It may seem simple, but I can not seem to find a good way to do this:
Provided that I have a known SNP by rs number, and an extensive list of SNPs on the other hand (almost a million), how would I find the SNP (or SNPs) that are in LD with the known SNP within this list?
It would be ideal if i could do this in a batch: provide a list of known SNPs, and receive lists of LD SNPs for each known SNP as output.
May there also be a way to do this with other types of variations, such as methylation sites?
I have checked PLINK's options but i can not seem to find a way to get this done using only known rs numbers (no known phenotypes, sometimes no known p-values).