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 Figure 15, where enrichment relative to genes in random sets of loci is indicated by red shading. To cluster DEPICT reconstituted gene sets, we used affinity propagation clustering71 and calculated the correlation between each resulting “exemplary gene set” in Figure 4. Genes, gene sets, and tissue/cell enrichments were considered significant when their false discovery rate was below 0.05. All such significant DEPICT results are reported in Supplementary Tables 17–19. PASCAL and DEPICT were also applied in the same fashion to the MTAG summary statistics (Supplementary Tables 34–39).
