We perform the clumping in Plink36. Note that we measure the LD between every pair of SNPs on each chromosome without regard to the physical distance between them. Therefore, if two SNPs on the same chromosome have pairwise r2 above 0.1, then they cannot both be lead SNPs. On the other hand, it is possible for two SNPs in close physical proximity both to be lead SNPs, provided their pairwise r2 is below 0.1. The Supplementary Note reports analyses of the sensitivity of the number of lead SNPs and loci to alternative definitions and to the choice of the reference file used to estimate LD.
