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- Ideal TOPite Genome (Annointed:)
- Ideal TOPite mtDNA-haplogroup:
- >http://www.phylotree.org/tree/index.htm
- >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC447592/table/TB2/?report=objectonly
- >http://www.cell.com/ajhg/pdf/S0002-9297(12)00146-2.pdf
- >http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156632
- >Based on the pelvic and the skull morphologies, the specimen was determined to be a female
- >Additionally, a comb only used by the lady in the era which was found amongst the relics of the tomb suggests that the individual was from a female
- >However it was noted that male traits were also observed on the remarkably inclined forehead, everted gonial and developed mental regions on the mandible. DNA-based sex determination was attempted but the analysis did not obtain any results regarding the sex. It was presumed that the nuclear DNA could not be amplified from the ancient specimen of human remains
- >the stature was estimated to be 154.9 ± 4.6 cm
- >Consensus mtDNA haplotype of the Silla individual was 16220C, 16254G, 16298C, 16362C, 73G, 152C, 249d, 263G, 310.1C
- >the Silla individual’s haplotype belongs to East Asian haplogroup F1b1a
- Ancestral Allele/Derived Allele/RNRS/L0/L1-6 - TOPite-Allele/Haplogroup
- 73 - (G/A;G;G;G) - A/R0
- 146 - (C/T;C;C;T) - T/L1'2'3'4'5'6
- 152 - (C/T;C;T;C) - C/L1'2'3'4'5'6/N10b, I2'3, N1a3a1, N1a3a3, N1b
- 182 - (C/T;C;C;T) - C/L1'2'3'4'5'6
- 195 - (C/T;C;C;C) - C/L2'3'4'6
- 200 - (A/G;G;A;A) - G/L0
- 249 - (A/-;A;A;-) - -/R9c1a, F, R21, S5, M20, M31a1, M36d1, M40a1a, M59, M80, L3x2
- 263 - (G/A;G;A;G) - A/H2a2a1
- 593 - (T/C;T;T;T) - C/L1-6
- 750 - (G/A;G;G;G) - A/H2
- 1048 - (C/T;C;T;C) - C/L1'2'3'4'5'6
- 1438 - (G/A;G;G;G) - A/H2
- 1719 - (G/A;G;G;G) - A/R
- 2706 - (G/A;G;G;G) - A/H
- 2758 - (A/G;A;A;G) - G/L1'2'3'4'5'6
- 3516 - (C/A;C;A;C) - C/L1'2'3'4'5'6
- 4312 - (T/C;T;T;C) - T/L1'2'3'4'5'6
- 4769 - (G/A;G;G;G) - A/L1'2'3'4'5'6
- 5442 - (T/C;T;C;T) - T/L1'2'3'4'5'6
- 5460 - (G/A;G;G;G) - A/H1
- 6185 - (T/C;T;C;T) - T/L1'2'3'4'5'6
- 7028 - (T/C;T;T;T) - C/H
- 7146 - (G/A;G;A;G) - A/L2'3'4'5'6
- 8701 - (G/A;G;G;G) - A/N
- 8860 - (G/A;G;G;G) - A/L
- 9042 - (C/T;C;T;C) - C/L1'2'3'4'5'6
- 9347 - (A/G;A;G;A) - A/L1'2'3'4'5'6
- 10589 - (G/A;G;A;G) - G/L1'2'3'4'5'6
- 10644 - (T/C;T;T;C) - T/L0
- 10915 - (C/T;C;C;T) - C/L0
- 11719 - (A/G;A;A;A) - G/R0
- 11914 - (A/G;A;A;G) - A/L0
- 11915 - (C/T;C;T;C) - T/L0
- 12007 - (G/A;G;A;G) - G/L1'2'3'4'5'6
- 12705 - (T/C;T;T;T) - C/L1'2'3'4'5'6
- 12720 - (A/G;A;G;A) - A/L1'2'3'4'5'6
- 12810 - (A/G;A;A;A) - G/V3
- 13105 - (G/A;G;G;G) - G/HV0
- 13276 - (G/A;G;G;A) - G/L1'2'3'4'5'6
- 13506 - (T/C;T;T;C) - C/L2,3,4,6
- 14766 - (T/C;T;T;T) - C/HV
- 15301 - (G/A;G;G;A) - G/N
- 15326 - (G/A;G;G;G) - A/H2a2a
- 15775 - (A/G;A;A;A) - G/W5
- 16129 - (A/G;A;A;G) - G/L2,3,4,6
- 16187 - (T/C;T;T;C) - C/L2,3,4,6
- 16220 - (A/C;A;A;A) - C/F3b
- 16223 - (T/C;T;T;T) - C/R
- 16230 - (G/A;G;G;A) - G/L1'2'3'4'5'6
- 16254 - (A/G;A;A;A) - G/L3a
- 16278 - (T/C;T;T;C) - C/L1'2'3'4'5'6
- 16298 - (T/C;T;T;T) - C/L3h1a1, F3, R30b1, N10b, M8, W1d
- 16362 - (T/C;T;T;T) - C/L3h1b2, L3b, L3c, L3d5, F3, F4a1, R9b2, F1a4a, O1, N10, I3c, W5a
- -
- A
- 001: 16q; ABAT (AA;) Position: 8750498
- \https://www.snpedia.com/index.php/Rs724159992
- \https://www.ncbi.nlm.nih.gov/clinvar/RCV000149900.1/
- \https://www.omim.org/entry/137150#0003
- >GATA-transaminase deficiency [...] c.275G-A transition
- 001b: 16q; ABAT (TT;) Position: 8768220
- \https://www.snpedia.com/index.php/Rs724159990
- \https://www.ncbi.nlm.nih.gov/clinvar/RCV000149898.1/
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=724159990
- >CTC [Leucine] -> TTC [Phenylalanine)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757431/#!po=21.0145
- \The variant (ABAT NM_000663.3 c.631C>T; NP_000654.2 p.Leu211Phe [...] Subject 1 (S1) [...] none of the individuals previously reported as having ABAT deficiency were noted to have mitochondrial dysfunction
- 001c: 16q; ABAT (GG;) Position: 8768248
- \https://www.snpedia.com/index.php/Rs121434578
- \https://www.ncbi.nlm.nih.gov/clinvar/RCV000017603.27/
- \https://www.omim.org/entry/137150#0001
- >GABA-transaminase deficiency [...] 754A-G transition in the ABAT gene [...] Vmax was reduced to 25% of wildtype activity
- 001d: 16q; ABAT (CC;) Position: 8781360
- \https://www.snpedia.com/index.php/Rs724159991
- \https://www.ncbi.nlm.nih.gov/clinvar/RCV000149899.1/
- \https://www.omim.org/entry/137150#0007
- >GABA-transaminase deficiency [...] c.1433T-C transition
- 002: 16q; ABCC1 (AA;) Position: 48224287
- \https://www.snpedia.com/index.php/Rs17822931
- >also known as c.538G>A [...] It is commonly (T;T)(AA) for East Asians and (C;C)(GA/GG) for Europeans and Africans
- \https://www.omim.org/entry/607040#0001
- >The AA genotype corresponds to dry ear wax, and GA and GG to the wet type
- -^
- 003: 9q; ABO (TT;) Position: 133273813
- \https://www.snpedia.com/index.php/Rs505922
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514387/
- \https://www.ncbi.nlm.nih.gov/pubmed/22642827
- >The protective allele (T) for rs505922 is in complete [...] (LD) [...] with the O allele
- -^
- 003b: 9q; ABO (GG;) Position: 133256205
- \https://www.snpedia.com/index.php/Rs7853989
- \http://www.redcross.org/images/MEDIA_CustomProductCatalog/m4440094_26_2_10.pdf
- >B (ABO*B1) nt 526C>G (rs7853989)
- -^
- 003c: 9q; ABO (GG;) Position: 133256028
- \https://www.snpedia.com/index.php/Rs8176743
- \http://www.redcross.org/images/MEDIA_CustomProductCatalog/m4440094_26_2_10.pdf
- >B (ABO*B1) nt 703G>A (rs8176743)
- -^
- 003d: 9q; ABO (CC;) Position: 133255935
- \https://www.snpedia.com/index.php/Rs8176746
- \http://www.redcross.org/images/MEDIA_CustomProductCatalog/m4440094_26_2_10.pdf
- >B (ABO*B1) nt 796C>A (rs8176746)
- -^
- 003e: 9q; ABO (GG;) Position: 133255928
- \https://www.snpedia.com/index.php/Rs8176747
- \http://www.redcross.org/images/MEDIA_CustomProductCatalog/m4440094_26_2_10.pdf
- >B (ABO*B1) nt 803G>C (rs8176747)
- -^
- 003f: 9q; ABO (-;-;) Position: 133257521
- \https://www.snpedia.com/index.php/Rs8176719
- \http://www.redcross.org/images/MEDIA_CustomProductCatalog/m4440094_26_2_10.pdf
- >O (ABO*O1) nt 261G/ΔG (rs8176719)
- -^
- 004: 3q; ADAMTS9 (TT;) Position: 64705365
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6795735
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >ADAMTS9, EA = C
- 005: 15q; ADAMTSL3 (CC;) Position: 84037709
- \https://www.snpedia.com/index.php/Rs950169
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631150/table/pgen-1000373-t001/?report=objectonly
- >rs950169 T frequency = Schizophrenia(0.23,) Controls(0.30)
- -^
- 006: 14q; AKT1 (CC;) Position: 104772855
- \https://www.snpedia.com/index.php/Rs2494732
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22831980/
- >C - greater odds of cannabis-associated psychosis
- -^
- 006b: 14q; AKT1 (GG;) Position: 104796031
- \https://www.snpedia.com/index.php/Rs2498786
- \https://www.ncbi.nlm.nih.gov/m/pubmed/26178916/
- >The CC frequency of AKT1 rs2498786 polymorphism in AD with T2D group and AD control group was significantly higher than that in healthy control group
- -^
- 006c: 14q; AKT1 (GG;) Position: 104772809
- \https://www.snpedia.com/index.php/Rs3803304
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652804/
- >G - associated with Ashkenazi Jewish Centenarians
- -^
- 007: 12q; ALDH2 (GG;) Position: 111803962
- \https://www.snpedia.com/index.php/Rs671
- >(G;G) Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19706845/
- -^
- 008: 18q; APCDD1 (CC;) Position: 10487921
- \http://publicatio.bibl.u-szeged.hu/4816/1/2746617_Nagy_JLife%20Sci.pdf
- >AGA (Androgenic Alopecia) patients - CC = n37, CT = n100, TT = 73
- >Controls - CC = n28, CT = n60, TT = 10
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3185480
- -^
- 009: 11q; APOC3 (CC;) Position: 116829268
- \https://www.snpedia.com/index.php/Rs2542052
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16602826/
- >The prevalence of homozygosity for the -641C allele in the APOC3 promoter (rs2542052) was higher in centenarians (25%) and their offspring (20%) than in controls (10%)
- -^
- 009b: 11q; APOC3 (AA;) Position: 116830844
- \https://www.snpedia.com/index.php/Rs147210663
- \http://www.nejm.org/action/showImage?doi=10.1056%2FNEJMoa1308027&iid=f02
- >A46T Effect allele = A, Triglyceride levels/allele = G(100% = n1,) A(53% of n1)
- -^
- 010: Xq; AR (AA;) Position: 67545785
- \https://www.snpedia.com/index.php/Rs6152
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21981665/
- >Three common polymorphisms of the AR gene were addressed: a StuI restriction-site polymorphism (rs6152, G>A) [...] Meta-analysis results identified a significant association between the G allele of the AR StuI polymorphism and the risk for AGA
- -^
- 010b: Xq; AR (GG;) Position: 67350329
- \https://www.snpedia.com/index.php/Rs2223841
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1226186/table/TB3/?report=objectonly
- >rs2223841 AGA(Androgenic alopecia) Frequency = A(0.954,) G(0.046,) Unaffected = A(0.688,) G(0.312)
- -^
- 010c: Xq; AR (CAG(n = 36;) Position: 67545318
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=193922933
- \http://omim.org/entry/313700#14
- \https://www.ncbi.nlm.nih.gov/m/pubmed/15198988/
- >There was on average a 1.7% decrease in activity for each additional glutamine repeat
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833274/
- >The mean CAG repeat lengths were Afro-Caribbean 19.6 ± 3.2, Caucasian 21.9 ± 2.9, Hispanic 22.6 ± 3.1, and Thai 23.1 ± 3.3
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402034/
- >A significant association was identified between transsexualism and the AR allele, with transsexuals having longer AR repeat lengths than non-transsexual male control subjects
- 011: Xq; AR/EDA2R (CC;) Position: 67270282
- \https://www.snpedia.com/index.php/Rs4258142
- \https://images.nature.com/original/nature-assets/ncomms/2016/160301/ncomms10815/extref/ncomms10815-s1.pdf
- >Balding [...] rs4258142 Ancestral/Derived allele = C>T, Derived Allele frequency = CEU(85%,) YRI(0%,) CHB(100%,) NAM(99%,) CAN(88%)
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4258142
- \https://www.ncbi.nlm.nih.gov/m/pubmed/11453914/
- >The prevalence of AGA in Korean men and women was lower than that in caucasians, as recorded in the literature. Korean men tend to have more frontal hairline preservation and show a more 'female pattern' of hair thinning than caucasians. Therefore, 'female pattern' should be added to the classification of AGA
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1113949/
- >By the age of 30, 30% of white men have androgenetic alopecia; by the age of 50, 50% do [...] White men are four times more likely to than black men develop premature balding (Note: white rate of AGA / 4 = Black AGA rate = Age30(7.5%,) Age50(12.5%) Therefore YRI-allele = AGA-, HCB-allele = AGA, and CEU-allele = AGA+
- -^
- 012: 20q; ASIP (TT;) Position: 34262569
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2424984
- \https://www.ncjrs.gov/pdffiles1/nij/grants/223980.pdf
- >Six markers have significant effects on hair total melanin: [...] dbSNPrs2424984 (ASIP) [...] When each are considered separately, these markers account for [...] 19.9% [...] (respectively) of the total trait variation [...] Five markers showed a significant effect on skin reflectance: [...] dbSNPrs2424984 (ASIP) [...] 15.6% [...] of the total trait variance [...] Eye color was significantly influenced by 5 markers: [...] and dbSNPrs2424984 (ASIP). When considered separately as single markers, these account for [...] 3.4% of the total trait variance
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2424984
- >Frequency = CEU(CC=0.017, CT=0.194, TT=0.787,) HCB(CC=0.069, CT=0.418, TT=0.511,) YRI(CC=0.619, CT=0.345, TT=0.035)
- 012b: 20q; ASIP (GG;) Position: 34262569
- \https://www.snpedia.com/index.php/Rs1015362
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1015362
- >Frequency = CEU(AA=0.053, AG=0.424, GG=0.522,) HCB(AA=0.023, AG=0.209, GG=0.767,) YRI(AA=0.681, AG=0.300, GG=0.017)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700213/
- >The haplotype near ASIP(rs4911414[T] and rs1015362[G]) was significantly associated with fair skin color (OR, 2.28; 95% CI, 1.46–3.57
- -^
- 012c: 20q; ASIP (TT;) Position: 34141638
- \https://www.snpedia.com/index.php/Rs4911414
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4911414
- >Frequency = CEU(GG=0.450, GT=0.459, TT=0.090,) HCB(GG=0.761, GT=0.214, TT=0.023,) YRI(GG=0.705, GT=0.276, TT=0.017)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700213/
- >The haplotype near ASIP(rs4911414[T] and rs1015362[G]) was significantly associated with fair skin color (OR, 2.28; 95% CI, 1.46–3.57
- -^
- 012d: 20q; ASIP (AA;) Position: 34269192
- \https://www.snpedia.com/index.php/Rs6058017
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?ss=ss1364626247
- >Frequency = EUR(A=0.896, G=0.103,) EAS(A=0.787, G=0.212,) AFR(A=0.208, G=0.791)
- \http://www.utm.utoronto.ca/~parraest/profile/PDF%20files/Bonilla%20et%20al.,%202005a.pdf
- >A single-nucleotide poly- morphism (SNP) in the 3¢-untranslated region (UTR) of ASIP (noted as g.8818A>G in the literature, dbSNP# rs6058017) has been reported to be associated with dark hair and brown eyes in European Americans
- -^
- 013: 1q; ASPM (GG;) Position: 197101567
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=41310927
- >Ancestral Allele: T
- >Fwd=T-to-A=Rev/Fwd=C-to-G=Rev, so T = A and C = G
- >A(S, Ser) -> G(G, Gly)
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?ss=ss1294110430
- >EUR(T=0.589, C=0.410,) EAS(T=0.836, C=0.163,) AFR(T=0.956, C=0.043)
- \http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034243
- >ASPM A44871G (rs41310927,Ser2562Gly [...] We found a significant positive correlation between Tone Perception and the [...] derived alleles for ASPM A44871G [...] Table 1. Association between load of ASPM-G allele and neural repetition suppression to tone repeat (1) and tone-change (2) conditions
- \https://academic.oup.com/hmg/article/15/12/2025/2355898
- >For ASPM, each additional A44871G allele was associated with a non- significant (df=1, 115, P=0.55) 10.9 cc decrease in brain volume [...] The 95% confidence interval for the change in brain volume per A44871G allele was -46.8 cc [...] We cannot exclude the possibility that these alleles might nonetheless be associated with small differences in brain volume [...]
- \http://science.sciencemag.org/content/309/5741/1720.long
- >Frequency of ASPM D-allele = Russians(38%,) French(50%,) Orkney Islands(40.6%,) Papuan(59.7%,) South African Bantu(0%,) San(0%,) Bakola Pygmy(0%)
- \http://www.sciencedirect.com/science/article/pii/S016028960200137X
- >African-descended people (Blacks) average cranial capacities of 1267 cm3, European-descended people (Whites) 1347 cm3 [...] It must be concluded that the race differences in average brain size are securely established [...] Blacks average an IQ of 85, Whites 100
- >Note: 1347 - 1267 = 80 / 2 = 40, therefore two copies of the 44871G allele could explain the observed 80cc of difference between blacks and whites
- -^
- 013b: 1q; ASPM (CC;) Position: 197117000
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=10922168
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/#!po=16.6667
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs10922168 42cc -/+ 38
- \http://www.pnas.org/content/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs10922168 T/C Minor allele frequency = 0.17
- -^
- 013c: 1q; ASPM (AA;) Position: 197101312
- \http://jmg.bmj.com/content/42/9/725
- >ASPM mutations identified in patients with primary microcephaly [...] In addition, we also identified four non-synonymous [...] 7939C->A [...] SNPs
- \https://www.snpedia.com/index.php/Rs3762271
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3762271
- >NM_018136.4:c.7939C>A
- \http://journals.sagepub.com/doi/full/10.1177/1099800416630621
- >The CC genotype of rs3762271 was significantly associated with birth weight [...] and body length
- -^
- B
- 001: 6q; BAT2 (GG;) Position: 31635190
- \https://www.snpedia.com/index.php/Rs1046089
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992315/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992315/table/T1/?report=objectonly
- >G allele = 0.48x odds of severe Malaria
- -^
- 002: 4q; BMP2K (AA;) Position: 78865702
- \https://www.snpedia.com/index.php/Rs2288255
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19927351/
- >1379 G/A (rs2288255) [...] frequency of A allele in the BMP2K gene 1379 G/A polymorphism showed a significant difference between cases and controls [...] subjects with either AA or AG genotype show higher risk than GG genotype
- \http://iovs.arvojournals.org/article.aspx?articleid=2124443
- 002b: 4q; BMP2K (GG;) Position: 78911552
- \https://www.snpedia.com/index.php/Rs12507099
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19927351/
- >3171 C/G (rs12507099) [...] 3171 C/G polymorphism was not significant
- \http://iovs.arvojournals.org/article.aspx?articleid=2124443
- -^
- 003: 14q; BMP4 (TT;) Position: 53950804
- \https://www.snpedia.com/index.php/Rs17563
- \https://www.ncbi.nlm.nih.gov/pubmed/21034624?dopt=Abstract
- >ossification of the posterior longitudinal ligament (OPLL) [...] the frequency of "TT" genotype in male OPLL patients was significantly higher than in male controls [...] A significant difference was also observed between the 6007C>T polymorphism and the number of ossified cervical vertebrae in OPLL patients
- -^
- 004: 9q; BNC2 (CC;) Position: 16680140
- \https://www.snpedia.com/index.php/Rs10738445
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28342042/
- >Adolescent idiopathic scoliosis [...] We found that patients have a significantly higher frequency of CC than the controls
- \https://www.ncbi.nlm.nih.gov/m/pubmed/26211971/
- >At higher doses, delayed or disturbed pigmentation was also observed in the embryos with severe body curva- ture
- \https://www.omim.org/entry/608669
- >A/A allele rendered the chromatin inaccessible, and the enhancer element was only slightly active, resulting in low expression of BNC2 and thus light skin pigmentation
- -^
- 004b: 9q; BNC2 (AA;) Position: 16885019
- \https://www.snpedia.com/index.php/Rs12350739
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=12350739
- \https://www.ncbi.nlm.nih.gov/m/pubmed/24916375/
- >When the rs12350739-AA allele is present, the chromatin at the region surrounding rs12350739 is inaccessible and the enhancer element is only slightly active, resulting in low expression of BNC2, corresponding with light skin pigmentation
- -^
- 004c: 9q; BNC2 (TT;) Position: 16864523
- \https://www.snpedia.com/index.php/Rs2153271
- \http://journals.plos.org/plosgenetics/article/figure?id=10.1371/journal.pgen.1000993.t002
- >Freckling associated with rs2153271 - assumed to be T based on CEU frequency
- -^
- 004d: 9q; BNC2 (GG;) Position: 16464982
- \https://www.snpedia.com/index.php/Rs10733310
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28057405/
- >association between SNP rs10733310 [...] and pigment spots [...] Pigment Forearm = GG(2.9,) TG(2.5,) TT(2.1)
- -^
- C
- 001: 3q; CCR2 (AA;) Position: 46357717
- \https://www.snpedia.com/index.php/Rs1799864
- \https://www.ncbi.nlm.nih.gov/m/pubmed/12556692/
- >individuals with one or two copies of CCR2-64I had a 58% lower risk of AIDS
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1799864
- >Ancestral Allele: G [...] GTC [Valine] -> ATC [Isoleucine]
- -^
- 002: 3q; CCR5 (0T;) Position: 46373456
- \https://www.snpedia.com/index.php/Rs333
- \https://www.ncbi.nlm.nih.gov/m/pubmed/8898752/
- \https://www.ncbi.nlm.nih.gov/m/pubmed/8898752/
- >A 32-nucleotide deletion (delta 32) within the beta-chemokine receptor 5 (CCR5) gene has been described in subjects who remain uninfected despite extensive exposure to HIV-1
- -^
- 003: 16q; CETP (GG;) Position: 56982180
- \https://www.snpedia.com/index.php/Rs5882
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20068209/
- >Compared with isoleucine homozygotes, valine homozygotes had significantly slower memory decline
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=5882
- >GTC [Valine] -> ATC [Isoleucine]
- -^
- 003b: 16q; CETP (TT;) Position: 56960616
- \https://www.snpedia.com/index.php/Rs17231506
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23372063/
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=17231506
- >rs17231506 (CETP c.-1337 C>T) [...] significantly modulate the capacity of whole-plasma to mediate cholesterol efflux from human macrophages
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684899/bin/NIHMS726871-supplement.docx
- >Supplementary Table 9, rs17231506 HDL-C = CC(48.99,) CT(51.23,) TT(54.01)
- -^
- 004: 17q; CD79B (TT;) Position: 63928899
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7921
- >Ancestral Allele = C [...] Fwd = C/T, Rev = A/G, C-A/T-G, so C=A, G=T [...] Frequency = CEU(CC=0.513, CT=0.415, TT=0.070,) HCB(CC=0.906, CT=0.069, TT=0.023,) YRI(CC=0.510, CT=0.361, TT=0.127)
- \https://www.sciencedirect.com/science/article/pii/S0888754397951715
- >Sequence analysis of the region between the GH1 gene and its most proximal HS (HSI) revealed a perfect match to the B-lymphocyte-specific CD79b gene
- \https://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs7921, Effect Allele = A, Effect(0.34)
- 005: 9q; CDK5RAP2 (GG;) Position: 120373094
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4836817
- >Ancestral Allele: C [...] Frequency = CEU(CC=0.477, CT=0.486, TT=0.035,) HCB(CC=0.813, CT=0.162, TT=0.023,) YRI(CC=0.875, CT=0.116, TT=0.008,) CHB(CC=0.804, CT=0.195, TT=0.000)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs4836817, Population(Males,) Effect Size([-]42-/+24cm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs4836817 = Major/minor allele = G(=C)/T
- >Note: 42+24=66cc, CEU(0(*0.477=0.477,)-66(*0.486=-32.076,)-132(*0.035=-4.62,)=-36.219cc) HCB(0(*0.813=0.813,)-66(*0.162=-10.692,)-132(*0.023=-3.036,)=-12.915cc) YRI(0.875=0.875,)-66(*0.116=-7.656,)-132(*0.008=-1.056,)=-7.837cc)
- 005b: 9q; CDK5RAP2 (GG;) Position: 120382296
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=10818453
- >Ancestral Allele: A [...] Frequency = CEU(AA=0.035, AG=0.526, GG=0.437,) HCB(AA=0.069, AG=0.279, GG=0.651,) YRI(AA=0.144, AG=0.441, GG=0.414
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs10818453, Population(Males,) Effect Size([-]63-/+35cm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs10818453 = Major/minor allele = G/A
- >Note: 63+35=98cc, CEU(-196(*0.035=-6.86,)-98(*0.526=-51.548,)0(0.437=0.437)=-57.971cc) HCB(-196(*0.069=-13.524,)-98(*0.279=-27.342,)0(0.651=0.651)=-40.215cc) YRI(-196(*0.144=-28.224,)-98(*0.441=-43.218,)0(0.414=0.414)=-71.028cc)
- 005c: 9q; CDK5RAP2 (GG;) Position: 120388175
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4836819
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.033, AG=0.576, GG=0.389,) HCB(AA=0.088, AG=0.177, GG=0.733,) YRI(AA=0.250, AG=0.466, GG=0.283)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs4836819, Population(Males,) Effect Size([-]61-/+34cm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs4836819 = Major/minor allele = G/A
- >Note: 61+34=95cc, CEU(-190(*0.033=-6.27,)-95(*0.576=-54.72,)0(0.389=0.389)=-60.601cc) HCB(-190(*0.088=-16.72,)-95(*0.177=-16.815,)0(0.733=0.733)=-32.802cc) YRI(-190(*0.250=-47.5,)-95(*0.466=-44.27,)0(0.283=0.283)=-91.487cc)
- 005d: 9q; CDK5RAP2 (GG:) Position: 120389401
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4836820
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.017, AG=0.513, GG=0.469,) HCB(AA=0.069, AG=0.116, GG=0.813,) YRI(AA=0.000, AG=0.283, GG=0.716)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs4836820, Population(Males,) Effect Size([-]72-/+33cm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs4836820 = Major/minor allele = G/A
- >Note: 72+33=105cc, CEU(-210(*0.017=-3.57,)-105(*0.513=-53.865,)0(0.469=0.469)=-60.601cc) HCB(-210(*0.069=-14.49,)-105(*0.116=-12.18,)0(0.813=0.813)=-25.857cc) YRI(-210(*0.000=-0.00,)-105(*0.283=-29.715,)0(0.716=0.716)=-28.999cc)
- 005e: 9q; CDK5RAP2 (GG;) Position: 120394313
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7859743
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.026, AG=0.522, GG=0.451,) HCB(AA=0.093, AG=0.186, GG=0.720,) YRI(AA=0.203, AG=0.469, GG=0.327)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs7859743, Population(Males,) Effect Size([-]60-/+33cm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs7859743 = Major/minor allele = G/A
- >Note: 60+33=93cc, CEU(-186(*0.026=-4.836,)-93(*0.522=-48.546,)0(0.451=0.451)=-52.931cc) HCB(-186(*0.093=-17.298,)-93(*0.186=-17.298,)0(0.720=0.720)=-33.876cc) YRI(-186(*0.203=-37.758,)-93(*0.469=-43.617,)0(0.327=0.327)=-81.048cc)
- 005f: 9q; CDK5RAP2 (GG;) Position: 120403882
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2297453
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.026, AG=0.455, GG=0.517,) HCB(AA=0.162, AG=0.395, GG=0.441,) YRI(AA=0.168, AG=0.460, GG=0.371)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs2297453, Population(Males,) Effect Size([-]72-/+34cm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs2297453 = Major/minor allele = G/A
- >Note: 72+34=106cc, CEU(-212(*0.026=-5.512,)-106(*0.455=-48.23,)0(0.517=0.517)=-53.225cc) HCB(-212(*0.162=-34.344,)-106(*0.395=-17.298,)0(0.441=0.441)=-51.201cc) YRI(-212(*0.168=-35.616,)-106(*0.469=-49.714,)0(0.371=0.371)=-81.048cc)
- 005g: 9q; CDK5RAP2 (GG;) Position: 120407440
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2282168
- >Ancestral Allele = G [...] Frequency = CEU(CC=0.017, CG=0.424, GG=0.557,) HCB(CC=0.046, CG=0.116, GG=0.837,) YRI(CC=0.035, CG=0.312, GG=0.652)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs2282168, Population(Males,) Effect Size([-]84-/+35wcm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs2282168 = Major/minor allele = G/A(=C)
- >Note: 84+35=119cc, CEU(-238(*0.017=-4.046,)-119(*0.424=-50.456,)0(0.557=0.557)=-53.945cc) HCB(-238(*0.046=-10.948,)-119(*0.116=-13.804,)0(0.837=0.837)=-23.915cc) YRI(-238(*0.035=-8.33,)-119(*0.312=-37.128,)0(0.652=0.652)=-44.806cc)
- 005h: 9q; CDK5RAP2 (AA;) Position: 120407793
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1888893
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.544, AG=0.428, GG=0.026, GT=0.000) HCB(AA=0.744, AG=0.186, GG=0.069, GT=0.000,) YRI1/YRI2/BANTU(AA=0.333, AG=0.333, GG=0.000, GT=0.333)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs1888893, Population(Males,) Effect Size([-]73-/+35wcm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs1888893 = Major/minor allele = G/G
- >Note: 73+35=108cc, does not include T-allele, CEU(0(*0.544=0.544,)-108(*0.428=-45.68,)-216(*0.026=-5.616)=-50.752cc) HCB(0(*0.774=0.774,)-108(*0.186=-20.088,)-216(0.069=-14.904)=-34.218cc) YRI(0(*0.500=0.500,)-108(*0.500=-54.0,)-216(0.000=-0.000)=-53.5cc)
- 005i: 9q; CDK5RAP2 (AA;) Position: 120407889
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=914592
- >Ancestral Allele = A [...] Frequency = CEU(AA=0.554, AG=0.427, GG=0.018,) HCB(AA=0.833, AG=0.119, GG=0.047,) YRI(AA=0.666, AG=0.297, GG=0.036)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs914592, Population(Males,) Effect Size([-]83-/+35wcm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs914592 = Major/minor allele = G/G
- >Note: 83+35=118cc, CEU(0(*0.554=0.554,)-118(*0.427=-50.386,)-236(*0.018=-4.248)=-54.08cc) HCB(0(*0.833=0.833,)-118(*0.119=-14.042,)-236(*0.047=-11.092)=-24.301cc) YRI(0(*0.666=0.666,)-118(*0.297=-35.046,)-236(0.036=-8.496)=-42.876cc)
- 005j: 9q; CDK5RAP2 (CC;) Position: 120407932
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=914593
- >Ancestral Allele = A [...] Frequency = CEU(CC=0.557, CG=0.424, GG=0.017,) HCB(CC=0.837, CG=0.116, GG=0.046,) YRI(CC=0.637, CG=0.300, GG=0.061)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/
- >rs914593, Population(Males,) Effect Size([-]80-/+35.6wcm3 [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs914593 = Major/minor allele = G/G
- >Note: 80+35.6=115.6cc, CEU(0(*0.557=0.557,)-115.6(*0.424=-49.0144,)-231.2(*0.017=-3.9304)=-54.08cc) HCB(0(*0.837=0.837,)-115.6(*0.116=-13.409,)-231.2(*0.046=-10.635)=-23.207cc) YRI(0(*0.637=0.637,)-115.6(*0.300=-34.68,)-231.2(0.036=-8.3232)=-42.3662cc)
- \http://www.sciencedirect.com/science/article/pii/S016028960200137X
- >It must be concluded that the race differences in average brain size are securely established [...] In the US and around the world, East Asians and their descendants average an IQ of about 106, Europeans and their descendants about 100, and Africans and their descendants about 85. The lowest average IQ scores are reported for sub-Saharan Africa, about 70 [...] Their study found that East Asians, Europeans, and Africans averaged cranial volumes of 1415, 1362, and 1268 cm3
- >Calculated average Racial cc adjustment = HCB(-302.507cc = +231.898 of AFR,) CEU(-534.405cc = AFR +10.5902,) YRI(-544.9952cc.) In 8/10 instances, the Derived allele is associated with lower brain volume/cortical area. 1,812.9952cc - 544.9952cc = 1268cc, 1,812.9952cc - 534.405cc = 1,278.5902cc, Kenya(Height=67",) Europe(Height=71",) 71" / 67" = 1.0597 * 1,278.5902cc = 1,354.92203494cc. 1,812.9952cc - 302.507cc = 1,510.4882cc China(Height=66.5",) 66.5" / 71" = 0.9366 * 1,510.4882cc = 1,414.72324812cc. The Amud neanderthal (55Kya, 1740cc, Height=70") 72.89655172413793"(70 * 1.041379310344828 = 72.89655172413793) / 70" = 1.041379310344828(1,812 / 1740 = 1.041379310344828) * 1740 = 1,812cc. The correlation between brain size and IQ is 0.33;
- \http://www.people.vcu.edu/~mamcdani/Big-Brained%20article.pdf
- >The best unbiased estimate of the population correlation between brain volume and intelligence is 0.33
- >Therefore, if 1362cc = 100IQ, than 100IQ = 449.46, 1268cc = 85IQ, than 85IQ = 418.44, 449.46 / 418.44 = 1.074132492113565 * 1268cc = 1,362cc, 1.074132492113565 - 1 = 0.074132492113565 / 2 = 0.037066246056782 + 1 = 1.037066246056782 * 1268cc = 1,315cc - 47 = 1268, 1,315 + 47 = 1362cc, 1.037066246056782 * 85IQ = 88.15063091482647. Therefore, 1362cc = 100IQ = 449.46, and 449.46 / n1(cc * 0.33) = n2 * n3(cc) = n4, or n1(0.33 * cc) / 449.46 = n3 * (1362cc/100IQ) = n4 = cc/IQ. Therefore n1=597.96(0.33 * 1,812cc) / 449.46 = n3(1.330396475770925) * (1,812cc/133IQ) = n4. 56 / 72.89655172413793 = 0.768211920529801 * 1,812cc = 1,392cc, 1,392cc / 1362cc = 1.022026431718062 * 100IQ = 102IQ.
- 006: 7q; CDK6 (GG;) Position: 92607515
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4272
- >Ancestral Allele = A [...] Frequency = CEU(AA=0.513, AG=0.433, GG=0.053,) HCB(AA=0.813, AG=0.139, GG=0.046,) YRI(AA=0.787, AG=0.185, GG=0.026)
- \https://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs4272, Effect Allele = A, Effect(-0.46)
- 007: 4q; CLOCK (CC;) Position: 55435202
- \http://snpedia.com/index.php/Rs1801260
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166621/
- >Clock Mutants Find Cocaine More Rewarding
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17221848/
- >carriers of the C allele had a similar degree of severity of depression, but showed higher activity levels in the evening, a delayed sleep onset (mean 79 min later), and a reduced amount of sleep during the night (mean 75 min less)
- -^
- 008: 8q; CNGB3 (TT;) Position: 86632768
- \https://www.snpedia.com/index.php/Rs121918344
- \https://omim.org/entry/605080#0001
- >total colorblindness, photophobia, nystagmus, 20/200 visual acuity, and a normal-appearing retina [...] Sequence analysis of exons showed a C-to-T transition
- 009: 6q; CNR1 (GG;) Position: 88143916
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1049353
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.044, AG=0.375, GG=0.580,) HCB(AA=0.000, AG=0.139, GG=0.860,) YRI(AA=0.000, AG=0.176, GG=0.823)
- \https://link.springer.com/article/10.1007%2Fs12020-007-0022-y
- >G1422A variant (rs1049353) [...] In obese men, CNR1 1422 A/A genotype was significantly associated with higher WHR (P = 0.009) and waist circumference (P = 0.008)
- 009b: 6q; CNR1 (CC;) Position: 88147601
- \https://www.snpedia.com/index.php/Rs806374
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28930056/
- >rs806374, was significantly associated with individual differences in level-but not growth-of cannabis use over time, such that C carriers were more likely to use cannabis more frequently
- 009c: 6q; CNR1 (CC:) Position: 88149004
- \https://www.snpedia.com/index.php/Rs806377
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155489/
- >To further analyse genotypic differences for each SNP that were significantly associated with gaze duration for happy faces, post hoc t-tests were conducted. In rs806377, the CC genotype was associated with longer gaze duration than the CT genotype
- 009d: 6q; CNR1 (CC;) Position: 88149832
- \https://www.snpedia.com/index.php/Rs806378
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20107430/
- >A common polymorphism in the cannabinoid receptor 1 (CNR1) gene is associated with antipsychotic-induced weight gain in Schizophrenia [...] rs806378 was nominally associated with weight gain in patients of European ancestry treated with clozapine or olanzapine [...] This translated into approximately 2.2 kg more weight gain in patients carrying the T allele than the patients homozygous for the CC genotype
- 009e: 6q; CNR1 (AA;) Position: 88154934
- \https://www.snpedia.com/index.php/Rs806380
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=806380
- >Ancestral Allele = A
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16917946/
- >Univariate (single-marker) association tests demonstrated that SNP rs806380, located in intron 2 of the CNR1 gene, was significantly associated with developing one or more cannabis dependence symptoms, with the G allele having a protective effect
- 010: 1q; CNR2 (CC;) Position: 23874672
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2229579
- >Ancestral Allele = C
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23846977/
- >Association of single-nucleotide polymorphisms in the cannabinoid receptor 2 gene with schizophrenia in the Han Chinese population [...] For rs2229579, the T allele frequencies of the case group were higher than the control
- 010b: 1q; CNR2 (GG;) Position: 23875153
- \http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=2501431
- >Fwd = A/G, Rev = C/T, A-T/G-C
- \https://www.snpedia.com/index.php/Rs2501431
- \https://www.ncbi.nlm.nih.gov/m/pubmed/29353877/
- >Gene variants and educational attainment in cannabis use: mediating role of DNA methylation
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802451/table/Tab5/?report=objectonly
- >Frequency = rs2501431, AA(Controls = 47.37%, MJ-Users = 58.97%,) AG(Controls = 41.05%, MJ-Users = 41.03%,) GG(Controls = 11.58%, MJ-Users = 0.00%)
- \https://www.ncbi.nlm.nih.gov/m/pubmed/26055357/
- >TT genotype of rs2501431 [...] had lower lumbar spine BMD and femoral neck BMD compared with the other genotypes
- 010c: 1q; CNR2 (TT;) Position: 23875430
- \https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=2501432
- \https://www.snpedia.com/index.php/Rs2501432
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23846977/
- >Association of single-nucleotide polymorphisms in the cannabinoid receptor 2 gene with schizophrenia in the Han Chinese population [...] rs2501432C/T [...] Our results suggest that the T allele of rs2501432 may be a protective factor, particularly in males
- 010d: 1q; CNR2 (GG;) Position: 23875429
- \https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=35761398
- >CAA(Q, Gln) -> CGG(R, Arg) [...] Fwd = C/T, A-C/G-T
- \https://www.snpedia.com/index.php/Rs35761398
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23707465/
- >Association between a polymorphism in cannabinoid receptor 2 and severe necroinflammation in patients with chronic hepatitis C [...] Patients with the CB2-63 QQ variant had higher serum levels of aminotransferase than those with the CB2-63 QR or RR variants [...] Patients with the CB2-63 QQ variant had higher serum levels of aminotransferase than those with the CB2-63 QR or RR variants [...] The CB2-63 QQ variant of CNR2 is associated with more severe inflammation and hepatocellular necrosis in patients with HCV infection
- 010e: 1q; CNR2 (AA;) Position:
- \https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=41311993
- >Fwd = G/T, Rev = C/A, G-C/T-A [...] C(L, Leu) -> A(I, Ile) [...] Frequency = EAS(G=1.000, T=0.000,) EUR(G=0.991, T=0.008,) AFR(G=1.000, T=0.000,) AMR(G=0.998, T=0.001,) SAS(G=0.996, T=0.003)
- \https://www.snpedia.com/index.php/Rs41311993
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21658778/
- >Genetic association between bipolar disorder and 524A>C (Leu133Ile) polymorphism of CNR2 gene, encoding for CB2 cannabinoid receptor [...] rs41311993 (524C>A; Leu133Ile [...] A statistically significant association was found between BD and the CNR2 524C>A; Leu133Ile
- 011: 22q; COMT (AA;) Position: 19963748
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4680
- >GTG [Valine] -> ATG [Methionine]
- \Citation: https://www.snpedia.com/index.php/Rs4680
- >COMT gene
- >(A;A): (worrier) advantage in memory and attention tasks
- >(A;G): multiple associations, see details
- >(G;G): (warrior) multiple associations, see details
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17008817/
- >Those with valine (Val158) alleles have increased greater COMT activity and lower prefrontal extracellular dopamine compared with those with the methionine
- -^
- 012: 5q; CPEB4 (GG;) Position: 173362458
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6861681
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >CPEB4, EA = A
- 013: Xq; CSF2RA (CC;) Position: 1029445
- \https://www.snpedia.com/index.php/Rs4129148
- \http://www.nature.com/mp/journal/v12/n6/fig_tab/4001983f2.html#figure-title
- \https://www.nature.com/articles/4001983
- >homozygosity for the C allele (−strand) was significantly associated with schizophrenia
- -^
- 013b: Xq; CSF2RA (GG;) Position: 1294564
- \https://www.snpedia.com/index.php/Rs28414810
- \http://www.nature.com/mp/journal/v12/n6/fig_tab/4001983t2.html#figure-title
- \https://www.nature.com/articles/4001983/tables/2
- >rs28414810 G allele Frequency = Schizophrenia(0.80,) Controls(0.63)
- -^
- 014: 15q; CYP1A2 (AA;) Position: 74750296
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=72547513
- >C allele = F[Phe] -> A allele = L[Leu]
- \http://jpet.aspetjournals.org/content/308/1/300.long
- >Metabolism and Kinetic Characterization of 7-Ethoxyresorufin O-Deethylation by CYP1A2 Variant Enzymes
- >The F186L Vmax value was 16-fold lower (p < 0.05) than that of the wild type
- \https://en.wikipedia.org/wiki/2-Hydroxyestradiol
- >CYP1A2 and CYP3A4 are the major enzymes catalyzing the 2-hydroxylation of estradiol
- >2-Hydroxyestradiol has been found to increase prolactin secretion when administered intravenously to women.[6] It was noted that this could be due to 2-hydroxyestradiol binding to and antagonizing the D2 receptor
- 015: 15q; CYP19A1 (13T;) Position: 15q21.1
- \https://academic.oup.com/jcem/article-lookup/doi/10.1210/jcem.83.4.4697
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC333565/?page=1
- \https://academic.oup.com/humrep/article/25/12/3146/550945
- >Association of aromatase (TTTAn) repeat polymorphism length and the relationship between obesity and decreased sperm concentration [...] Men with high repeats had higher estradiol
- 015b: 15q; CYP19A1 (TT;) Position: 51287401
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16949385/
- >TT genotype was associated with [...] lower testosterone and higher E2 levels
- \https://www.snpedia.com/index.php/Rs936306
- -^
- 015c: 15q; CYP19A1 (GG;) Position: 51266534
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16949385/
- >AA genotype of the CYP 19 rs749292 [...] had lower testosterone and E2 levels but higher levels of sex hormone-binding globulin (SHBG)
- \https://www.snpedia.com/index.php/Rs749292
- -^
- 015d: 15q; CYP19A1 (AA;) Position: 51237582
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16949385/
- >lower SHBG levels among those with the AA genotype of the CYP 19 rs2414096
- \https://www.snpedia.com/index.php/Rs2414096
- -^
- 015e: 15q; CYP19A1 (TT;) Position: 51210789
- \http://cebp.aacrjournals.org/content/18/5/1617.long
- >alleles [...] rs10046(T) [...] were associated with higher levels of estrogens
- \https://www.snpedia.com/index.php/Rs10046
- -^
- 015f: 15q; CYP19A1 (TT;) Position: 51210789
- \http://cebp.aacrjournals.org/content/18/5/1617.long
- >rs727479(T) [...] were associated with higher levels of estrogens
- \https://www.snpedia.com/index.php/Rs727479
- -^
- 015g: 15q; CYP19A1 (GG;) Position: 51210647
- \http://cebp.aacrjournals.org/content/18/5/1617.long
- >alleles [...] rs4646(G) were associated with higher levels of estrogens
- \https://www.snpedia.com/index.php/Rs4646
- -^
- 015h: 15q; CYP19A1 (GG;) Position: 51236915
- \http://cebp.aacrjournals.org/content/18/5/1617.long
- >The Val80 (rs700518) G allele was found to be associated with elevated aromatase expression
- \https://www.snpedia.com/index.php/Rs700518
- -^
- 015i: 15q; CYP19A1 (CC;) Position: 51321614
- \https://www.snpedia.com/index.php/Rs1004982
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760732/
- >The risk of breast cancer with (but not without) proliferative fibrocystic conditions was increased among women homozygous for the minor allele of rs1004982 (C)
- -^
- 015j: 15q; CYP19A1 (TT;) Position: 51287401
- \https://www.snpedia.com/index.php/Rs936306
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760732/
- >The risk of breast cancer with (but not without) proliferative fibrocystic conditions was increased among women homozygous for the minor allele of [...] rs936306 (T)
- -^
- 015k: 15q; CYP19A1 (CC;) Position: 51243825
- \https://www.snpedia.com/index.php/Rs4775936
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760732/
- >The risk of breast cancer with (but not without) proliferative fibrocystic conditions was increased among women homozygous for the minor allele of [...] and rs4775936 (C)
- -^
- 015l: 15q; CYP19A1 (GG;) Position: 51255741
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20417295/
- >GG genotype at rs1062033 was associated with an increased risk of knee OA
- \https://www.snpedia.com/index.php/Rs1062033
- -^
- 015m: 15q; CYP19A1 (CC;) Position: 51211017
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/17815/
- \https://www.snpedia.com/index.php/Rs121434534
- \https://www.omim.org/entry/107910#0001
- >Aromatase deficiency [...] C-to-T transition
- 015n: 15q; CYP19A1 (CC;) Position: 51211017
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/17818/
- \https://www.snpedia.com/index.php/Rs121434536
- \https://omim.org/entry/107910#0004
- >Aromatase deficiency [...] C-to-T transition
- 015o: 15q; CYP19A1 (GG;) Position: 51222349
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/17826/
- \https://www.snpedia.com/index.php/Rs121434538
- \https://omim.org/entry/107910#0012
- >Aromatase deficiency [...] G-to-A transition
- 015p: 15q; CYP19A1 (GG;) Position: 51231710
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17216495/
- >Men carrying AA/AG genotypes in the rs12594287 SNP had a 30% reduced risk of having extreme low femoral neck BMD
- \https://www.snpedia.com/index.php/Rs12594287
- -^
- 015q: 15q; CYP19A1 (CC;) Position: 51223154
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17216495/
- >TT/TC genotypes in the rs16964201 SNP had a 40% reduced risk of having extreme low femoral neck BMD
- \https://www.snpedia.com/index.php/Rs16964201
- -^
- 015r: 15q; CYP19A1 (CC;) Position: 51237900
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17216495/
- >Men with TC/CC genotypes in the rs17703883 SNP had a 1.5 times higher risk of having extreme low femoral neck BMD
- \https://www.snpedia.com/index.php/Rs17703883
- -^
- 015s: 15q; CYP19A1 (GG;) Position: 51302775
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681277/table/T4/?report=objectonly
- >AA = E2(17.5pg/ml-/+6.2,) AG = E2(18.8pg/ml-/+6.1,) GG = E2(19.8pg/ml-/+6.2)
- \https://www.snpedia.com/index.php/Rs2470152
- -^
- 015t: 15q; CYP19A1 (GG;) Position: 51314513
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3751591
- >Ancestral Allele = T [...] Fwd = C/T, Rev = A/G, C-A/T-G, A=C/G=T, so Ancestral Allele = G(Fwd)/T(Rev)
- \https://www.snpedia.com/index.php/Rs3751591
- \http://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs3751591, Effect allele: A, Effect: +0.25
- -^
- 015u: 15q; CYP19A1 (CC;) Position: 51243825
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19064562/
- >breast cancer with (but not without) proliferative fibrocystic conditions was increased among women homozygous for the minor allele of [...] rs4775936 (C) relative to those homozygous for the major allele
- \https://www.snpedia.com/index.php/Rs4775936
- -^
- 015v: 15q; CYP19A1 (CC;) Position: 51215771
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=700519
- \https://www.snpedia.com/index.php/Rs700519
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613759/table/T3/?report=objectonly
- \rs700519 CC = Estradiol(9.3-11.1,) CT/TT = Estradiol(8.6-11.1)
- -^
- 015w: 15q; CYP19A1 (AA;) Position: 51242350
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19124504/
- \A alleles of rs749292 and rs727479) have been associated with a 10% to 20% increase in circulating estrogen levels
- \https://www.snpedia.com/index.php/Rs727479
- -^
- 015x: 15q; CYP19A1 (AA;) Position: 51266534
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812905/table/T4/?report=objectonly
- >rs749292 GG = Estradiol(98.0-113.1,) GA = Estradiol(99.9-115.1,) AA = Estradiol(104.9-121.7)
- \https://www.snpedia.com/index.php/Rs749292
- -^
- 016: 10q; CYP2E1 (CC;) Position: 133536297
- \https://www.snpedia.com/index.php/Rs1329149
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19706845/
- >A novel polymorphism rs1329149 of CYP2E1 [...] are associated with colorectal cancer [...] The adjusted OR was [...] 4.04 for the rs1329149 T/T genotype
- -^
- 016b: 10q; CYP2E1 (CC;) Position: 133537633
- \https://www.snpedia.com/index.php/Rs2070676
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19381774/
- >We found an association between allele and genotype frequencies of the C/G polymorphism at intron 7 (rs2070676) of this gene and PD(Parkinsons disease) (P value of 0.026 and 0.027, respectively
- -^
- 017: 7q; CYP3A (GG;) Position: 99784473
- \https://www.snpedia.com/index.php/Rs2740574
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165281/
- >prostate cancer (PCa [...] Recent papers have reported that men with a Gleason score of >7 had lower intraprostatic DHT than men with a Gleason score of <6, suggesting that a low-androgen microenvironment predisposes to development or progression for high-grade PCa or CRPC
- >Note: Hypoactive DHT synthesis will lead to excess T. If CYP3A4 metabolizes T and estradiol into 2-Hydroxyestradiol, and 17b-HSD synthesis is hypoactive leading to a buildup of Estrone, than a CYP3A4 allele that leads to prostate cancer will also lead to hypoactive 2-Hydroxyestradiol synthesis due to a lack of Estradiol substrate and impaired CYP3A4 function.
- \http://cebp.aacrjournals.org/content/8/10/901.long
- >The G variant was not found in the Chinese or Japanese populations
- >In this case, being homozygous for the CYP3A4 variant appeared to increase the risk of presenting with high grade/stage
- >A comparison of men with AG to AAand GG to AA showed a slight increasing trend for Gleason grade
- >We report consistent positive associations between the CYP3A4 variant and clinical characteristics in African-American men with prostate cancer
- \https://www.omim.org/entry/124010#39
- >They referred to the polymorphism as CYP3A4-V (124010.0001
- >The CYP3A4*1B allele (124010.0001) may decrease the oxidative deactivation of testosterone (Rebbeck et al., 1998). African Americans have the highest documented rates of prostate cancer in the world
- >The overlap between these blocks in these 2 groups contained only 2 of the investigated 26 SNPs, and 1 of them was the CYP3A4*1B allele. The region centromeric of CYP3A4*1B on 7q exhibited high haplotype homozygosity in European Caucasians as opposed to African Americans. CYP3A4*1B showed a moderate effect on CYP3A4 mRNA and protein expression
- \https://en.wikipedia.org/wiki/2-Hydroxyestradiol
- >CYP1A2 and CYP3A4 are the major enzymes catalyzing the 2-hydroxylation of estradiol
- >2-Hydroxyestradiol has been found to increase prolactin secretion when administered intravenously to women.[6] It was noted that this could be due to 2-hydroxyestradiol binding to and antagonizing the D2 receptor
- 017b: 7q: CYP3A4 (TT;) Position: 99758183
- \https://www.snpedia.com/index.php/Rs67666821
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16580902/
- >Identification and characterization of CYP3A4*20, a novel rare CYP3A4 allele without functional activity
- \https://www.pharmgkb.org/haplotype/PA165819244
- >CYP3A4*20
- >Location: rs67666821
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=67666821
- >Ancestral allele = G, Derived allele = -/T(Fwd)
- D
- 001: 13q; DAOA (AA;) Position: 105487313
- \https://www.snpedia.com/index.php/Rs947267
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17293043/
- >Our findings showed that the SNP rs947267 was significantly associated with schizophrenia [...] in particular those formed by the A allele of rs947267
- -^
- 001b: 13q; DAOA (AA;) Position: 105467097
- \https://www.snpedia.com/index.php/Rs2391191
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19482054/
- >Two haplotypes G-A of M12 (rs3916965)-M15 (rs2391191) [...] also showed associations with methamphetamine psychosis
- -^
- 001c: 13q; DAOA (AA;) Position: 105484383
- \https://www.snpedia.com/index.php/Rs7139958
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22122005/
- >rs7139958 AA [...] rs7139958 A [...] genotypes were associated with higher scores on the PANSS positive subscale among patients with schizophrenia, possibly reflecting their greater susceptibility to the development of more severe positive symptoms
- -^
- 001d: 13q; DAOA (AA;) Position: 105489886
- \https://www.snpedia.com/index.php/Rs778294
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19763662/
- >for rs778294, 50% of probands with the AA genotype, but only 22% of probands with a GG or GA genotype progressed to psychosis
- -^
- 001e: 13q; DAOA (TT;) Position: 105486017
- \https://www.snpedia.com/index.php/Rs9558571
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22122005/
- >rs9558571 TT [...] rs9558571 T genotypes were associated with higher scores on the PANSS positive subscale among patients with schizophrenia, possibly reflecting their greater susceptibility to the development of more severe positive symptoms
- -^
- 002: 9q; DBH (CC;) Position: 133658547
- \https://www.snpedia.com/index.php/Rs129882
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25975715/
- >Specifically, the C allele of the ADHD-associated rs129882 SNP produced a 2-fold decrease [...] in luciferase activity [...] Reduced DBH expression would be consistent with decreased conversion of dopamine to noradrenaline
- -^
- 002b: 9q; DBH (TT;) Position: 133635393
- \https://www.snpedia.com/index.php/Rs1611115
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17625104/
- >The T allele associated with lower serum DBH in both groups [...] −1021C->T polymorphism of DBH (rs1611115)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728391/table/T3/?report=objectonly
- >rs1611115 T allele frequency = Schizophrenics(0.774,) Controls(0.733)
- \https://www.nature.com/articles/5201838
- >we also examined the association of rs161115 to pDβH [...] Subjects with CC had the highest square-root plasma DβH activity (N=36, 4.56±1.65), followed by subjects with CT (N=14, 3.96-/+1.61) and TT (N=5, 1.35-/+0.60)
- -^
- 002c: 9q; DBH (GG;) Position: 133638697
- \https://www.snpedia.com/index.php/Rs2007153
- \https://www.ncbi.nlm.nih.gov/pubmed/19673036?dopt=Abstract
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728391/table/T3/?report=objectonly
- >rs2007153 G allele frequency = Schizophrenics(0.658,) Controls(0.470)
- -^
- 002d: 9q; DBH (CC;) Position: 133650175
- \https://www.snpedia.com/index.php/Rs2283123
- \https://www.ncbi.nlm.nih.gov/pubmed/19673036?dopt=Abstract
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728391/table/T3/?report=objectonly
- >rs2283123 T allele frequency = Schizoprenics(0.020,) Controls(0.063)
- 002e: 9q; DBH (TT;) Position: 133644512
- \https://www.snpedia.com/index.php/Rs2519152
- \http://www.nature.com/ejhg/journal/v15/n8/fig_tab/5201838t1.html#figure-title
- \https://www.nature.com/articles/5201838/tables/1
- >rs2519152 plasma DBH activity = CC(5.47-/+1.83,) CT(5.33-/+1.87,) TT(3.85-/+2.05)
- -^
- 002g: 9q; DBH (AA;) Position: 133647854
- \https://www.snpedia.com/index.php/Rs267606761
- \https://www.ncbi.nlm.nih.gov/clinvar/?term=rs267606761
- \https://www.omim.org/entry/609312#0004
- >In a patient with dopamine beta-hydroxylase deficiency [...] identified [...] a 259G-A transition in exon 1, resulting in a val87-to-met (V87M) substitution, and a 991G-A transition
- 002h: 9q; DBH (CC;) Position: 133636712
- \https://www.snpedia.com/index.php/Rs74853476
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/1750/
- \https://www.omim.org/entry/609312#0002
- \2 unrelated patients with dopamine beta-hydroxylase deficiency [...] identified a heterozygous T-to-C transition
- -^
- 002i: 9q; DBH (AA;) Position: 133636712
- \https://www.snpedia.com/index.php/Rs75215331
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/217765/
- \https://www.ncbi.nlm.nih.gov/clinvar/RCV000201828/
- >NM_000787.3:c.1085C>A [...] NP_000778.3:p.Ala362Glu [...] Protein change:
- A348E [...] dbSNP: 75215331
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059068/?report=reader#!po=49.0741
- >Strikingly, media from all three mutant forms of DBH showed [...] undetectable (in the case of A348E [...] amounts of proteins
- -^
- 003: 18q; DCC (AA;) Position: 53530928
- \https://www.snpedia.com/index.php/Rs227095
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2270954
- >MAF = A
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22418395/
- >rs2270954 [...] schizophrenia; patients were less likely to be heterozygous at this locus and more likely to be homozygous for the minor allele
- -^
- 004: 1q; DISC1 (AA;) Position: 231694549
- \https://www.snpedia.com/index.php/Rs3738401
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17673452/
- >A of [...] rs3738401 at the 5' end of DISC1 was over-transmitted to males with psychotic disorder
- -^
- 004b: 1q; DISC1 (CC;) Position: 231818355
- \https://www.snpedia.com/index.php/Rs6675281
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736903/
- >Schizophrenia risk-associated polymorphisms [...] rs6675281 (Leu607Phe) [...] on the expression of Δ7Δ8 mRNA [...] T (Phe) carriers (the 3 T/T subjects combined and the C/T subjects) showed significantly higher expression than C/C (Leu/Leu) individuals [by 22%
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736903/figure/F2/?report=objectonly
- >Δ7Δ8 mRNA levels = Controls(90,) Schizophrenics(130)
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6675281
- >CTC [Leucine] -> TTC [Phenylalanine]
- 004c: 1q; DISC1 (TT;) Position: 231632793
- \https://www.snpedia.com/index.php/Rs751229
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17673452/
- >T [...] of rs751229 [...] at the 5' end of DISC1 was over-transmitted to males with psychotic disorder
- -^
- 004d: 1q; DISC1 (TT;) Position: 231931311
- \https://www.snpedia.com/index.php/Rs821577
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19188535/
- >minor allele of rs821577 was significantly associated with higher scores on social and physical anhedonia
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=821577
- >MAF = T
- -^
- 005: 1q; DNM3 (AA;) Position: 1723465448
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1011731
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >DNM3, EA = G
- 005b: 1q; DNM3 (TT;) Position: 172084147
- \https://www.snpedia.com/index.php/Rs17346452
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955183/bin/NIHMS225625-supplement-1.doc
- \Hundreds of variants clustered in genomic loci and biological pathways affect human height [...] rs17346452 Effect Allele = T(-0.038)
- -^
- 006: 5q; DRD1 (CC;) Position: 175443899
- \https://www.snpedia.com/index.php/Rs265981
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18205172/
- >associations of the rs265981-C [...] with more severe problems in social interaction, greater difficulties with nonverbal communication and increased stereotypies
- -^
- 006b: 5q; DRD1 (AA;) Position: 175443147
- \https://www.snpedia.com/index.php/Rs4532
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18205172/
- >associations of [...] rs4532-A [...] alleles [...] with more severe problems in social interaction, greater difficulties with nonverbal communication and increased stereotypies
- -^
- 006c: 5q; DRD1 (TT;) Position: 175441697
- \https://www.snpedia.com/index.php/Rs686
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18205172/
- >associations of [...] rs686-T alleles [...] with more severe problems in social interaction, greater difficulties with nonverbal communication and increased stereotypies
- 007: 11q; DRD2 (CC;) Position: 113425552
- \https://www.snpedia.com/index.php/Rs1079598
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21247255/
- >The DRD2 rs1079598 CC genotype was overrepresented in aggressive children compared to controls
- _^
- 007b: 11q; DRD2 (CC;) Position: 113447023
- \https://www.snpedia.com/index.php/Rs17601612
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=17601612
- >MAF = C
- \https://www.ncbi.nlm.nih.gov/pubmed/25184405?dopt=Abstract
- >Reports of higher subclinical psychotic experiences were associated with DRD2 SNPs rs17601612
- -^
- 007c: 11q; DRD2 (-;-;) Position: 113475529
- \https://www.snpedia.com/index.php/Rs1799732
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1799732
- \https://www.ncbi.nlm.nih.gov/pubmed/19547807?dopt=Abstract
- >Thus the -141C Ins/Del polymorphism of the DRD2 gene (allele Ins) was associated to the SCZ phenotype
- \https://www.ncbi.nlm.nih.gov/pubmed/20146828?dopt=Abstract
- >significant association of -141C Ins allele [...] of DRD2 with alcohol dependence
- \http://www.sciencedirect.com/topics/neuroscience/dopamine-hypothesis-of-schizophrenia
- >studies have shown an increased density of the dopamine D2 receptor in postmortem brain tissue of schizophrenia sufferers
- \http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010670
- >Thalamic Dopamine D2 Receptor Densities Are Negatively Related to Psychometric Creativity in Healthy Individuals [...] The results show a negative correlation between divergent thinking scores and D2 density in the thalamus [...] We suggest that decreased D2 receptor densities in the thalamus lower thalamic gating thresholds, thus increasing thalamocortical information flow. In healthy individuals, who do not suffer from the detrimental effects of psychiatric disease, this may increase performance on divergent thinking tests
- -^
- 007d: 11q; DRD2 (CC;) Position: 113412755
- \https://www.snpedia.com/index.php/Rs6275
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6275
- \https://www.ncbi.nlm.nih.gov/pubmed/18477981?dopt=Abstract
- >association study of the DRD2 gene C939T polymorphism and schizophrenia [...] the frequency of the TT genotype being higher in patients compared to the controls
- -^
- 007e: 11q; DRD2 (TT;) Position: 113412737
- \https://www.snpedia.com/index.php/Rs6277
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6277
- \https://www.ncbi.nlm.nih.gov/pubmed/18255274?dopt=Abstract
- >Association study of three polymorphisms in the dopamine D2 receptor gene and schizophrenia in the Russian population [...] Frequency of the C allele, corresponding to a normal wild-type level of expression, was higher in patients compared to controls, and that of the T allele was lower
- -^
- 008: 3q; DRD3 (AA;) Position: 114157428
- \https://www.snpedia.com/index.php/Rs167771
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324694/
- >Insistence on Sameness (IS) [...] Individuals carrying the AA variant of the rs167771 SNP scored significantly higher on the IS-factor
- \https://www.nature.com/articles/tpj200926/tables/4
- >A common variant in DRD3 gene is associated with risperidone-induced extrapyramidal symptoms
- >DRD3 rs16771 Associated allele = G, G Frequency = Cases(0.45,) Controls(0.2)
- -^
- 008b: 3q; DRD3 (AA;) Position: 114171968
- \https://www.snpedia.com/index.php/Rs6280
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18320559/
- >The rate of positive symptom remission, defined as all PANSS positive items less than three (minimal or absent symptoms) was also tested for association with ser-9-gly genotypes [...] Approxi- mately 39% of patients with the gly/gly genotype were remitters compared with 14% patients with ser/ser or ser/gly genotypes
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6280
- >G(Gly) -> A(Ser)
- -^
- 009: 11q; DRD4 (CC;) Position: 641191
- \https://www.snpedia.com/index.php/Rs11246226
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728391/table/T3/?report=objectonly
- >Association of Tagging Single Nucleotide Polymorphisms on 8 Candidate Genes in Dopaminergic Pathway with Schizophrenia in Croatian Population
- >Alleles = (Major/minor)A/C, C Frequency = Controls(0.183,) Cases(0.078)
- -^
- 009b: 11q; DRD4 (CC;) Position: 636784
- \https://www.snpedia.com/index.php/Rs1800955
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1800955
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1705471/table/Tab1/?report=objectonly
- >Association and synergistic interaction between promoter variants of the DRD4 gene in Japanese schizophrenics
- >rs1800955 Frequency = Controls(CC=0.19, CT=0.48, TT=0.34,) Cases(CC=0.16, CT=0.50, TT=0.34)
- -^
- 010: 6q; DTNBP1 (TT;) Position: 15656839
- \https://www.snpedia.com/index.php/Rs1018381
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21130223/
- >rs1018381 [...] suggesting that the minor allele carriers of these SNPs had lower cognitive ability scores than the major allele homozygotes
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19497374/
- >heterozygous risk-allele carriers (T/C) and homozygous non-carriers (C/C [...] Stronger right hemispherical brain activation in anterior cingulate gyrus (BA 24), superior (BA 22, 38) and middle (BA 21) temporal gyrus was observed in the carriers compared to non-carriers
- \https://en.wikipedia.org/wiki/Dysbindin
- >schizophrenic patients carrying the high-risk haplotype demonstrated visual processing deficits [...] damping down the DTNBP1 expression led to an increase in cell surface dopamine D2-receptor levels
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC33999/
- >increase in the level of dopamine as well as an increase in the number of D2 receptors in schizophrenia
- -^
- 010b: 6q; DTNBP1 (CC;) Position: 15572843
- \https://www.snpedia.com/index.php/Rs742105
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19369910/
- >Patients with [...] allele T of marker rs742105 (P1333) have better response to clozapine
- 010c: 6q; DTNBP1 (CC;) Position: 15650901
- \https://www.snpedia.com/index.php/Rs760761
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19800201/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783814/table/T1/?report=objectonly
- >DTNBP [...] is associated with schizophrenia [...] rs760761 Major allele = C, Frequency(of C) = Cases(0.809,) Controls(0.742)
- -^
- 010d: 6q; DTNBP1 (CC;) Position: 15544505
- \https://www.snpedia.com/index.php/Rs9370822
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20615671/
- >Homozygotes for the C allele of rs9370822 were more than two and a half times as likely to have schizophrenia
- -^
- 011: 18q; DYN (CC;) Position: 49081890
- \https://www.snpedia.com/index.php/Rs833497
- \https://www.nature.com/articles/jhg201072/tables/1
- >rs833497 CC = Affected(0.13,) Controls(0.10,) TC = Affected(0.45,) Controls(0.40,) TT = Affected(0.42,) Controls(0.50)
- E
- 001: 2q; EDAR (CC;) Position: 108897145
- \https://www.snpedia.com/index.php/Rs3827760
- \https://omim.org/entry/604095#0011
- >HAIR MORPHOLOGY 1, HAIR THICKNESS [...] C allele was present at a frequency of 87.6% in 180 Chinese and Japanese samples, compared to 0% in 120 European and African samples [...] A further study [...] showed a significant association of the 1540T/C SNP with cross-sectional area of hairs [...] a follow-up study, Fujimoto et al. (2008) found a significant association between 1540C and increased hair cross-sectional area [...] of a possible association between the T1540C polymorphism and shovel-shaped incisors, see 147400
- \https://omim.org/entry/147400
- >Kimura et al. (2009) measured crown diameter and tooth-shoveling grade in 102 individuals from around Tokyo and 100 from the Sakishima Islands, then analyzed the correlation between dental traits and a T1540C polymorphism (rs3827760) in the EDAR gene (604095.0011 [...] EDAR 1540C alleles in an individual strongly correlated with the tooth-shoveling [...] the effect of the allele was additive and explained 18.9% of total variance in shoveling [...] 1540C significantly affected overall tooth size
- 002: Xq; EDA2R (CC;) Position: 66605144
- \https://www.snpedia.com/index.php/Rs1385699
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18385763/
- >rs1385699 was revealed to have the strongest association [...] (T-allele kinship-corrected frequencies cases=0.92, controls=0.7
- -^
- 003: 2q; EN1 (CC;) Position: 119545994
- \http://www.pdgene.org/view?poly=rs11692564
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714/table/T2/
- >We identified a low-frequency non-coding variant near a novel locus, EN1 [...] rs11692564[T], MAF = 1.7% [...] which was also associated with a decreased risk of fracture (OR = 0.85 [...] an En1Cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass
- \http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538659/
- \We propose that these high levels of En1 serve to drive the formation of eccrine glands at the expense of hair follicles
- \http://www.nature.com/nature/journal/v526/n7571/abs/nature14878.html
- \Using an En1cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover
- \EN1+ = BMD+, Eccrine Glands+, Hair follicles-
- \EN1- = BMD-, Eccrine Glands-, Hair follicles+
- 003b: 2q; EN1 (GG;) Position: 118855868
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=188303909
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714/table/T2/
- >Variant rs188303909 was in moderate LD with rs11692564
- 003c: 2q; EN1 (TT;) Position: 118772253
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=55983207
- >MAF = C
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714/table/T2/
- >We also identified an additional association signal, arising from rs55983207 (MAF = 4%), 17 kb downstream of rs11692564 (r2 = 0.001) to be associated with femoral neck BMD
- 003d: 2q; EN1 (GG;) Position: 118397296
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6542457
- >MAF = C
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714/table/T2/
- >we also observed two additional novel genome-wide significant variants for lumbar spine BMD near EN1, rs6542457 (MAF = 6.7%
- 004: 2q; EPAS1 (GG;) Position: 46329206
- \https://www.snpedia.com/index.php/Rs13419896
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25792003/
- >frequencies of the G allele of EPAS1 SNP rs13419896 were significantly higher in the HAPC group than in the control group
- 004b: 2q; EPAS1 (AA;) Position: 46348249
- \https://www.snpedia.com/index.php/Rs4953354
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25792003/
- >A alleles of rs12619696 and rs4953354 were prevalent in the HAPC group
- 004c: 2q; EPAS1 (AA;) Position: 46463303
- \https://www.snpedia.com/index.php/Rs12619696
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25792003/
- >A alleles of rs12619696 and rs4953354 were prevalent in the HAPC group
- 004: 2q; ERBB4 (AA;) Position: 211951364
- \https://www.snpedia.com/index.php/Rs839523
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22115776/
- >Three common ERBB4 single nucleotide polymorphisms that were previously associated with schizophrenia and impaired frontotemporal-related information processing (rs7598440, rs839523, and rs707284 [...] GGG haplotype homozygotes were associated with "protective" effects on VWM performance and PE(Psychotic experiences,) AAA "risk" haplotype carriers were associated with worse VWM performance and simultaneously exhibited significantly elevated PE
- 004b: 2q; ERBB4 (AA;) Position: 211974321
- \https://www.snpedia.com/index.php/Rs707284
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22115776/
- >Three common ERBB4 single nucleotide polymorphisms that were previously associated with schizophrenia and impaired frontotemporal-related information processing (rs7598440, rs839523, and rs707284 [...] GGG haplotype homozygotes were associated with "protective" effects on VWM performance and PE(Psychotic experiences,) AAA "risk" haplotype carriers were associated with worse VWM performance and simultaneously exhibited significantly elevated PE
- 004c: 2q; ERBB4 (AA;) Position: 211928473
- \https://www.snpedia.com/index.php/Rs7598440
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22115776/
- >Three common ERBB4 single nucleotide polymorphisms that were previously associated with schizophrenia and impaired frontotemporal-related information processing (rs7598440, rs839523, and rs707284 [...] GGG haplotype homozygotes were associated with "protective" effects on VWM performance and PE(Psychotic experiences,) AAA "risk" haplotype carriers were associated with worse VWM performance and simultaneously exhibited significantly elevated PE
- 005: 6q; ESR1 (AA;) Position: 151975965
- \https://www.snpedia.com/index.php/Rs2179922
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18350145/
- >Homozygote carriers of the G-allele of the SNP rs2179922 were on average 0.90 cm taller
- 005b: 6q; ESR1 (TT;) Position: 152061176
- \https://www.snpedia.com/index.php/Rs2273206
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18424448/
- >The T allele of another intron 6 SNP was part of a 3' haplotype less common in schizophrenia [rs2273206(T), rs2273207(G), rs2228480(G)
- 005c: 6q; ESR1 (GG;) Position: 152061190
- \https://www.snpedia.com/index.php/Rs2273207
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18424448/
- >The T allele of another intron 6 SNP was part of a 3' haplotype less common in schizophrenia [rs2273206(T), rs2273207(G), rs2228480(G)
- 005d: 6q; ESR1 (GG;) Position: 152098960
- \https://www.snpedia.com/index.php/Rs2228480
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18424448/
- >The T allele of another intron 6 SNP was part of a 3' haplotype less common in schizophrenia [rs2273206(T), rs2273207(G), rs2228480(G)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2276716/
- >Dopamine Inhibits Basal Prolactin Release
- \https://www.ncbi.nlm.nih.gov/m/pubmed/7449733/
- >estradiol benzoate (25 microgram/kg, sc) daily for 5 days resulted in a marked elevation of the serum PRL
- \https://www.mayoclinic.org/diseases-conditions/prolactinoma/symptoms-causes/syc-20376958
- >The major effect is decreased levels of some sex hormones — estrogen in women and testosterone in men
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793919/#!po=26.0417
- >The subjective effects of stimulant drugs vary across the menstrual cycle, with subjective reports from women in the follicular phase, when estradiol is low, being more similar to reports from men, while rising estradiol during the luteal phase, as well as the administration of exogenous estradiol, enhances the subjective effects of stimulants like cocaine and amphetamine [...] In the striatum and NAc, estradiol is able to acutely enhance DA signaling in females but not males
- \http://www.tandfonline.com/doi/pdf/10.5455/bcp.20141212113905
- >Negative symptom scores in the group with hyperprolactinemia were significantly higher than in the non-hyperprolactinemic group
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848766/
- \male patients had more negative symptoms
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775856/
- \Negative symptoms were the most common in male patients
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908169/
- >lisdexamfetamine (LDX), a pro-drug of amphetamine licensed for use in ADHD, has been investigated for its possible treatment of negative symptoms in schizophrenia. Favorable results were published based on an open-label, randomized withdrawal phase trial demonstrating improvement in negative symptoms with LDX
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23756608/
- >In adults with clinically stable schizophrenia, open-label LDX appeared to be associated with significant improvements in negative symptoms without positive symptom worsening
- >Dopamine+ = Prolactin-, Estrogen+ = Prolactin+/Dopamine+
- >Male = Prolactin+, Female = Prolactin-, and the elevated striatum and NAc DA signally caused by estridiol is likely the cause. Elevated DA in females also seems to reduce negative symptoms, based on efficacy of DA agonists to improve negative symtoms. If elevated DA causes schizophrenia, than an ESR1 allele with positive correlation for the disease entails DA- as DA agonists are protective against negative symptoms which are likely the basis for the increased rate of schizophrenia diagnosis among males. If decreased DA causes schizophrenia, than an ESR1 allele with positive correlation for the disease entails DA- as well - which contradicts the observed decrease in negative symptoms in females, who exhibit DA+. Therefore, a Schizophrenia+ ESR1 allele = Estrogen-, or;
- >If Estrogen+ = Schizo- and Negative-, than Schizo+ = Negative+,
- >If DA+ = Negative-, than Estrogen+ = Negative-,
- >If Estrogen+ = Negative-, than Estrogen+ = DA+,
- >Than Estrogen- = DA- = Schizo+ = Male+/Female-
- >Therefore DA+ = Male-/Female+.
- 005d: 6q; ESR1 (CC;) Position: 151949537
- \https://www.snpedia.com/index.php/Rs3020314
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18636124/
- \rs3020314 homozygous variant IVS4+5029CC genotype was associated with a 58% reduced risk of FL (follicular lymphoma)
- \https://www.jcpsp.pk/archive/2009/Apr2009/14.pdf
- >25-year-old female having asymptomatic edema of unilateral leg was provisionally diagnosed as a case of psoas abscess. Later, she turned out to be a case of non-Hodgkin’s lymphoma [...] She had diffuse ache in left lower limb, noticed swelling of left foot, which gradually progressed, proximally involving calf, thigh and groin
- 005e: 6q; ESR1 (AA;) Position: 151951263
- \https://www.snpedia.com/index.php/Rs3020377
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25218601/
- >Among individuals with the COMT val allele, those with 2 copies of the ESR1 rs3020377 minor A allele exhibit reduced COMT activity, increased bodily pain, and poorer self-reported health
- 005f: 6q; ESR1 (TT;) Position: 151959418
- \https://www.snpedia.com/index.php/Rs3798759
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23450473/
- >Single factor analysis stratified by sex also found that frequencies of rs3798759 GG and TG genotypes and G allele were significantly higher in female schizophrenia patients
- 005g: 6q; ESR1 (AA;) Position: 151996005
- \https://www.snpedia.com/index.php/Rs7757956
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17105837/
- >For rs7757956, the difference in total body less head ABMC in late puberty was 50% less in individuals homozygous or heterozygous for the A allele
- 005h: 6q; ESR1 (AA;) Position: 151842246
- \https://www.snpedia.com/index.php/Rs9340799
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613912/
- >rs9340799 were associated with endometrial cancer risk so that subjects homozygous for the rarer alleles [...] were at decreased risk as compared to homozygotes for the most common allele
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613912/table/T6/?report=objectonly
- F
- 001a: 15q; FBN1 (CC;) Position: 48428423
- \https://www.snpedia.com/index.php/Rs137854457
- \https://www.ncbi.nlm.nih.gov/clinvar/?term=rs137854457
- >G[Cys] ->C[Ser]
- \https://www.omim.org/entry/134797#0002
- >MARFAN SYNDROME, MILD VARIABLE [...] Some affected adults were unaware of their status before the molecular diagnosis [...] cysteine-to-serine substitution at codon 2307 (C2307S) in an EGF-like motif from one fibrillin allele
- -^
- 001b: 15q; FBN1 (AA;) Position: 48425483
- \https://www.snpedia.com/index.php/Rs137854464
- \https://www.omim.org/entry/134797#0015
- >the phenotype also included 'some skeletal manifestations, but no symptoms at all in the cardiovascular system
- >mutation was detected in the DNA of all subjects with dislocated lenses, as well as in the DNA of 3 other members of the family with only skeletal manifestations
- >In a 4-generation family with predominant ectopia lentis and only mild skeletal features of the Marfan syndrome but no sign of cardiovascular abnormality [...] found a G-to-A transition at nucleotide 7339
- 001c: 15q; FBN1 (TT;) Position: 48600217
- \https://www.snpedia.com/index.php/Rs137854467
- \https://www.omim.org/entry/134797#0018
- >proband was 21 years old when he was referred to a rheumatologist because of pain in the hands during motion and episodes of knee joint effusions. There were no joint deformities, no scoliosis, and no cardiac symptoms. He had had spherophakia and lens dislocation since childhood
- >One or several episodes of knee joint effusion with moderate pain had occurred in 5 individuals. These episodes may have been related to moderate physical activity. Physical examination did not reveal ongoing joint effusion or other signs of synovitis in any of the family members
- >Stahl-Hallengren et al. (1994) identified a C-to-T transition at nucleotide 364. This mutation substituted a cysteine for arginine-122 (R122C
- >Stevenson et al. (1982) gave the clinical description of 2 families with ectopia lentis in association with dolichostenomelia and joint stiffness
- 002: 4q; FGF5 (-/-) Position: 80266984
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=587777579
- \https://www.omim.org/entry/165190#0001
- >1-BP DEL [...] Whole-mount immunofluorescence studies of plucked forearm hair fibers demonstrated complete absence of FGF5 and very low levels of FGF5S in patient hair compared to controls
- \https://en.wikipedia.org/wiki/FGF5
- >In numerous genetic studies of long haired phenotypes of animals it has been shown that small changes in the FGF5 gene can disrupt its expression, leading to an increase in the length of the anagen phase of the hair cycle, resulting in phenotypes with extremely long hair
- >This has been demonstrated in many species, including cats [9],,[10] dogs [11], [12] mice,[8] rabbits,[13] donkeys,[14] sheep and goats,[15] where it is often referred to as the angora mutation
- >Blocking FGF5 in the human scalp extends the hair cycle, resulting in less hair fall, faster hair growth rate and increased hair growth
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115575/
- >Here, we present, to our knowledge, the first human counterpart of the angora phenotype, showing that FGF5 underlies trichomegaly and is a crucial regulator of hair growth in humans.
- 002b: 4q; FGF5 (--/--) Position: 80266984
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=587777580
- \https://www.omim.org/entry/165190#0002
- >In affected members of a large consanguineous Pakistani family with trichomegaly (TCMGLY; 190330), Higgins et al. (2014) identified homozygosity for a 2-bp deletion (c.159_160delTA
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115575/
- >Here, we present, to our knowledge, the first human counterpart of the angora phenotype, showing that FGF5 underlies trichomegaly and is a crucial regulator of hair growth in humans.
- 002c: 4q; FGF5 (-/-) Position: 80286385
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=587777581
- >Allele T Y[TYR] -> Allele G D[Asp]
- \https://www.omim.org/entry/165190#0003
- >In a Pakistani patient with trichomegaly (TCMGLY; 190330), Higgins et al. (2014) identified homozygosity for a c.520T-C transition in exon 3 of the FGF5 gene, resulting in a tyr174-to-his (Y174H) substitution
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115575/
- >Here, we present, to our knowledge, the first human counterpart of the angora phenotype, showing that FGF5 underlies trichomegaly and is a crucial regulator of hair growth in humans.
- 003: 6q; FOXO3 (GG;) Position: 108587315
- \https://www.snpedia.com/index.php/Rs2802292
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18765803/
- >Long-lived men also exhibited several biological markers indicative of greater insulin sensitivity and this was associated with homozygosity for the FOXO3A GG genotype
- 003b: 6q; FOXO3 (TT;) Position: 108613258
- \https://www.snpedia.com/index.php/Rs2764264
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992870/bin/NIHMS250473-supplement-Table_1.doc
- \Oldest Old = CC(8.77,) CT(41.28,) TT(49.95)
- 003c: 6q; FOXO3 (GG;) Position: 108659993
- \https://www.snpedia.com/index.php/Rs12212067
- \https://www.ncbi.nlm.nih.gov/m/pubmed/24035192/
- >We identify a noncoding polymorphism in FOXO3A (rs12212067: T > G) at which the minor (G) allele, despite not being associated with disease susceptibility, is associated with a milder course of Crohn's disease and rheumatoid arthritis and with increased risk of severe malaria
- 003d: 6q; FOXO3 (TT;) Position: 108678084
- \https://www.snpedia.com/index.php/Rs1935949
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652804/table/T4/?report=objectonly
- \AJC(Ashkenazi Jewish Centenarians) = OR(Odds ratio) CC(-,) CT(1.3,) TT(2.08)
- 004: 2q; FSHR (AA;) Position: 48962782
- \https://www.snpedia.com/index.php/Rs6166
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20335500/
- >AA rs6166 women showed a lower BMD (femoral neck and total body), lower stiffness index (calcaneal QUS), and higher serum levels of bone turnover markers compared to GG rs6166 women. The prevalence of osteoporosis was significantly higher in AA rs6166 women compared with GG rs6166 women
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16630814/
- >Bone mass is increased and osteoclastic resorption is decreased in haploinsufficient FSHbeta+/- mice with normal ovarian function, suggesting that the skeletal action of FSH is estrogen independent
- >We suggest that high circulating FSH causes hypogonadal bone loss
- \https://en.wikipedia.org/wiki/Follicle-stimulating_hormone
- >When the follicle matures and reaches 8–10 mm in diameter it starts to secrete significant amounts of estradiol [...] The sharp increase in estradiol production [...] cause a positive effect on the hypothalamus and pituitary and rapid GnRH pulses occur and an LH surge results. [...] The increase in serum estradiol levels cause a decrease in FSH production by inhibiting GnRH production
- \https://en.wikipedia.org/wiki/Estradiol#Skeletal_system
- >Estradiol has a profound effect on bone. Individuals without it (or other estrogens) will become tall and eunuchoid, as epiphyseal closure is delayed or may not take place. Bone structure is affected also, resulting in early osteopenia and osteoporosis.[21] Also, women past menopause experience an accelerated loss of bone mass due to a relative estrogen deficiency.[22]
- \https://en.wikipedia.org/wiki/Aromatase_excess_syndrome
- >FSH levels are said to be consistently low in the condition, while LH levels are in the low to normal range
- \https://en.wikipedia.org/wiki/Follicle-stimulating_hormone_receptor
- >Estrogen upregulates FSH receptor sites
- \FSH+ = Estradiol+ = GnRH-/BMD+/FSHR+ = FSH- (rs6166-G)
- \FSH- = Estradiol- = GnRH+/BMD-/FSHR- = FSH+ (rs6166-A)
- 004b: 2q; FSHR (TT;) Position: 48974189
- \https://www.snpedia.com/index.php/Rs2268363
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2268363
- \MAF = G
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20932654/
- >SNPs) Associated with the Development of Erectile Dysfunction in African-American Men Following Radiotherapy for Prostate Cancer
- >rs2268363, MAF frequency = Cases(6.11,) Controls(0.183)
- >MAF frequency = CEU(0.1,) YRI(0.592)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628192/table/T2/?report=objectonly
- >FSH = Decreased (Libido)(7.6,) Normal (Libido)(8.9)
- >Therefore T = FSH+, G = FSH-
- 005: 16q; FTO (AA;) Position: 53809247
- \http://www.pdgene.org/view?poly=rs1121980
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs1121980, Waist size(cm)/Trunk total fat %/Leg total fat % = GG(92.6|53.2/33.6,) GA(98.0|53.3/34.1,) AA(94.0|50.6/35.9)
- 005b: 16q; FTO (CC;) Position: 53800954
- \http://www.pdgene.org/view?poly=rs1421085
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs1421085, Waist size(cm)/Trunk total fat %/Leg total fat % = TT(90.4|52.9/34.0,) TC(98.7|53.3/34.0,) CC(95.4|49.7/36.4)
- 005c: 16q; FTO (AA;) Position: 53803574
- \http://www.pdgene.org/view?poly=rs1558902
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs1558902, Waist size(cm)/Trunk total fat %/Leg total fat % = TT(91.4|53.2/33.8,) TA(98.9|53.4/33.9,) AA(95.7|49.8/36.3)
- 005d: 16q; FTO (TT;) Position: 53818460
- \http://www.pdgene.org/view?poly=rs3751812
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs3751812, Waist size(cm)/Trunk total fat %/Leg total fat % = GG(92.3|53.4/33.5,) GT(97.7|53.4/33.9,) TT(97.7|48.8/37.9)
- 005e: 16q; FTO (GG;) Position: 53830465
- \http://www.pdgene.org/view?poly=rs9930506
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs9930506, Waist size(cm)/Trunk total fat %/Leg total fat % = AA(92.4|53.0/33.7,) AG(97.3|53.3/34.0,) GG(97.8|50.9/35.9)
- 005f: 16q; FTO (AA;) Position: 53820527
- \http://www.pdgene.org/view?poly=rs9939609
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs9930609, Waist size(cm)/Trunk total fat %/Leg total fat % = TT(92.3|53.5/33.5,) TA(97.4|53.1/34.2,) AA(100.0|50.0/36.6)
- 005g: 16q; FTO (TT;) Position: 53825488
- \http://www.pdgene.org/view?poly=rs9941349
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- >rs9941349, Waist size(cm)/Trunk total fat %/Leg total fat % = CC(92.5|53.2/33.6,) CT(97.3|53.2/34.1,) TT(97.7|50.9/35.9)
- G
- 001: 2q; GAD1 (GG;) Position: 170816965
- \https://www.snpedia.com/index.php/Rs3749034
- \http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758549/?report=classic
- >As predicted, patients with the risk-associated G/G genotype at rs3749034 had a significant decrease in KCC2 mRNA expression in the hippocampus
- >In the hippocampus of patients with schizophrenia, GAD25/GAD67 and NKCC1/KCC2 ratios are increased and KCC2 levels are decreased, reflecting a potentially immature state of the GABA system
- >Remarkably, these increased GAD25/GAD67 and NKCC1/KCC2 expression ratios in hippocampus are associated with the GAD1 genotype, with risk alleles predicting the relatively less mature pattern
- 001b: 2q; GAD1 (AA;) Position: 170852920
- \https://www.snpedia.com/index.php/Rs769391
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594692/#!po=6.00000
- >low CSF GABA concentrations are observed in a variety of epileptic syndromes, including genetic models of epilepsy
- >Figure 2b shows that 14.6% of subjects with the AA genotype had PTS activity, while 3.7% of those with the AG genotype and 6.25% of those with the GG genotype had PTS activity
- 002: 10q; GAD2 (GG;) Position: 26216567
- \https://www.snpedia.com/index.php/Rs2236418
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25966064/
- >The frequency distributions of the AA, AG, and GG genotypes in the polymorphic site rs2236418 in the diabetes GAD-Ab-positive group were 45.9, 42.8, and 11.4%, respectively, whereas those in the control group were 36.6, 43.7, and 19.8%
- 002b: 10q; GAD2 (AA;) Position: 26216756
- \https://www.snpedia.com/index.php/Rs185649317
- \https://www.geneticsmr.com/articles/relationship-between-serum-gadab-and-the-genetic-polymorphisms-of-gad2-and-type-2-diabetes-mellitus.pdf
- >The frequency distributions of AA, AG, and GG in theT2-DM group were 6.6, 39.4, and 53.9%, respectively. The frequency distributions of AA, AG, and GG in the healthy control group were 6.0, 40.6, and 53.4%
- 002c: 10q; GAD2 (TT;) Position: 26216765
- \https://www.snpedia.com/index.php/Rs8190590
- \https://www.geneticsmr.com/articles/relationship-between-serum-gadab-and-the-genetic-polymorphisms-of-gad2-and-type-2-diabetes-mellitus.pdf
- >The frequency distributions of CC, CT, and TT in the T2-DM group were 52.1, 36.4, and 11.5%, respectively. The frequency distributions of CC, CT, and TT in the control group were 44.4, 39.4, and 16.2%
- 003: 10q; GATA3 (GG;) Position: 8272081
- \https://www.snpedia.com/index.php/Rs17143387
- \https://www.ncbi.nlm.nih.gov/snp/rs17143387#frequency_tab
- >African (T=0.946, G=0.054,) East Asian (T=0.532, G=0.468)
- \http://www.nature.com/articles/ncomms10815/tables/1
- >Hair shape [...] GATA3 [...] Alleles ancestral>derived: T>G
- 004: 17q; GH1 (AA;) Position: 61995030
- \http://www.pdgene.org/view?poly=rs2665802
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20650818/
- >+1169A allele of the A/T single nucleotide polymorphism (SNP; rs2665802
- >the +1169A allele contributes directly to the observed reduction in both GH1 gene expression and GH secretion
- 004b: 17q; GH1 (AA;) Position: 63918016
- \https://www.snpedia.com/index.php/Rs71640277
- \https://www.omim.org/entry/139250#0009
- >Cogan et al. (1995) reported a G-to-A transition of the first base of the donor splice site of intron 3 (IVS3+1G-A) in the GH1 gene in subjects with isolated growth hormone deficiency type II
- 004c: 17q; GH1 (AA;) Position: 63917337
- \https://www.snpedia.com/index.php/Rs137853223
- \https://www.omim.org/entry/139250#23
- >In a large kindred with dominant growth hormone deficiency (IGHD2; 173100) Gertner et al. (1998) detected a heterozygous G-to-A transition at nucleotide 6664 in exon 5 of the GH1 gene, resulting in an arg183-to-his substitution (R183H
- >Hess et al. (2007) studied the phenotype-genotype correlation of subjects with IGHD2 caused by an R183H mutation
- >The affected subjects in family 1 were significantly shorter (-2.6 vs -0.1 standard deviation score (SDS), p less than 0.0001) and had significantly lower IGF1 (147440) serum levels (-1.9 vs -0.5 SDS, p less than 0.0001), compared with family members with a normal genotype
- >The affected adults exhibited great variability in their stature, ranging from -4.5 to -1.0 SD (mean -2.8 SDS), with 5 members being of normal height (greater than -2 SDS
- 005: Xq; GPR143 (CC;) Position: 9759390
- \https://www.snpedia.com/index.php/Rs137852296
- \https://www.omim.org/entry/300808#3
- >In a patient with OA1 (300500), Schnur et al. (1998) identified a missense mutation that converted codon 133 from TGG (trp) to CGG (arg) (W133R). The patients also showed developmental delay and renal and immune dysfunction. In another family, the same W133R mutation was found. That family was of interest because a manifesting female had a 45,XO karyotype (Turner syndrome
- 005b: Xq; GPR143 (AA;) Position: 9743637
- \https://www.snpedia.com/index.php/Rs137852297
- \https://www.omim.org/entry/300808#5
- >a patient with OA1 (300500) characterized by the presence of giant pigment granules in melanocytes, Schnur et al. (1998) identified a thr232-to-lys (T232K) missense mutation resulting from a change of ACG to AAG in the OA1 gene. The mother had a normal fundus examination; the mother and the affected grandfather had 'vitiligo
- 005c: Xq; GPR143 (TT;) Position: 9760811
- \https://www.snpedia.com/index.php/Rs137852298
- \https://www.omim.org/entry/300808#9
- >NYSTAGMUS, 6, CONGENITAL, X-LINKED
- >In a large 6-generation Chinese family in which 8 males had congenital nystagmus (NYS6; 300814), Liu et al. (2007) identified a 266C-T transition in exon 2 of the GPR143 gene, resulting in a ser89-to-phe (S89F) substitution
- 005d: Xq; GPR143 (AA;) Position: 9759332
- \https://www.snpedia.com/index.php/Rs58933950
- \https://www.omim.org/entry/300808#4
- >In a patient with ocular albinism (OA1; 300500) and giant pigment granules in melanocytes, Schnur et al. (1998) demonstrated a mutation changing codon 152 from AGC (ser) to AAC (asn) (S152N) in the OA1 gene
- 005e: Xq; GPR143 (AA;) Position: 9765714
- \https://www.snpedia.com/index.php/Rs62635018
- \https://www.omim.org/entry/300808#8
- >In a study of 9 families with X-linked ocular albinism (OA1; 300500), Rosenberg and Schwartz (1998) identified 7 pathogenic mutations. Only 1 of these, gly35 to asp (G35D
- >https://www.nature.com/articles/5200226.pdf
- >In all patients an aberrant SSCA pattern was found. Direct sequencing revealed the mutations 164G>A (G35D)
- 006: 2q; GRB14 (CC;) Position: 165513091
- \Citations: http://www.pdgene.org/view?poly=rs10195252
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >GBR14, EA = T
- 007: 10q; GRID1 (TT;) Position: 86233584
- \https://www.snpedia.com/index.php/Rs2814331
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2814331
- \http://www.nature.com/articles/ncomms10815/tables/1
- H
- 001: 15q; HERC2 (GG;) Position: 28111713
- \https://www.snpedia.com/index.php/Rs1129038
- \https://www.ncbi.nlm.nih.gov/pubmed/18172690?dopt=Abstract
- 001b: 15q; HERC2 (CC;) Position: 28120472
- \https://www.snpedia.com/index.php/Rs12913832
- \https://www.nature.com/articles/jhg201138
- >carriers possessing CC, CA or AA genotypes in rs12896399 with CC genotype in rs12913832 are all classified into the group of ‘high-risk’ of having blue eye colour [...] Detailed analysis indicates that the chances of having blue eye colour rise with A allele in rs12896399 [...] and the highest chances of having blue eye colour are with AA genotype in rs12896399, but only on condition of possessing CC genotype in rs12913832. The allele T in rs12913832 in HERC2 masks this effect and, independently of the genotype in rs12896399, individuals possessing the T allele in rs12913832 are classified into the group of ‘low-risk’ of having blue eye colour
- 001c: 15q; HERC2 (GG;) Position: 28285036
- \https://www.snpedia.com/index.php/Rs1667394
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >Blue versus brown eyes = rs1667394-A = Discovery OR(29.43,) Replication OR(18.46,) Netherlands OR(15.34) [...] Blue versus green eyes = Discovery OR(6.74,) Replication OR(5.83,) Netherlands OR(5.96) [...] Red versus non-red hair = rs1667394-A = Discovery OR(0.91,) Replication OR(0.81,) Netherlands OR(1.44) [...] Blond versus brown hair = rs1667394-A = Discovery OR(4.94,) Replication OR(5.96,) Netherlands OR(5.51)
- 001d: 15q; HERC2 (CC;) Position: 28208069
- \https://www.snpedia.com/index.php/Rs2238289
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18172690/
- 001e: 15q; HERC2 (TT;) Position: 28182840
- \https://www.snpedia.com/index.php/Rs7170852
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18172690/
- 001f: 15q; HERC2 (AA;) Position: 28120587
- \https://www.snpedia.com/index.php/Rs7183877
- \https://www.ncbi.nlm.nih.gov/pubmed/18172690?dopt=Abstract
- 001g: 15q; HERC2 (CC;) Position: 28243742
- \https://www.snpedia.com/index.php/Rs8028689
- \https://www.ncbi.nlm.nih.gov/pubmed/18172690?dopt=Abstract
- 001h: 15q; HERC2 (AA;) Position: 28268218
- \https://www.snpedia.com/index.php/Rs916977
- \https://www.ncbi.nlm.nih.gov/pubmed/18172690?dopt=Abstract
- 001i: 15q; HERC2 (GG;) Position: 27985172
- \https://www.snpedia.com/index.php/Rs1800407
- \https://www.nature.com/articles/jhg201138
- >Green versus non-green eye colour is, according to MDR, best predicted by a three-factor model consisting of rs12913832 in HERC2, rs1408799 in TYRP1 and rs1800407 in OCA2 [...] The rs12913832 position removes 0.28% of ‘uncertainty’ in green eye colour prediction, rs1408799 removes 0.23% and the interaction between them eliminates an additional 1.23%
- \https://www.nature.com/articles/jhg201138/figures/2
- >rs1800407, Green/non-Green eyes, AA=0/2, AG=18/58, GG=15/210
- 002: 6q; HLA-DQA1 (AA;) Position: 32638107
- \https://www.snpedia.com/index.php/Rs2187668
- \https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-016-0211-8#Tab2
- 003: 6q; HMGA1 (CC;) Position: 34246545
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1150781
- >Ancestral Allele = G [...] G(G, Gly) -> C(A, Ala) [...] Frequency = CEU(CC=0.862, CG=0.137, GG=0.000,) HCB(CC=0.822, CG=0.155, GG=0.022,) YRI(CC=0.305, CG=0.491, GG=0.203)
- \https://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs1150781, Effect Allele = C, Effect(0.73)
- 004: 12q; HMGA2 (TT;) Position: 65964567
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1042725
- >Ancestral Allele = C [...] Frequency = CEU(CC=0.283, CT=0.424, TT=0.292,) HCB(CC=0.023, CT=0.441, TT=0.534,) YRI(CC=0.401, CT=0.508, TT=0.089)
- \https://www.snpedia.com/index.php/Rs1042725
- \http://www.nature.com/ng/journal/v39/n10/abs/ng2121.html
- >We estimate that rs1042725 explains ∼0.3% of population variation in height (∼0.4 cm increased adult height per C allele)
- >Note: HMGA2 is much more generally expressed throughout the body than HMGA1, and if the ancestral allele is associated with greater height it's probably also associated with a general archaic appearance. As well, rs1150781-C of HMGA1 is derived while being associated with greater stature, while rs1042725-C is ancestral while being associated with greater height.
- 004b: 12q; HMGA2 (CC;) Position: 65950030
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=10784502
- >Ancestral Allele = T [...] Frequency = CEU(CC=0.265, CT=0.415, TT=0.318,) HCB(CC=0.000, CT=0.232, TT=0.767,) YRI(CC=0.327, CT=0.495, TT=0.176)
- \https://www.snpedia.com/index.php/Rs10784502
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635491/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635491/bin/NIHMS378125-supplement-supp_tables.docx
- >rs10784502, Effect Allele = T, non-Effect Allele = C, Effect(-11860.7)
- 004c: 12q; HMGA2 (TT;) Position: 65961131
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=867633
- >Ancestral Allele = C [...] Fwd = C/T, Rev = A/G, T-A/G-T, so A=C, G=T [...] Frequency = CEU(CC=0.416, CT=0.383, TT=0.200,) HCB(CC=0.022, CT=0.355, TT=0.622,) YRI(CC=0.533, CT=0.383, TT=0.083)
- \https://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs867633, Effect Allele = A, Effect(-0.39)
- 005: 12q; HOXC10 (AA;) Position: 54384387
- \Citations: http://www.pdgene.org/view?poly=rs7302703
- \https://academic.oup.com/hmg/article/23/9/2498/632550/Gene-centric-meta-analyses-for-central-adiposity
- \was associated with increased WHR [...] as was rs7302703-G in HOXC10
- 006: 12q; HOXC13 (CC;) Position: 54342684
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1443512
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >HOXC13, EA = A
- 007: 2q; HOXD3 (AA;) Position: 176139387
- \https://www.snpedia.com/index.php/Rs4078756
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28691018/
- 007b: 2q; HOXD3 (TT;) Position: 176151087
- \https://www.snpedia.com/index.php/Rs13418078
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20686522/
- 007c: 2q; HOXD3 (AA;) Position: 176150242
- \https://www.snpedia.com/index.php/Rs1867863
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028147/#!po=38.8889
- 008: 2q; HOXD10 (AA;) Position: 176119164
- \https://www.snpedia.com/index.php/Rs104893634
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/14878/
- 009: 17q; HSD17B1 (AA;) Position: 42552898
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=201739205
- \https://www.ncbi.nlm.nih.gov/m/pubmed/26694100/
- >point mutation vIV (A -> C) was located in the putative TATA box of the EDH17B2 gene [...] the mutation vIV decreases EDH17B2 promoter activity by an average of 45%
- \https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/hsd17b1
- >The type 1 enzyme (HSD17B1) is referred to as the “estrogenic” 17β-HSD because it catalyzes the final step in estrogen biosynthesis by preferentially reducing the weak estrogen estrone to yield the potent estrogen 17β-estradiol
- 010: 13q; HTR2A (GG;) Position: 46867572
- \https://www.snpedia.com/index.php/Rs1328674
- 010b; 13q; HTR2A (TT;) Position: 46897343
- \https://www.snpedia.com/index.php/Rs6311
- 010c; 13q; HTR2A (TT;) Position: 46895805
- \https://www.snpedia.com/index.php/Rs6313
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18006541/
- 010d; 13q; HTR2A (TT;) Position: 46834899
- \https://www.snpedia.com/index.php/Rs6314
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18006541/
- 010e; 13q; HTR2A (GG;) Position: 46854476
- \https://www.snpedia.com/index.php/Rs643627
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16814396/
- 010f; 13q; HTR2A (AA;) Position: 46835968
- \https://www.snpedia.com/index.php/Rs7322347
- \http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117792
- 010g; 13q; HTR2A (CC;) Position: 46855311
- \https://www.snpedia.com/index.php/Rs7984966
- \https://www.ncbi.nlm.nih.gov/m/pubmed/27230021/
- 010h; 13q; HTR2A (GG;) Position: 46837850
- \https://www.snpedia.com/index.php/Rs7997012
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16642436/
- 011: 2q; HTR2B (CC;) Position: 231115305
- \https://www.snpedia.com/index.php/Rs10194776
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19455600/
- 011b: 2q; HTR2B (AA;) Position: 231116063
- \https://www.snpedia.com/index.php/Rs16827801
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19455600/
- 011c: 2q; HTR2B (TT;) Position: 231123707
- \https://www.snpedia.com/index.php/Rs79874540
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21179162/
- 012: Xq; HTR2C (GG;) Position: 114903581
- \https://www.snpedia.com/index.php/Rs1414334
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558473/
- 012b: Xq; HTR2C (GG;) Position: 114765807
- \https://www.snpedia.com/index.php/Rs2428707
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28260903/
- 012c: Xq; HTR2C (TT;) Position: 114584047
- \https://www.snpedia.com/index.php/Rs3813929
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19434072/
- 012d: Xq; HTR2C (TT;) Position: 114849062
- \https://www.snpedia.com/index.php/Rs4272555
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28260903/
- 012e: Xq; HTR2C (TT;) Position: 114590222
- \https://www.snpedia.com/index.php/Rs498177
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21185157/
- 012f: Xq; HTR2C (CC;) Position: 114584109
- \https://www.snpedia.com/index.php/Rs518147
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19434072/
- 012g: Xq; HTR2C (AA;) Position: 114583441
- \https://www.snpedia.com/index.php/Rs521018
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21185157/
- I
- 001: 15q; IGFR1 (AA;) Position: 98908747
- \https://www.snpedia.com/index.php/Rs34516635
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265137/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265137/table/T2/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=34516635
- 001b: 15q; IGFR1 (AA;) Position: 98693273
- \https://www.snpedia.com/index.php/Rs1976667
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22172258/
- 001c: 15q; IGFR1 (AA;) Position: 98934996
- \https://www.snpedia.com/index.php/Rs2229765
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19460140/
- 002: Xq; IL3RA (CC;) Position: 1352044
- \https://www.snpedia.com/index.php/Rs6422441
- \http://www.nature.com/mp/journal/v12/n6/fig_tab/4001983t2.html#figure-title
- 002b: Xq; IL3RA (GG;) Position: 1352245
- \https://www.snpedia.com/index.php/Rs6603272
- \http://www.nature.com/mp/journal/v12/n6/fig_tab/4001983t2.html#figure-title
- 002c: Xq; IL3RA (CC;) Position: 1352649
- \https://www.snpedia.com/index.php/Rs17883192
- \http://www.nature.com/mp/journal/v12/n6/fig_tab/4001983t2.html#figure-title
- 003: 7q; IL6 (GG;) Position: 22727026
- \https://www.snpedia.com/index.php/Rs1800795
- \https://www.ncbi.nlm.nih.gov/m/pubmed/15664628/
- \https://www.ncbi.nlm.nih.gov/m/pubmed/22695063/
- 003b: 7q; IL6 (TT;) Position: 22727518
- \https://www.snpedia.com/index.php/Rs2069830
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18727828/
- 004: Xq; IRAK1 (TT;) Position: 154018741
- \https://www.snpedia.com/index.php/Rs1059702
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21933552/
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21898345/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848422/
- 004b: Xq; IRAK1 (TT;) Position: 154013378
- \https://www.snpedia.com/index.php/Rs1059703
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23233309/
- 004c: Xq; IRAK1 (AA;) Position: 154010439
- \https://www.snpedia.com/index.php/Rs3027898
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20500689/
- 004: 6q; IRF4 (TT;) Position: 396321
- \https://www.snpedia.com/index.php/Rs12203592
- \http://www.nature.com/articles/ncomms10815/tables/1
- 005: 16q; ITGAL (CC;) Position: 30481502
- \https://www.snpedia.com/index.php/Rs1064524
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4043868/
- 006: 12q; ITPR2 (AA;) Position: 26344550
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=718314
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >ITPR2, EA = G
- J
- K
- 001: 12q; KITLG (TT;) Position: 88934558
- \https://www.snpedia.com/index.php/Rs12821256
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >Blue versus brown eyes = rs12821256-C = Discovery OR(1.13,) Replication OR(1.20,) Netherlands OR(0.96) [...] Blue versus green eyes = rs12821256-C = Discovery OR(0.92,) Replication OR(1.09,) Netherlands OR(1.18) [...] Red versus non-red hair = rs12821256-C = Discovery OR(1.01,) Replication OR(0.88,) Netherlands OR(0.65) [...] Blond versus brown hair = rs12821256-C = Discovery OR(2.32,) Replication OR(1.90,) Netherlands OR(2.43)
- 001b: 12q; KITLG (GG;) Position: 88905969
- \https://www.snpedia.com/index.php/Rs642742
- \https://omim.org/entry/184745#0002
- >The frequency of the ancestral A allele is at least 92% in West Africans, whereas the frequency of the derived G allele is at least 86% in Europeans and East Asians. Admixture mapping suggested that replacement of 2 West African alleles (AA) with 2 European alleles (GG) may account for a lightening of a person's skin by 6 to 7 melanin units. In comparison, the overall skin reflectance difference between West Africans and Europeans is 30 melanin units
- 001c: 12q; KITLG (CC;) Position: 88559549
- \https://www.snpedia.com/index.php/Rs3782179
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865677/
- >testicular germ cell tumors (TGCT [...] TGCT risk was increased three-fold per copy of the major A-allele in KITLG rs3782179
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3782179
- 001d: 12q; KITLG (GG;) Position: 88560182
- \https://www.snpedia.com/index.php/Rs4474514
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865677/
- >testicular germ cell tumors (TGCT [...] TGCT risk was increased three-fold per copy of the major A-allele in KITLG [...] and rs4474514
- 001e: 12q; KITLG (AA;) Position: 88559882
- \https://www.snpedia.com/index.php/Rs4590952
- \http://www.cell.com/cell/fulltext/S0092-8674(13)01154-9
- >rs4590952, G/A [...] However, the PWM score decreases dramatically with the A allele
- 002: 3q; KPNA4 (CC;) Position: 160508519
- \https://www.snpedia.com/index.php/Rs17236529
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4043868/
- L
- 001: 1q; LEPR (GG;) Position: 66058513
- \http://www.pdgene.org/view?poly=rs1137101
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- 002: 11q; LRP5 (GG;) Position: 68192346
- \Citations: http://www.pdgene.org/view?poly=rs599083
- \>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321886/?report=classic
- \>These revealed that adipocyte numbers in android fat tended to be lower in carriers of the low BMD-associated allele at rs599083 (GG, GT) versus homozygous carriers of the common allele (TT) (p = 0.05
- 003: 6q; LY86 (AA;) Position: 6688148
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1294421
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >LY86, EA = G
- 004: 1q; LYPLAL1 (TT;) Position: 217817340
- \Citations: https://www.genome.gov/pages/research/dir/waisthipratio.pdf
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926774/
- \TT-allele carriers showed furthermore lower scores for Hunger (74%, p < 0.001), lower Disinhibition (53%, p < 0.001), and higher Cognitive restraint (21%, p = 0.017) than GG/GT carriers
- 004b: 1q; LYPLAL1 (TT;) Position: 217817340
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4846567
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >LYPLAL1, EA = G
- M
- 001: 2q; MAP2 (GG;) Position: 209633537
- \https://www.snpedia.com/index.php/Rs9288410
- \https://www.ncbi.nlm.nih.gov/books/NBK25535/
- 002: 17q; MAP3K3 (TT;) Position: 63647335
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=8081612
- >Ancestral Allele = T [...] Frequency = CEU(CC=0.522, CT=0.389, TT=0.088,) HCB(CC=0.930, CT=0.069, TT=0.000,) YRI(CC=0.026, CT=0.238, TT=0.734)
- \https://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs8081612, Effect Allele = T, Effect(0.37)
- 003: 16q; MC1R (AT;) Position: 89919733
- \https://www.snpedia.com/index.php/Rs104894523
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894523
- 003b: 16q; MC1R (TT;) Position: 89919728
- \https://www.snpedia.com/index.php/Rs104894524
- 003c: 16q; MC1R (TT;) Position: 89919722
- \https://www.snpedia.com/index.php/Rs1110400
- 003d: 16q; MC1R (AA;) Position: 89919683
- \https://www.snpedia.com/index.php/Rs11547464
- 003e: 16q; MC1R (TT;) Position: 89919436
- \https://www.snpedia.com/index.php/Rs1805005
- 003f: 16q; MC1R (AA;) Position: 89919510
- \https://www.snpedia.com/index.php/Rs1805006
- 003g: 16q; MC1R (TT;) Position: 89919709
- \https://www.snpedia.com/index.php/Rs1805007
- >rs1805007, known as Arg151Cys or R151C
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >Red versus non-red hair = rs1805007-T = Discovery OR(12.47,) Replication OR(6.12,) Netherlands OR(13.02) [...] Blond versus brown hair = rs1805007-T = Discovery OR(2.34,) Replication OR(2.0,) Netherlands OR(1.59)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338132/
- >Several studies have been conducted with mixed results since our initial report of increased Parkinson's disease risk in individuals with red hair and/or red hair‐associated p.R151C variant of the MC1R gene
- >We found that red hair (pooled odds ratios = 1.68, 95% confidence intervals: 1.07, 2.64) and p.R151C (pooled odds ratios = 1.10, 95% confidence intervals: 1.00, 1.21), but not p.R160W, were associated with greater risk for Parkinson's disease. Our results support potential roles of pigmentation and its key regulator MC1R in the pathogenesis of Parkinson's disease
- 003h: 16q; MC1R (TT;) Position: 89919736
- \https://www.snpedia.com/index.php/Rs1805008
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >Red versus non-red hair = rs1805008-T = Discovery OR(7.86,) Replication OR(4.53,) Netherlands OR(3.71) [...] Blond versus brown hair = rs1805008-T = Discovery OR(1.88,) Replication OR(1.74,) Netherlands OR(1.93)
- 003i: 16q; MC1R (CC;) Position: 89920138
- \https://www.snpedia.com/index.php/Rs1805009
- 003j: 16q; MC1R (AA;) Position: 89919532
- \https://www.snpedia.com/index.php/Rs2228479
- 003k: 16q; MC1R (AA;) Position: 89919746
- \https://www.snpedia.com/index.php/Rs885479
- 004: 2q; MCM6 (TT;) Position: 135851076
- \https://www.snpedia.com/index.php/Rs4988235
- \http://www.nature.com/ejcn/journal/v71/n1/full/ejcn2016164a.html?foxtrotcallback=true
- 004b: 2q; MCM6 (AA;) Position: 135859184
- \https://www.snpedia.com/index.php/Rs182549
- \http://omim.org/entry/601806
- 004c: 2q; MCM6 (CC;) Position: 135851176
- \https://www.snpedia.com/index.php/Rs145946881
- \http://www.omim.org/entry/601806#0003
- 004d: 2q; MCM6 (GG;) Position: 135851081
- \https://www.snpedia.com/index.php/Rs41380347
- \http://www.omim.org/entry/601806#0004
- 005: 8q; MCPH1 (CC;) Position: 6444662
- \https://www.snpedia.com/index.php/Rs930557
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=930557
- >Ancestral Allele: G [...] G(D, Asp) -> C(H, His) [...] Frequency = CEU(CC=0.616, CG=0.333, GG=0.050,) HCB(CC=0.644, CG=0.288, GG=0.066,) YRI(CC=0.100, CG=0.483, GG=0.416)
- \https://academic.oup.com/hmg/article/16/6/600/610971
- >To test the hypothesis that the recent selective sweep at ASPM and Microcephalin is due to increased intelligence, we genotyped the diagnostic sites that distinguish the adaptive derived allele (D-allele) from the ancestral allele (A-allele [...] Australian (Largest) sample = MCPH1, AA(FIQ=112.7-/+12.2,) AD(FIQ=113.3-/+12.3,) DD(FIQ=114.2-/+12.7) [...] Genotyping of Microcephalin was performed by automated sequencing of the diagnostic G37995C SNP
- \http://www.sciencedirect.com/science/article/pii/S016028960200137X
- >African-descended people (Blacks) average cranial capacities of 1267 cm3, European-descended people (Whites) 1347 cm3 [...] It must be concluded that the race differences in average brain size are securely established [...] Blacks average an IQ of 85, Whites 100
- 005b: 8q; MCPH1 (AA;) Position: 5917813
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2816514
- >Ancestral Allele = C [...] Frequency = CEU(AA=0.150, AC=0.349, CC=0.500,) HCB(AA=0.022, AC=0.155, CC=0.822,) YRI(AA=0.000, AC=0.100, CC=0.899)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/?report=objectonly
- >rs2816514, Population(Females,) Effect Size([+]44-/+23cm3) [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs2816514 = Major/minor = C/A
- 005c: 8q; MCPH1 (AA;) Position: 5920479
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2816517
- >Ancestral Allele = A [...] Frequency = CEU(AA=0.237, AC=0.406, CC=0.355,) HCB(AA=0.022, AC=0.222, CC=0.755,) YRI(AA=0.000, AC=0.250, CC=0.750)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/?report=objectonly
- >rs2816517, Population(Females,) Effect Size([+]37-/+20cm3) [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs2816514 = Major/minor = C/A
- 005d: 8q; MCPH1 (CC;) Position: 6208094
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=11779303
- >Ancestral Allele = C [...] CEU(CC=0.026, CG=0.380, GG=0.592,) HCB(CC=0.000, CG=0.116, GG=0.883,) YRI(CC=0.000, CG=0.09, GG=0.909,) MKK(CC=0.076, CG=0.300, GG=0.622)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/#!po=16.6667
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/table/t01/?report=objectonly
- >rs11779303, Population(Females,) Effect Size([+]62-/+33cm3) [...] The effect sizes represent increase in volume and area per extra copy of the minor allele
- \http://www.pnas.org/content/pnas/suppl/2009/12/16/0908454107.DCSupplemental/st02.doc
- >rs11779303 = Major/minor = G/C
- 005e: 8q; MCPH1 (CC;) Position: 6621521
- \https://www.snpedia.com/index.php/Rs1057090
- \https://academic.oup.com/hmg/article/17/9/1329/571192
- >SNP2 = rs930557, SNP3 = rs1057090, SNP4 = rs2912016 [...] we observed a significant positive correlation between the CCC haplotype (27.7%) and the cranial volume (P = 0.004) while the CTC haplotype (20.4%) [...] This result indicates that the derived C allele of rs1057090 contributes to the larger cranial volume in the studied males [...] SNP2(C,)SNP3(T,)SNP4(C)=Hap-score(-2.92,) SNP2(C,)SNP3(C,)SNP4(C)=Hap-score(2.93)
- 005f: 8q; MCPH1 (AA;) Position: 6621657
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2912016
- >Ancestral Allele: A
- \https://academic.oup.com/hmg/article/17/9/1329/571192
- >SNP2 = rs930557, SNP3 = rs1057090, SNP4 = rs2912016 [...] we observed a significant positive correlation between the CCC haplotype (27.7%) and the cranial volume (P = 0.004) while the CTC haplotype (20.4%) [...] This result indicates that the derived C allele of rs1057090 contributes to the larger cranial volume in the studied males [...] SNP2(C,)SNP3(T,)SNP4(C)=Hap-score(-2.92,) SNP2(C,)SNP3(C,)SNP4(C)=Hap-score(2.93)
- 006: Xq; MECP2 (AA;) Position: 154031941
- \https://www.snpedia.com/index.php/Rs2075596
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006b: Xq; MECP2 (CC;) Position: 154033423
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3027933
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006c: Xq; MECP2 (AA;) Position: 154045127
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3027939
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006d: Xq; MECP2 (TT;) Position: 154046529
- \https://www.snpedia.com/index.php/Rs17435
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=17435
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006e: Xq; MECP2 (AA;) Position: 154057430
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7884370
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006f: Xq; MECP2 (CC;) Position: 154059995
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1734787
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006g: Xq; MECP2 (AA;) Position: 154065469
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1734791
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006h: Xq; MECP2 (AA;) Position: 154075609
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1734792
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 006i: Xq; MECP2 (AA;) Position: 154082978
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2239464
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/table/T1/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734382/
- 007: 5q; MEGF10 (AA;) Position: 127348117
- \https://www.snpedia.com/index.php/Rs27388
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18179784/
- 008: 20q; MMP24 (GG;) Position: 35231612
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2425019
- >Ancestral Allele = G [...] Frequency = CEU(AA=0.292, AG=0.548, GG=0.159,) HCB(AA=0.465, AG=0.418, GG=0.116,) YRI(AA=0.000, AG=0.000, GG=1.000)
- \https://www.sciencedirect.com/science/article/pii/S000292971000594X#!
- >Table 1. Sixty-Four Loci Showing Significant Evidence for Association with Adult Height [...] rs2425019, Effect Allele = A, Effect(-0.32)
- >Note: Predominantly expressed in the cerebellum. Yoruba(YRI) Africans are fixed for the G allele, suggesting that rs2425019-G leads to a larger cortex and greater height due to the induction of a long-limbed 'equatorial' phenotype. The archaic (Mesolithic) phenotype of Europe had an average cranial capacity of 1567cc, while modern Europeans average 1362-1391cc;
- \https://www.sciencedirect.com/science/article/pii/S0018442X14000900
- >The most comprehensive records are those from Europe, where Henneberg (1988, 1990) has examined the records of thousands of skulls. He reports a “Mesolithic” mean volume for males of 1567 ml [...] while the males of post-Mediaeval and recent times yielded a mean of 1391 ml
- 009: 8q; MSRA (CC;) Position: 9860080
- \Citations: http://www.pdgene.org/view?poly=rs545854
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110388/?report=classic
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- 010: 11q; MTNR1B (CC;) Position: 92975544
- \https://www.snpedia.com/index.php/Rs10830963
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597741/table/pone-0003962-t003/
- 010b: 11q; MTNR1B (TT;) Position: 92972141
- \https://www.snpedia.com/index.php/Rs12804291
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597741/table/pone-0003962-t003/
- 010c: 11q; MTNR1B (CC;) Position: 92980341
- \https://www.snpedia.com/index.php/Rs3781638
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597741/table/pone-0003962-t003/
- 010d: 11q; MTNR1B (CC;) Position: 92968430
- \https://www.snpedia.com/index.php/Rs4753426
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17632395/
- 011: 1q; mTOR (TT;) Position: 11262571
- \https://www.snpedia.com/index.php/Rs2295080
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23209702/
- N
- 001: 16q; NET (TT;) Position: 55692146
- \https://www.snpedia.com/index.php/Rs11568324
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587507/
- 001b: 16q; NET (GG;) Position: 55670130
- \https://www.snpedia.com/index.php/Rs187715
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21070505/
- 002: 7q; NFE2L3 (CC;) Position: 25871109
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1055144
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >NFE2L3, EA = T
- 003: 4q; NFKB1 (AA;) Position: 102523317
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1585215
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720066/
- >Polymorphic variation in NFKB1 and other aspirin-related genes and risk of Hodgkin lymphoma
- >rs1585215, Cases(AA=111, AG=250, GG=82,) Controls(AA=151, AG=169, GG=33)
- \https://www.ncbi.nlm.nih.gov/pubmed/26663363
- >The importance of Nfkb1 function can be seen in mouse models, where Nfkb1(-/-) mice display increased inflammation and susceptibility to certain forms of DNA damage, leading to cancer, and a rapid ageing phenotype
- 003b: 4q; NFKB1 (AA;) Position: 102522412
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1599961
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720066/
- >Polymorphic variation in NFKB1 and other aspirin-related genes and risk of Hodgkin lymphoma
- >rs1599961, Cases(GG=170, GA=221, AA=66,) Controls(GG=128, GA=175, AA=64)
- 003c: 4q; NFKB1 (TT;) Position: 102575280
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4648022
- >MAF = T
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735864/
- >SNP rs4648022 is an intronic SNP, with a MAF of 0.06 in cases and 0.10 in controls. The ordinal OR was 0.59 for each variant allele (95% CI 0.41-0.84), and this association was similar for CLL/SLL (OR=0.58; 95% CI 0.32-1.02), follicular lymphoma (OR=0.58; 95% CI 0.32-1.05), and DLBCL (OR=0.56; 95% CI 0.26-1.20)
- 004: 3q; NISCH (CC;) Position: 52506426
- \Citations: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6784615
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >NISCH, EA = T
- 005: 8q; NRG1 (CC;) Position: 32168933
- \https://www.snpedia.com/index.php/Rs10093107
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040109/table/T1/?report=objectonly
- 005b: 8q; NRG1 (CC;) Position: 32039076
- \https://www.snpedia.com/index.php/Rs1462906
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21179114/
- 005c: 8q; NRG1 (TT;) Position: 32553698
- \https://www.snpedia.com/index.php/Rs16879552
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024406/table/pone-0016181-t001/?report=objectonly
- 005d: 8q; NRG1 (TT;) Position: 31638065
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19594860/
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17925794/
- 006: 14q; NRXN3 (GG;) Position: 79945162
- \http://www.pdgene.org/view?poly=rs10146997
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419359/table/T3/
- O
- 001: 15q; OCA2 (GG;) Position: 27752101
- \https://www.snpedia.com/index.php/Rs17565841
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=17565841
- >Frequency, CEU = (A=0.016, G=0.816,) YRI = (A=0.05, G=0.94)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758866/#!po=28.8462
- >Genomewide association study for onset age in Parkinson disease
- >The most highly associated SNP in both the additive and dominant three sample meta-analyses, rs17565841, is located approximately 3 kb from the 3' end of the gene OCA2 on chromosome 15 [...] This SNP was associated with an average 2.8 years younger onset age (p = 2.6 × 10-6) under an additive model and a 3.3 years younger onset age (p = 2.1 × 10-6) under a dominant model
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758866/table/T2/?report=objectonly
- >SNP = rs17565841, Minor allele = A
- 001b: 15q; OCA2 (GG;) Position: 28099092
- \https://www.snpedia.com/index.php/Rs7495174
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >Blue versus brown eyes = rs7495174-A = Discovery OR(6.9,) Replication OR(5.56,) Netherlands OR(4.87) [...] Blue versus green eyes = rs7495174-A = Discovery OR(1.41,) Replication OR(2.02,) Netherlands OR(1.45) [...] Red versus non-red hair = rs7495174-A = Discovery OR(1.49,) Replication OR(1.26,) Netherlands OR(1.15) [...] Blond versus brown hair = rs7495174-A = Discovery OR(4.94,) Replication OR(5.96,) Netherlands OR(5.51)
- 001c: 15q; OCA2 (TT;) Position: 28093567
- \https://www.snpedia.com/index.php/Rs4778241
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427173/
- \The highest association for blue:nonblue (green/hazel or brown) eye color was found with three SNPs in intron 1: rs7495174 T/C, rs6497268 (now rs4778241) G/T, and rs11855019 (now rs4778138) T/C. We found the TGT/TGT diplotype in 62.2% of samples, and this was the major blue-eye genotype, with a frequency of 91% in blue- or green-eyed individuals, compared with only 9.5% in those with brown eyes
- 001d: OCA2 (CC;) Position: 28090674
- \https://www.snpedia.com/index.php/Rs4778138
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427173/
- \The highest association for blue:nonblue (green/hazel or brown) eye color was found with three SNPs in intron 1: rs7495174 T/C, rs6497268 (now rs4778241) G/T, and rs11855019 (now rs4778138) T/C. We found the TGT/TGT diplotype in 62.2% of samples, and this was the major blue-eye genotype, with a frequency of 91% in blue- or green-eyed individuals, compared with only 9.5% in those with brown eyes
- 001e: OCA2 (CC;) Position: 28082689
- \https://www.snpedia.com/index.php/Rs4778137
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4778137
- >Frequency = CEU(C=0.465, G=0.534,) HCB(CC=0.04, CG=0.24, GG=0.711,) JPT(CC=0.681, CG=0.272, GG=0.659,) YRI(CC=0.101, CG=0.508, GG=0.389)
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20308648/
- >Association between a germline OCA2 polymorphism at chromosome 15q13.1 and estrogen receptor-negative breast cancer survival
- >the rare G allele being associated with increased overall survival (HR of death per rare allele carried = 0.56
- 002: Xq; OPN1LW (TT;) Position: 154154734
- \https://www.snpedia.com/index.php/Rs104894912
- \https://www.omim.org/entry/300822#1
- >BLUE CONE MONOCHROMACY [...] In the male proband from a 4-generation BCM family with 3 affected individuals, who had been previously studied by Reitner et al. (1991) (patient 'MP'), Nathans et al. (1993) identified a single red pigment gene carrying a C-T transition in exon 4, resulting in an arg247-to-ter (R247X) substitution
- 002b: Xq; OPN1LW (AA;) Position: 154158844
- \https://www.snpedia.com/index.php/Rs104894913
- \https://www.omim.org/entry/300822#4
- >COLORBLINDNESS, PROTAN [...] In a person with protan colorblindness (CBP; 303900), Ueyama et al. (2002) found a gly338-to-glu (GGG to GAG; G338E) mutation in the single red pigment gene. The mutant opsin showed no absorbance
- 002c: Xq; OPN1LW (CC;) Position: 154154602
- \https://www.snpedia.com/index.php/Rs121434621
- \https://www.omim.org/entry/300822#3
- >BLUE CONE MONOCHROMACY [...] In the male proband from a 3-generation family with 8 individuals with blue cone monochromacy (BCM; 303700), Nathans et al. (1993) identified a cys203-to-arg (C203R) mutation
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121434621
- >T(T, Cys) -> C(R, Arg)
- 003: Xq; OPN1MW (CC;) Position: 154191716
- \https://www.snpedia.com/index.php/Rs104894914
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894914
- >T(T, Cys) -> C(R, Arg)
- \https://www.omim.org/entry/300821#1
- >DEUTERANOMALY [...] Jagla et al. (2002) observed the C203R mutation among 5 of 50 multigene deuteranopes (see 303800) of middle European ancestry, suggesting a founder effect for this mutation
- 003b: Xq; OPN1MW (AA;) Position: 154187939
- \https://www.snpedia.com/index.php/Rs104894915
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894915
- \https://www.omim.org/entry/300821#3
- >In a Japanese subject with deutan colorblindness (CBD; 303800), Ueyama et al. (2002) found an asn94-to-lys (AAC to AAA) missense mutation in the single green pigment gene
- 003c: Xq; OPN1MW (AA;) Position: 154195934
- \https://www.snpedia.com/index.php/Rs104894916
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894916
- \https://www.omim.org/entry/300821#4
- >In a Japanese male with deutan colorblindness (CBD; 303800), Ueyama et al. (2002) found an arg330-to-gln (CGA to CAA) mutation in both green pigment genes
- 003d: Xq; OPN1MW (CC;) Position: 154190173
- \https://www.snpedia.com/index.php/Rs267606927
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=267606927
- >T(W, Trp) -> C(R, Arg)
- \https://www.omim.org/entry/300821#6
- >CONE DYSTROPHY 5, X-LINKED [...] long-range PCR and sequence analysis in a 3-generation British family with X-linked cone dystrophy mapping to Xq27.3 (see 303700), Gardner et al. (2010) demonstrated that the cone opsin gene array in affected members consisted of an LW gene containing a 529T-C transition in an MW exon 3, resulting in a trp177-to-arg (W177R) substitution at a highly conserved residue, followed by an MW gene containing an identical W177R mutation in exon 3
- 003e: Xq; OPN1MW (CC;) Position: 154182566
- \https://www.snpedia.com/index.php/Rs724159983
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=724159983
- >Contig allele = A
- \https://www.omim.org/entry/300821#5
- >COLORBLINDNESS, DEUTAN [...] In 32 of 37 (86.5%) Japanese subjects with deutan colorblindness (CBD; 303800) and a normal genotype, Ueyama et al. (2003) identified a -71A-C transversion in the green pigment gene at the second position in the array
- 004: 7q; OPN1SW (AA;) Position: 128775556
- \https://www.snpedia.com/index.php/Rs104894031
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894031
- \https://www.omim.org/entry/613522#1
- >In 4 individuals with tritanopia (190900), Weitz et al. (1992) identified a 644G-A transition in the BCP gene, resulting in a gly79-to-arg (G79R) substitution in the second transmembrane domain of the blue-sensitive opsin
- 004b: 7q; OPN1SW (CC;) Position: 128774545
- \https://www.snpedia.com/index.php/Rs104894032
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894032
- >T(S, Ser) -> C(P, Pro)
- \https://www.omim.org/entry/613522#2
- >In an individual with tritanopia (190900), Weitz et al. (1992) identified a 1049C-T transition in exon 3 of the BCP gene, resulting in a ser214-to-pro (S214P) substitution in the fifth transmembrane domain of the blue-sensitive opsin
- 004c: 7q; OPN1SW (TT;) Position: 128773786
- \https://www.snpedia.com/index.php/Rs104894033
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894033
- >C(P, Pro) -> T(S, Ser)
- \https://www.omim.org/entry/613522#3
- >In 3 unrelated persons with tritanopia (190900), Weitz et al. (1992) identified a 1199C-T transition in the BCP gene, resulting in the substitution of serine for proline-264 (P264S
- 005: 3q; OXTR (TT;) Position: 8752859
- \https://www.snpedia.com/index.php/Rs1042778
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1042778
- >Frequency = CEU(GG=0.398, GT=0.469, TT=0.132,) YRI(GG=0.08, GT=0.482, TT=0.437,) HCB(GG=0.88, GT=0.119, TT=0.0)
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187267/#!po=14.7959
- >the G allele of the OXTR rs1042778 were each implicated in prosocial decision making (Israel et al., 2009), and carriers of the rs1042778 G allele exhibited more parenting behaviour and had higher plasma OT levels than T carriers
- \http://www.sciencedirect.com/science/article/pii/S0091305711001985
- >The post hoc analysis revealed that only the QNP-treated males spent more time in close contact with the scented male relative to the unscented (novel) male
- >OT (Oxytocin) receptor antagonists block partner preferences induced by D2-type receptor agonists like QNP
- \http://www.sciencedirect.com/science/article/pii/S0006322309007628
- >oxytocin increased the envy ratings [...] Oxytocin also increased the ratings of gloating
- \https://www.sciencedirect.com/science/article/pii/S0306453013003326
- >Results indicate that homosexual in comparison to heterosexual men display higher sensitivity to oxytocin's enhancing impact on social approach tendencies
- \https://en.wikipedia.org/wiki/Quinpirole
- >At least one study has found that quinpirole induces compulsive behavior symptomatic of obsessive compulsive disorder in rats
- 005b: 3q; OXTR (CC;) Position: 8761057
- \https://www.snpedia.com/index.php/Rs13316193
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20347913/
- >Additionally, significant association was also found for rs13316193 (F=3.09, p=0.05) with post-hoc tests demonstrating that the CC genotype was significantly associated with poorer social ability than the TT genotype
- 005c: 3q; OXTR (TT;) Position: 8755399
- \https://www.snpedia.com/index.php/Rs2268490
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2268490
- >Frequency = CEU(CC=0.761, CT=0.238,) HCB(CC=0.325, CT=0.511, TT=0.162,) YRI(CC=0.557, CT=0.389, TT=0.05)
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23547247/
- >C-rs2268490) was associated with lower levels of post-betrayal satisfaction
- 005d: 3q; OXTR (TT;) Position: 8760360
- \https://www.snpedia.com/index.php/Rs2268494
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23547247/
- >T-rs2268494) was significantly associated with faster retaliation post-betrayal
- 005e: 3q; OXTR (AA;) Position: 8755356
- \https://www.snpedia.com/index.php/Rs237887
- \https://www.ncbi.nlm.nih.gov/m/pubmed/23547247/
- >A-rs237887 [...] was associated with higher levels of post-betrayal satisfaction
- 005f: 3q; OXTR (AA;) Position: 8762685
- \https://www.snpedia.com/index.php/Rs53576
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19934046/
- >Compared with individuals homozygous for the G allele of rs53576 (GG), individuals with one or two copies of the A allele (AG/AA) exhibited lower behavioral and dispositional empathy
- P
- 001: 2q; PAX3 (TT;) Position: 222272282
- \https://www.snpedia.com/index.php/Rs12995399
- \https://www.ncbi.nlm.nih.gov/pubmed/23751107?dopt=Abstract
- 001b: 2q; PAX3 (CC;) Position: 222202200
- \https://www.snpedia.com/index.php/Rs2855268
- \https://www.ncbi.nlm.nih.gov/pubmed/23751107?dopt=Abstract
- 001c: 2q; PAX3 (TT;) Position: 222297305
- \https://www.snpedia.com/index.php/Rs6754024
- \https://www.ncbi.nlm.nih.gov/pubmed/23751107?dopt=Abstract
- 001d: 2q; PAX3 (AA;) Position: 222203567
- \https://www.snpedia.com/index.php/Rs7559271
- \https://www.ncbi.nlm.nih.gov/pubmed/22341974?dopt=Abstract
- 001e: 2q; PAX3 (TT;) Position: 222291868
- \https://www.snpedia.com/index.php/Rs7600206
- \https://www.ncbi.nlm.nih.gov/pubmed/23751107?dopt=Abstract
- 002: 11q; PAX6 (CC;) Position: 31809109
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3026354
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002b: 11q; PAX6 (CC;) Position: 31793814
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=667773
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002c: 11q; PAX6 (AA;) Position: 31791961
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3026390
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002d: 11q; PAX6 (GG;) Position: 31791034
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2071754
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002e: 11q; PAX6 (TT;) Position: 31790667
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3026393
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002f: 11q; PAX6 (AA;) Position: 31788750
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1506
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002g: 11q; PAX6 (GG;) Position: 31787774
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=12421026
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002h: 11q; PAX6 (GG;) Position: 31787522
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=662702
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002i: 11q; PAX6 (AA;) Position:
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3026401
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002j: 11q; PAX6 (GG:) Position: 31778325
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7125966
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002k: 11q; PAX6 (GG;) Position: 31657400
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=964112
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002l: 11q; PAX6 (AA;) Position: 31584349
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=11031419
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 002m: 11q; PAX6 (TT;) Position: 31513808
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=509628
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093386/table/pone-0019587-t002/?report=objectonly
- 003: 20q; PDYN (TT;) Position: 1994212
- \https://www.snpedia.com/index.php/Rs1997794
- \https://link.springer.com/article/10.1007%2Fs00702-009-0238-5
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1997794
- 003b: 20q; PDYN (AA;) Position: 1979580
- \https://www.snpedia.com/index.php/Rs910080
- \http://onlinelibrary.wiley.com/store/10.1111/j.1601-183X.2012.00785.x/asset/j.1601-183X.2012.00785.x.pdf?v=1&t=j7b8zk9p&s=63a99164dd7bcd367abf3602ac245547c640a0a0
- 003c: 20q; PDYN (GG;) Position: 1979293
- \https://www.snpedia.com/index.php/Rs2235749
- \https://www.ncbi.nlm.nih.gov/pubmed/27074815?dopt=Abstract
- 003d: 20q; PDYN (AA;) Position: 1989288
- \https://www.snpedia.com/index.php/Rs2235751
- \https://www.ncbi.nlm.nih.gov/pubmed/19468819?dopt=Abstract
- 004: 17q; PEMT (TT;) Position: 17439793
- \Citations: http://www.pdgene.org/view?poly=rs936108
- \https://academic.oup.com/hmg/article/23/9/2498/632550/Gene-centric-meta-analyses-for-central-adiposity
- \was associated with increased WHR [...] as was [...] rs936108-C in PEMT
- 005: 16q; PRSS53 (CC;) Position: 31087690
- \https://www.snpedia.com/index.php/Rs11150606
- \http://dx.doi.org/10.1038/ncomms10815
- 006: 1q; PROX1 (GG;) Position: 213985643
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340875
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006b: 1q; PROX1 (TT;) Position: 213987186
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340874
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006c: 1q; PROX1 (GG;) Position: 213987186
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340873
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006d: 1q; PROX1 (TT;) Position: 213987205
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340872
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006e: 1q; PROX1 (AA;) Position: 213988477
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340839
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006f: 1q; PROX1 (TT;) Position: 213989230
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340838
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006g: 1q; PROX1 (GG;) Position: 213989391
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340837
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006h: 1q; PROX1 (CC;) Position: 213989726
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340836
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006i: 1q; PROX1 (GG;) Position: 213990332
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=340835
- \http://diabetes.diabetesjournals.org/content/62/5/1738#F1
- \http://diabetes.diabetesjournals.org/content/diabetes/62/5/1738/F2.large.jpg?width=800&height=600&carousel=1
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298567/
- 006: 9q; PTCH1 (TT;) Position: 95479134
- \https://www.snpedia.com/index.php/Rs199476090
- \https://www.omim.org/entry/601309#0003
- 006b: 9q; PTCH1 (GAGA;) Position: 87864514
- \https://www.snpedia.com/index.php/Rs1057524874
- \https://www.ncbi.nlm.nih.gov/m/pubmed/27426521/
- 007: 2q; PTH2R (GG;) Position: 208477369
- \https://www.snpedia.com/index.php/Rs897083
- \https://www.ncbi.nlm.nih.gov/pubmed/24378925?dopt=Abstract
- 008: 20q; PTGIS (TT;) Position: 49505441
- \https://www.snpedia.com/index.php/Rs5602
- \https://www.ncbi.nlm.nih.gov/m/pubmed/27186408/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27215/#!po=11.5854
- 008b: 20q; PTGIS (CC;) Position: 49513169
- \https://www.snpedia.com/index.php/Rs5629
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19147528/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929860/
- 009: 12q; PTPRQ (CC;) Position: 80506078
- \https://www.snpedia.com/index.php/Rs147541734
- \https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=147541734
- 009b: 12q; PTPRQ (TT;) Position: 80460829
- \https://www.snpedia.com/index.php/Rs183258549
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=183258549
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/156333/
- 009c: 12q; PTPRQ (GG;) Position: 80539915
- \https://www.snpedia.com/index.php/Rs190166486
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=190166486
- 009d: 12q; PTPRQ (GG;) Position: 80460707
- \https://www.snpedia.com/index.php/Rs281865414
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=281865414
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/156332/
- 009e: 12q; PTPRQ (-A;) Position: 80669467
- \https://www.snpedia.com/index.php/Rs749210663
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=749210663
- Q
- R
- 001: 1q; RHD (CC;) Position: 25303452
- \https://www.snpedia.com/index.php/Rs590787
- \http://www.biorxiv.org/content/biorxiv/suppl/2017/07/30/164400.DC2/164400-1.pdf
- \pp69, bloodtype
- 002: 22q; RTN4R (AA;) Position: 20242546
- \https://www.snpedia.com/index.php/Rs74315509
- \http://www.omim.org/entry/605566#0002
- 002b: 22q; RTN4R (TT;) Position: 20242778
- \https://www.snpedia.com/index.php/Rs74315508
- \http://www.omim.org/entry/605566#0001
- 002c: 22q; RTN4R (GG;) Position: 20241019
- \https://www.snpedia.com/index.php/Rs701428
- \https://www.ncbi.nlm.nih.gov/pubmed/28139055?dopt=Abstract
- 003: 6q; RSPO3 (CC;) Position: 127452639
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=9491696
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >RSPO3, EA = G
- 004: 6q; RUNX2 (CC;) Position: 45421552
- \https://www.snpedia.com/index.php/Rs7771980
- \http://journals.plos.org/plosone/article/file?type=supplementary&id=info:doi/10.1371/journal.pone.0083218.s009
- 004b: 6q; RUNX2 (AA;) Position: 45512277
- \https://www.snpedia.com/index.php/Rs104893988
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104893988
- \http://www.omim.org/entry/600211#2
- S
- 001: 11q; SBF2 (TT;) Position: 10207181
- \https://www.snpedia.com/index.php/Rs1867138
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667283/
- 002: 2q; SCN9A (GG;) Position: 166286562
- \https://www.snpedia.com/index.php/Rs121908908
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121908908
- \http://www.omim.org/entry/603415#0005
- 002b: 2q; SCN9A (AA;) Position: 166277133
- \https://www.snpedia.com/index.php/Rs121908909
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121908909
- \http://www.omim.org/entry/603415#0007
- 002c: 2q; SCN9A (TT;) Position: 166303162
- \https://www.snpedia.com/index.php/Rs121908916
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121908916
- \http://www.omim.org/entry/603415#0014
- 002d: 2q; SCN9A (AA;) Position: 166293354
- \https://www.snpedia.com/index.php/Rs121908917
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121908917
- \http://www.omim.org/entry/603415#0015
- 003: 7q; SDK1 (GG;) Position: 4150281
- \https://www.snpedia.com/index.php/Rs645106
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19851296/
- 004: 17q; SHBG (AA;) Position: 7630105
- \https://www.snpedia.com/index.php/Rs1799941
- \https://www.ncbi.nlm.nih.gov/pubmed/19574343?dopt=Abstract
- 004b: 17q; SHBG (TT;) Position: 7631360
- \https://www.snpedia.com/index.php/Rs6258
- \http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002313
- 005: 1q; SHC1 (GG;) Position: 154944156
- \Citations: http://www.pdgene.org/view?poly=rs12076073
- \https://academic.oup.com/hmg/article/23/9/2498/632550/Gene-centric-meta-analyses-for-central-adiposity
- \rs12076073-A in SHC1 (frequency = 0.96) increased WHR by 0.101 units (SE = 0.021) among females
- 006: 10q; SIRT1 (TT;) Position: 67883584
- \https://www.snpedia.com/index.php/Rs3758391
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17895433/
- 006b: 10q; SIRT1 (CC;) Position: 67917073
- \https://www.snpedia.com/index.php/Rs4746720
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20633545/
- 007: 12q; SLC15A4 (CC;) Position: 128793765
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3765107
- \http://www.cell.com/cell/fulltext/S0092-8674(17)30128-9
- \http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl1&pii=S0092867417301289
- 008: 14q; SLC24A4 (CC;) Position: 92307319
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=12896399
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >Blue versus brown eyes = rs12896399-T = Discovery OR(1.15,) Replication OR(1.29,) Netherlands OR(1.12) [...] Blue versus green eyes = rs12896399-T = Discovery OR(2.06,) Replication OR(1.49,) Netherlands OR(2.08) [...] Red versus non-red hair = rs12896399-T = Discovery OR(1.06,) Replication OR(1.07,) Netherlands OR(0.88) [...] Blond versus brown hair = rs12896399-T = Discovery OR(2.56,) Replication OR(2.34,) Netherlands OR(1.86)
- 009: 15q; SLC24A5 (AA;) Position: 48134287
- \https://www.snpedia.com/index.php/Rs1426654
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1426654
- 009b: 15q; SLC24A5 (AA;) Position: 48124702
- \https://www.snpedia.com/index.php/Rs16960620
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=16960620
- 009c: 15q; SLC24A5 (GG;) Position: 48127189
- \https://www.snpedia.com/index.php/Rs2555364
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2555364
- 010: 5q; SLC45A2 (CC;) Position: 33986304
- \https://www.snpedia.com/index.php/Rs13289
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17358008/
- 010b: 5q; SLC45A2 (GG;) Position: 33951588
- \https://www.snpedia.com/index.php/Rs16891982
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=16891982
- >TTC(F, Phe) -> TTG(L, Leu) [...] Frequency = CEU(C=0.03, G=0.96,) YRI = (C=1.0, G=0.0)
- \https://www.ncjrs.gov/pdffiles1/nij/grants/223980.pdf
- >Six markers have significant effects on hair total melanin: dbSNP rs16891982 (MATP) (SLC45A2,) [...] When each are considered separately, these markers account for 57.8% [...] (respectively) of the total trait variation
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18806926/
- >the L374 allele is ancestral [...] Fernandez et al. (2008) also observed that the L374 allele is linked with darker pigmentation
- 010c: 5q; SLC45A2 (CC;) Position: 33963765
- \https://www.snpedia.com/index.php/Rs26722
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=26722
- 010d: 5q; SLC45A2 (AA;) Position: 33955221
- \https://www.snpedia.com/index.php/Rs35390
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=35390
- 010e: 5q; SLC45A2 (CC;) Position: 33955568
- \https://www.snpedia.com/index.php/Rs35391
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=35391
- 010f: 5q; SLC45A2 (CC;) Position: 33969523
- \https://www.snpedia.com/index.php/Rs35414
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=35414
- 011: 5q; SLC6A3 (9T/9T;) Position: 1411740
- \https://www.snpedia.com/index.php/Rs3836790
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414865/#!po=26.5432
- 011b: 5q; SLC6A3 (CC;) Position: 1432710
- \https://www.snpedia.com/index.php/Rs460000
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20091113/
- 012: 17q; SLC6A4 (GG;) Position: 30197993
- \https://www.snpedia.com/index.php/Rs1042173
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657929/figure/F3/?report=objectonly
- 012b: 17q; SLC6A4 (AA;) Position: 30211514
- \https://www.snpedia.com/index.php/Rs140701
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18663369/
- 012c: 17q; SLC6A4 (AA;) Position: 30237328
- \https://www.snpedia.com/index.php/Rs25531
- \https://www.ncbi.nlm.nih.gov/m/pubmed/20090673/
- 012d: 17q; SLC6A4 (TT;) Position: 30237152
- \https://www.snpedia.com/index.php/Rs25532
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18055562/
- 012e: 17q; SLC6A4 (AA;) Position: 30204775
- \https://www.snpedia.com/index.php/Rs3794808
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18663369/
- 012f: 17q; SLC6A4 (GG;) Position: 30211697
- \https://www.snpedia.com/index.php/Rs4583306
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18663369/
- 013: 5q; SRD5A1 (GG;) Position: 6633779
- \Citations: http://www.pdgene.org/view?poly=rs248793
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083475/#!po=14.1791
- \For SRD5A1, the exon 1 synonymous SNP rs248793 (G>C) has been associated with the ratio of dihydrotestosterone to testosterone, such that individuals homozygous for the minor C-allele had a higher ratio than G-allele homozygotes and heterozygote
- 014: 2q; SRD5A2 (GG;) Position: 31580823
- \https://www.snpedia.com/index.php/Rs104893667
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/3350/
- 014b: 2q; SRD5A2 (TT;) Position: 31567511
- \https://www.snpedia.com/index.php/Rs13395648
- \https://www.ncbi.nlm.nih.gov/pubmed/22735779?dopt=Abstract
- 015: 17q; SSTR2 (CC;) Position: 73169179
- \https://www.snpedia.com/index.php/Rs1466113
- \https://www.ncbi.nlm.nih.gov/pubmed/20948194?dopt=Abstract
- 016: 3q; SYN2 (CC;) Position: 12167171
- \https://www.snpedia.com/index.php/Rs795009
- \https://www.ncbi.nlm.nih.gov/m/pubmed/15449241/
- T
- 001: 1q; TAS1R3 (TT;) Position: 1334174
- \https://www.snpedia.com/index.php/Rs307377
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19587085/
- 002: 1q; TAS2R38 (GG;) Position: 141973545
- \https://www.snpedia.com/index.php/Rs713598
- \https://www.ncbi.nlm.nih.gov/m/pubmed/21763010/
- 002b: 1q; TAS2R38 (TT;) Position: 141972905
- \https://www.snpedia.com/index.php/Rs1726866
- \http://omim.org/entry/607751
- 002c: 1q; TAS2R38 (TT;) Position: 141972905
- \https://www.snpedia.com/index.php/Rs1726866
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19782709/
- 003: 1q; TBX15 (CC;) Position: 119503843
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=984222
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >TBX15, EA = G
- 003b: 1q; TBX15 (CC;) Position: 118884844
- \https://www.snpedia.com/index.php/Rs61730011
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302847/table/T2/?report=objectonly
- >Low-frequency variants associated with adult height [...] The direction of the effect (Beta, standard deviation units) and effect allele frequency (AF) is given for the alternate (Alt) allele
- >rs61730011, Ref/Alt:A/C , TBX15, Alt = C, Beta = -0.059
- 004: 10q; TCF7L2 (GG;) Position: 113047288
- \https://www.snpedia.com/index.php/Rs11196205
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618330/#!po=56.6667
- 004b: 10q; TCF7L2 (GG;) Position: 113049143
- \https://www.snpedia.com/index.php/Rs12255372
- \https://www.ncbi.nlm.nih.gov/m/pubmed/25185411/
- 004c: 10q; TCF7L2 (AA;) Position: 112971038
- \https://www.snpedia.com/index.php/Rs12573128
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28404897/
- 004d: 10q; TCF7L2 (GG;) Position: 113041766
- \https://www.snpedia.com/index.php/Rs7895340
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7895340
- 004e: 10q; TCF7L2 (TT;) Position: 112998590
- \https://www.snpedia.com/index.php/Rs7903146
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266211/table/Tab3/
- 005: 1q; TCHH (TT;) Position: 152110849
- \https://www.snpedia.com/index.php/Rs11803731
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775823/figure/fig1/?report=objectonly
- \With more T alleles, the proportion of straight hair increases
- 006: 5q; TERT (GG;) Position: 1297373
- \https://www.snpedia.com/index.php/Rs2736108
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174246/
- 006b: 5q; TERT (GG;) Position: 1296644
- \https://www.snpedia.com/index.php/Rs2736109
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174246/
- 006c: 5q; TERT (AA;) Position: 1288432
- \https://www.snpedia.com/index.php/Rs2853676
- \https://www.ncbi.nlm.nih.gov/m/pubmed/26042809/
- 006d: 5q; TERT (AA;) Position: 1285859
- \https://www.snpedia.com/index.php/Rs7705526
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670748/
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7705526
- 006e: 6q; TFAP2B (AG;) Position: 50803050
- \Citations: http://www.pdgene.org/view?poly=rs987237
- \http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110388/?report=classic
- 007: 19q; TGFB1 (TT;) Position: 41353016
- \https://www.snpedia.com/index.php/Rs1800470
- \https://www.ncbi.nlm.nih.gov/m/pubmed/16807529/
- \http://iovs.arvojournals.org/article.aspx?articleid=2124443
- 008: 1q; TGFB2 (CC;) Position: 218442109
- \https://www.snpedia.com/index.php/Rs991967
- \https://www.ncbi.nlm.nih.gov/m/pubmed/19710942/
- \http://iovs.arvojournals.org/article.aspx?articleid=2124443
- 009: 11q; TH (TT;) Position: 2172610
- \https://www.ncbi.nlm.nih.gov/m/pubmed/24417771/
- 010: 3q; TMCC1 (CC;) Position: 129582884
- \Citations: http://www.pdgene.org/view?poly=rs2811337
- \https://academic.oup.com/hmg/article/23/9/2498/632550/Gene-centric-meta-analyses-for-central-adiposity
- \rs2811337-G near TMCC1 was associated with increased WHR
- 011: 17q; TP53 (CC;) Position: 7676154
- \https://www.snpedia.com/index.php/Rs1042522
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2118619/
- 012: 11q; TPCN2 (AA;) Position: 69078931
- \https://www.snpedia.com/index.php/Rs35264875
- \http://omim.org/entry/612163
- 012b: 11q; TPCN2 (AA;) Position: 69087895
- \https://www.snpedia.com/index.php/Rs3829241
- \http://omim.org/entry/612163
- 013: 11q; TPH1 (AA;) Position: 18068882
- \http://www.pdgene.org/view?poly=rs4537731
- \http://pubmedcentralcanada.ca/pmcc/articles/PMC3766405/
- \For SNP1, the allele (A) we found to be associated with better cognition and higher QOL has previously been associated with lower serotonin levels
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T3/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T2/?report=objectonly
- 013b: 11q; TPH1 (CC;) Position: 18060353
- \http://www.pdgene.org/view?poly=rs684302
- \http://pubmedcentralcanada.ca/pmcc/articles/PMC3766405/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T3/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T2/?report=objectonly
- 013c: 11q; TPH1 (TT;) Position: 18055304
- \http://www.pdgene.org/view?poly=rs211105
- \http://pubmedcentralcanada.ca/pmcc/articles/PMC3766405/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T3/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T2/?report=objectonly
- 013d: 11q; TPH1 (CC;) Position: 18047816
- \http://www.pdgene.org/view?poly=rs1800532
- \http://pubmedcentralcanada.ca/pmcc/articles/PMC3766405/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T3/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T2/?report=objectonly
- 014: 12q; TPH2 (GG;) Position: 72331923
- \http://www.pdgene.org/view?poly=rs4570625
- \http://pubmedcentralcanada.ca/pmcc/articles/PMC3766405/
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T3/?report=objectonly
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766405/table/T2/?report=objectonly
- 014b: 12q; TPH2 (TT;) Position: 71979053
- \https://www.snpedia.com/index.php/Rs120074176
- \http://www.nature.com/mp/journal/v13/n4/full/4002152a.html?foxtrotcallback=true
- 015: 11q; TYR (CC;) Position: 89178528
- \https://www.snpedia.com/index.php/Rs1042602
- \https://omim.org/entry/606933#8
- >SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN [...] SKIN/HAIR/EYE PIGMENTATION 3, FRECKLING, INCLUDED TYR, SER192TYR [...] Based on analysis of HapMap samples, the A allele of rs1042602, associated with the absence of freckles, is found at a frequency of approximately 35% in European populations, while the ancestral C allele is fixed in Asian and Nigerian Yoruba populations
- 015b: 11q; TYR (GG;) Position: 89277878
- \https://www.snpedia.com/index.php/Rs1393350
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1393350
- >Frequency = CEU(AA=0.079, AG=0.292, GG=0.628,) HCB(GG=1.000,) YRI(GG=1.000)
- \https://www.ncbi.nlm.nih.gov/m/pubmed/17952075/
- >The association of the A allele of rs1393350 with blue versus green eye color was close to reaching genome-wide significance [...] Red versus non-red hair = rs1393350-A = Discovery OR(1.04,) Replication OR(1.05,) Netherlands OR(0.79) [...] Blond versus brown hair = rs1393350-A = Discovery OR(1.29,) Replication OR(1.36,) Netherlands OR(1.22)
- 016: 9q; TYRP1 (CC;) Position: 12672097
- \https://www.snpedia.com/index.php/Rs1408799
- \https://www.nature.com/articles/jhg201138
- >Green versus non-green eye colour is, according to MDR, best predicted by a three-factor model consisting of rs12913832 in HERC2, rs1408799 in TYRP1 and rs1800407 in OCA2 [...] The rs12913832 position removes 0.28% of ‘uncertainty’ in green eye colour prediction, rs1408799 removes 0.23% and the interaction between them eliminates an additional 1.23%
- \https://www.nature.com/articles/jhg201138/figures/2
- >rs12913832-TT, rs1408799-CC = Green eyes(n=21,) non-Green eyes(n=112)
- 016b: 9q; TYRP1 (-;-) Position: 12695626
- \https://www.snpedia.com/index.php/Rs104894130
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=104894130
- >T(Ser) -> G(Del)
- \https://www.omim.org/entry/115501#2
- >ALBINISM, OCULOCUTANEOUS, TYPE II, MODIFIER OF, INCLUDED TYRP1, SER166TER [...] Chiang et al. (2008) reported a Hispanic girl with oculocutaneous albinism type II (OCA2; 203200) caused by compound heterozygous mutations in the OCA2 gene (611409). She had pale skin, blue irides, and visual defects, including horizontal nystagmus, irides that transilluminated light, absence of foveal reflexes, albinotic fundi, and decreased visual acuity. However, she also had curly reddish-blonde hair, which was unusual for the OCA2 phenotype [...] Further genetic analysis identified heterozygosity for the S166X mutation in the TYRP1 gene in the girl
- \http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=79433
- >Visual anomalies, such as nystagmus, are frequently undetectable and patients usually present with one of two phenotypes: rufous OCA (ROCA), characterized by red-bronze skin color, blue or brown irises and ginger-red hair, or brown OCA (BOCA), characterized by light to brown hair and a light to brown or tan skin color. The clinical features of OCA3 have been considered as rather mild, and in the rare cases of non-African patients, reddish hair color has been reported
- 016c: 9q; TYRP1 (AA;) Position: 12702424
- \https://www.snpedia.com/index.php/Rs281865424
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=281865424
- >G(R, Arg) -> A(Q, Gln)
- \https://www.omim.org/entry/115501#4
- >In a Caucasian German boy with oculocutaneous albinism (OCA3; 203290), Rooryck et al. (2006) identified compound heterozygosity for mutations in the TYRP1 gene: a 1066G-A transition in exon 5, resulting in an arg356-to-glu (R356E [...] patient had yellow-gold hair with orange highlights, fair eyelashes, blue-green eyes with defects of the iris and nystagmus, several pigmented nevi, and pale yellow skin that did not tan but burned easily
- 016d: 9q; TYRP1 (-;-) Position: 12704547
- \https://www.snpedia.com/index.php/Rs387906560
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=387906560
- >A(K, Lys) -> ;(S, Ser)
- \https://www.omim.org/entry/115501#4
- >In an African American fraternal twin with type III oculocutaneous albinism (OCA3; 203290), Boissy et al. (1996) found a single basepair deletion (A) in codon 368 in exon 6 of the TYRP1 gene, which led to a premature stop at codon 384 [...] Manga et al. (1997) analyzed the TYRP1 gene in 19 unrelated southern African blacks with so-called 'rufous' OCA (ROCA) and identified compound heterozygosity for 368delA and a ser166-to-ter nonsense mutation (S166X; 115501.0002) in 17 of the 19 patients
- 016e: 9q; TYRP1 (-;-) Position: 12702414
- \https://www.snpedia.com/index.php/Rs387906562
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=387906562
- >AAC(N, Asn) -> -(V, Val)
- \https://www.omim.org/entry/115501#6
- >ALBINISM, OCULOCUTANEOUS, TYPE III [...] In a boy of Asian Indian origin with oculocutaneous albinism (OCA3; 203290), who had reddish hair color, brown irides, nystagmus, and lightly pigmented skin, Chiang et al. (2009) identified homozygosity for a 4-bp deletion (1057delAACA) in exon 5 of the TYRP1 gene. The unaffected parents were both heterozygous for the deletion
- U
- 001: 2q; UGT1A1 (TAn=8;) Position: 233760234
- \https://www.snpedia.com/index.php/Rs34815109
- \https://www.ncbi.nlm.nih.gov/m/pubmed/3999324/
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3064744
- 001b: 2q; UGT1A1 (GG;) Position: 233763993
- \https://www.snpedia.com/index.php/Rs6742078
- 001c: 2q; UGT1A1 (GG;) Position: 233759924
- \https://www.snpedia.com/index.php/Rs887829
- 001d: 2q; UGT1A1 (GG;) Position: 233763993
- \https://www.snpedia.com/index.php/Rs6742078
- 001e: 2q; UGT1A1 (CC;) Position: 233770738
- \https://www.snpedia.com/index.php/Rs11563251
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838666/table/T3/?report=objectonly
- \https://www.cdc.gov/cholesterol/facts.htm
- 002: 21q; UMODL1 (TT;) Position: 42134346
- \https://www.snpedia.com/index.php/Rs2839471
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18535602/
- \http://iovs.arvojournals.org/article.aspx?articleid=2124443
- 003: 20q; UQCC1 (CC;) Position: 35319358
- \https://www.snpedia.com/index.php/Rs6060369
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914680/table/T2/?report=objectonly
- V
- 001: 12q; VDR (AA;) Position: 47879016
- \https://www.snpedia.com/index.php/Rs121909790
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7745/
- 001b: 12q; VDR (AA;) Position: 47865106
- \https://www.snpedia.com/index.php/Rs121909791
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7746/
- 001c: 12q; VDR (AA;) Position: 47846679
- \https://www.snpedia.com/index.php/Rs121909792
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7747/
- 001d: 12q; VDR (AA;) Position: 47865085
- \https://www.snpedia.com/index.php/Rs121909793
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7749/
- 001e: 12q; VDR (AA;) Position: 47865175
- \https://www.snpedia.com/index.php/Rs121909794
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7750/
- 001f: 12q; VDR (TT;) Position: 47857512
- \https://www.snpedia.com/index.php/Rs121909795
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7751/
- 001g: 12q; VDR (TT;) Position: 47846743
- \https://www.snpedia.com/index.php/Rs121909796
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7752/
- 001h: 12q; VDR (AA;) Position: 47878977
- \https://www.snpedia.com/index.php/Rs121909797
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7753/
- 001i: 12q; VDR (GG;) Position: 47846444
- \https://www.snpedia.com/index.php/Rs121909798
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7754/
- 001j: 12q; VDR (GG;) Position: 47846444
- \https://www.snpedia.com/index.php/Rs121909799
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7755/
- 001k: 12q; VDR (GG;) Position: 47844859
- \https://www.snpedia.com/index.php/Rs121909800
- \https://www.ncbi.nlm.nih.gov/clinvar/?term=rs121909800
- 001l: 12q; VDR (AA;) Position: 47846374
- \https://www.snpedia.com/index.php/Rs121909802
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7748/
- 001m: 12q; VDR (AA;) Position: 47846052
- \https://www.snpedia.com/index.php/Rs1544410
- \https://www.ncbi.nlm.nih.gov/m/pubmed/10770213/
- 001n: 12q; VDR (AA;) Position: 47844994
- \https://www.snpedia.com/index.php/Rs267607169
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/7759/
- 001o: 12q; VDR (CC;) Position: 47844840
- \https://www.snpedia.com/index.php/Rs886037890
- \https://www.ncbi.nlm.nih.gov/clinvar/variation/264697/
- 002: 6q; VEGFA (GG;) Position: 43758873
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=6905288
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >VEGFA, EA = A
- 003: 8q; VMAT1 (GG;) Position: 20180955
- \https://www.snpedia.com/index.php/Rs2270641
- \https://www.ncbi.nlm.nih.gov/m/pubmed/18451639/
- \https://www.ncbi.nlm.nih.gov/m/pubmed/28476685/
- W
- 001: 2q; Wnt6 (GG;) Position: 218860595
- \https://www.snpedia.com/index.php/Rs6747776
- \https://www.ncbi.nlm.nih.gov/pubmed/21547848?dopt=Abstract
- 001b: 2q; Wnt6 (GG;) Position: 218867420
- \https://www.snpedia.com/index.php/Rs6754599
- \https://www.ncbi.nlm.nih.gov/pubmed/21547848?dopt=Abstract
- X
- Y
- Z
- 001: 22q; ZDHHC8 (GG;) Position: 20140031
- \https://www.snpedia.com/index.php/Rs175174
- \https://www.ncbi.nlm.nih.gov/m/pubmed/15489219/
- 002: 22q; ZNRF3 (GG;) Position: 29451671
- \https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4823006
- \https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000924/table/T1/?report=objectonly
- >aEffect Allele: WHR increasing allele on the forward strand;
- >ZNRF3, EA = A
- 002b: 22q; ZNRF3 (TT;) Position: 28904318
- \https://www.snpedia.com/index.php/Rs16986825
- \https://www.ncbi.nlm.nih.gov/pubmed/25086665?dopt=Abstract
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