Using RNA-seq data from 166 unrelated donors (median sequencing depth 38M reads), we next mapped eQTLs in a 1 Mb cis-window from the gene start. We identified 6,631 genes with an eQTL (FDR 5%, hereafter ‘eGenes’), 598 of which had a significant secondary eQTL (Supplementary Table 4). Power to discover eGenes in iPSCs was comparable to that in somatic tissues24 given our sample size, and iPSC eQTLs showed similar genomic properties to eQTLs in cell lines and tissues (Extended Data Fig. 7; Supplementary Table 5).
