To identify independent signals among the regression results, signals were amalgamated into putative associated loci using the same two-step strategy and parameters as PGC (Supplementary Table 14). In this procedure, regular LD clumping is performed (r2 = 0.1, P < 1×10−4; window size < 3 Mb) to obtain independent index SNPs. Afterward, loci are defined for each index SNP as the genomic region that contains all other imputed SNPs within the region with r2 ≥ 0.6. To avoid inflating the number of signals in gene-dense regions or in those with complex LD, all loci within 250 kb of each other were annealed.
