We first tested whether eQTLs in iPSCs and somatic tissues (lead variants and their high-LD proxies, control variants as before) showed global enrichment in this final set of disease-associated variants compared with matched sets of variants (Extended Data Fig. 9b). Fold enrichments were derived from a comparison to 100 sets of matched controls (mean of control overlaps per tissue). For iPSCs, we additionally tested enrichment for individual traits, deriving an empirical P-value. Traits with an adjusted P < 0.05 (Benjamini-Hochberg) and minimum five observed overlaps were considered enriched (Supplementary Table 6c).
