We performed stepwise conditional analyses of 248 loci that were genome wide significant in the core PGC dataset looking for independent associations. We performed association testing and meta-analysis across each locus, adding the allele dosages of the index SNP as a covariate. Where a second SNP had a conditional p-value of less than 1×10−6, we considered this as evidence for a second signal and repeated the process adding this as an additional covariate. We repeated this until no additional SNPs in the region achieved p<1×10-6. We also searched for long range dependencies. Here we tested the all pairs of independent signals for conditional independence (Supplementary Note).
