In (a and b), SNPs are pruned for LD using PLINK 22 with threshold r 2 value of 0.1, 0.3, 0.5 and 0.7. In (c and d), SNPs are pruned based on physical distance so that any pair of SNPs are at least 1 Mb away from each other. In (e and f), 10, 30, 50 and 70 % SNPs are randomly sampled from all of the SNPs.