We next identified iPSC eQTLs that may be associated with disease. iPSC eQTLs tagged 322 variants associated in genome-wide association studies with 145 different disease traits, corresponding to a 1.4-fold global enrichment over control variants (Fisher’s exact P = 1.4x10-6), and trait-specific enrichments for seven traits (Supplementary Table 6), a comparable level of enrichment to eQTLs from most somatic tissues (Extended Data Fig. 9). We also observed that iPSC eQTLs tagged a larger number of known cancer genes (COSMIC cancer census 27/04/201620) than somatic tissue eQTLs, with only cancer eQTLs tagging more (Extended Data Fig. 9).
