win_size<-c(15000, 30000, 50000, 100000)

for (i in 1:length(win_size)){
windows<-sapply(snp_ids$pos, function(x) (ceiling(x/win_size[i])))
snp_ids$window<-as.numeric(paste(snp_ids$chr, windows, sep="."))
}

snp_id  chr  pos window_15000  window_30000
Chr01__912   1  912    1.1        1.1
Chr01__944   1  944    1.1        1.1
Chr01__1107  1 1107    1.1        1.1
Chr01__1118  1 1118    1.1        1.1
Chr01__1146  1 1146    1.1        1.2
Chr01__1160  1 1160    1.1        1.2