somatic tissue-specific eQTLs were also driven by alternative regulatory variants, with only testis showing a substantial fraction (16%) of eQTLs attributable to tissue-specific gene expression (Fig. 4b). Using alternative methods for eQTL detection and assessing the extent of sharing between eQTLs in iPSCs and GTEx tissues, we confirmed that our conclusions were robust to methodological differences between GTEx and our study (Extended Data Fig. 8). However, due to variation in sample size, we cannot rule out that a fraction of the iPSC-specific eQTLs may have a weak effect on gene expression in some somatic tissues.
