We applied the same clumping algorithm to the GWAS and MTAG results to identify each set of “lead SNPs.” Our clumping algorithm is the same as in the previous SSGAC study.11 First, the SNP with the smallest P value was identified in the meta-analysis results. This SNP was designated the index SNP of clump 1. Second, we identified all SNPs on the same chromosome whose LD with the index SNP exceeds R2 = 0.1 and assigned them to clump 1. To generate the second clump, we removed the SNPs in clump 1 and then iterated the process to identify further index SNPs and their corresponding clumps until no SNPs remain.
