snp     chr     pos     pvalue
LOC105758527    1       55001   0.469590
LOC105758527    1       65001   0.067909
LOC105758527    1       75001   0.220712
LOC100218126    1       85001   0.174872
LOC105758529    1       125001  0.023420
NRF1    1       155001  0.242222
NRF1    1       165001  0.202569
NRF1    1       175001  0.327963
UBE2H   1       215001  0.063989
UBE2H   1       225001  0.542340

snp     chr     pos     pvalue
LOC105758527    1       55001   0.191300
NRF1    1       155001  0.257584
UBE2H   1       215001  0.063989
UBE2H   1       225001  0.3031645

awk 'BEGIN { FS = OFS = "t" }
        { y[$1] += $4; $4 = y[$1]; x[$2] = $0; }
END { for (i in x) { print x[i]; } }' file

CAPN6         6   18705001   1.63482
DACH1         3   67845001   3.39277
HSP90AB1      5   31175001   0.179808
LARS          16  415001     0.478678
DACH2         6   4065001    3.03408
LOC100219438  4   155435001  0.133995
CAPN8         5   8395001    0.655674
NEB           10  38455001   2.09714
CAPN9         5   42275001   0.236643
AVL9          4   65205001   0.502827