We conducted a manual review of all genes implicated within each locus, overlap with the GWAS catalogue (Supplementary Table 33), and all pathways identified by PASCAL and DEPICT (described below). We considered a gene to be implicated if it harbored variation in LD with a conditionally independent genome-wide significant variant, or if a gene was located within the locus and was significant by the PASCAL gene-based test. PASCAL69 was used for gene based and pathway analysis to test genes and canonical pathways from MSigDb (Supplementary Tables 20–21). Default settings were used to test all variants within all genes. DEPICT70 was used to identify enrichment within tissues/cell types, and reconstituted gene sets (also known as “pathways”). For each phenotype, variants from the GWAS were clumped using 500 kb flanking regions with the LD cutoff r2 > 0.1 (based on 1000 Genomes phase 1 release v3, the default in DEPICT). We used DEPICT to understand genetic signals beyond the genome-wide significant loci that surpass the conventional 5×10−8, and so included all variants with p<5×10−5. DEPICT tissue enrichment results are displayed in Supplementary
