How to compute LD for pairs of variants with Plink I have a set of SNPs (single nucleotide polymorphisms) { S1, S2, ..., SN } from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By this I mean e.g. I would like to compute e.g. LD between S1 and S2, S3, S4, but not the LD between S2 and S3. 

Could this calculation be performed in PLINK?
Yes, you can do this with plink.  

You can use the flag --ld-snp &lt;variant_id&gt; to calculate LD between your SNP of interest and all other SNPs.
If you have multiple SNPs of interest, and want each of those compared with every SNP in your dataset, use --ld-snps &lt;snp1-snp100,snp102,snp104&gt;
A final option to calculate LD between a specific pair of SNPs is --ld &lt;variant_id1&gt; &lt;variant_id2&gt;  

This the relevant plink manual page