head (sap_ids)
       snp_id    chr  pos
    Chr01__15043   1 15043
    Chr01__15079   1 15079
    Chr01__15139   1 15139
    Chr01__15165   1 15165
    ...
    ...
    ...
    Chr17__214708424  17 214708424        14314
    Chr17__214708451  17 214708451        14314
    Chr17__214708484  17 214708484        14314
    Chr17__214708508  17 214708508        14314
    Chr17__214708574  17 214708574        14314

win_size<-c(15000,30000,50000,100000)
res<- cbind(snp_ids,
       data.frame(lapply(setNames(win_size, paste("window",win_size, sep = "_")),
       function(x)as.numeric(ceiling(snp_ids$pos/x)))))

for instance, as I you see in the example below in window 4 I get SNPs from chromosomes 1,3 and 5

snp_id     chrom poistion   window
Chr01__58332   1 58332            4
Chr01__58335   1 58335            4
Chr01__58341   1 58341            4
Chr01__58450   1 58450            4
Chr01__58471   1 58471            4
Chr01__58530   1 58530            4
Chr01__58542   1 58542            4
Chr01__58641   1 58641            4
Chr03__45457   3 45457            4
Chr03__45604   3 45604            4
Chr04__56873   4 56873            4
Chr04__57387   4 57387            4
Chr04__57399   4 57399            4
Chr04__57528   4 57528            4
Chr04__58419   4 58419            4
Chr04__59670   4 59670            4
Chr04__59704   4 59704            4