This is a shut in the dark unless you'd like to check pairwise LD in one of the HapMap reference populations. The rest is relatively straightforward in Bioconductor:

> library(LDheatmap)
> data("CEUData")
> MyHeatmap <- LDheatmap(CEUSNP, CEUDist, LDmeasure = "r",
+ title = "Pairwise LD in r^2", add.map = TRUE,
+ SNP.name = c("rs4648356", "rs6687680"), color = grey.colors(20),
+ name = "myLDgrob", add.key = TRUE)

You can write a bash script to read from your snpList.file and pass it to the R. You may find this helpful!