We first clumped the European-only GWAS-based meta-analysis summary statistics using 500 kb flanking regions, LD r2 > 0.1 and excluded SNPs with P ≥ 5 × 10−4; which resulted in a list of 590 independent SNPs. HapMap phase II CEU genotype data37 was used to compute LD and genomic coordinates were defined by genome build GRCh38. Because the GWAS meta-analysis was based on both GWAS and Metabochip studies, there were discrepancies in the index SNPs that are referenced in Table 1 of the paper and the ones used in DEPICT, which was run on the GWAS data only. Therefore we forced in GWS index SNPs from the GWAS plus Metabochip GWA meta-analysis into the DEPICT GWAS-only based analysis. This enabled a more straightforward comparison of genes in DEPICT loci and genes in GWS loci highlighted by manual lookups, and did not lead to any significant bias towards SNPs on Metabochip (data not shown). We forced in 62 of the GWS loci in Table 1, so all of the 97 SNPs were among the 590 SNPs. The 590 SNPs were further
