Polymorphism data was downloaded from HapMap Project Phase 2 (release 24, November 2008). For each ascertained SNP, we downloaded two data sets: (i) genotypes for the associated SNP and (ii) genotypes for a 600-SNP window centered on the associated SNP. We downloaded all genotypes for all unrelated samples from the three populations of European and East Asian ancestry (CEU, JPT and CHB). JPT and CHB samples were clustered together due to their close genetic relationship.
