Population differences in local patterns of Linkage Disequilibrium (LD) around disease associated SNPs were measured with the varLD software (www.nus-cme.org.sg/software/varld.html) [3], using the targeted option for 50-SNP windows. For each population and genomic region, varLD builds a matrix of pairwise signed r2 values among all the SNP pairs and provides a raw score corresponding to the absolute difference in the eigen-decompositions between two matrices. This score is a summary measure of the overall LD levels in a given genomic region between two populations. We used it to measure the extent of differences in local LD between two kind of genomic regions: these containing replicated and non-replicated SNPs. To rule out the possibility that differences in LD between replicated and non-replicated SNPs are not related to the presence of the disease associated SNP, we scanned varLD differences in consecutive windows of the same size (50 SNP), starting 300 SNPs upstream of the disease associated SNP and finishing 300 SNPs downstream, with an step of 5 SNPs. In total, we checked 121 consecutive windows around the disease associated SNP. On average, we were examining a window of 503.61 Kb centered on each associated SNP.
