With a goal of identifying hepatic cis-regulatory variation, we mapped genome-wide cis-eQTLs in the iPSCs, HLCs, and GTEx livers using linear models as implemented in Matrix eQTL (Shabalin, 2012) (Figure 1A). We identified a total of 3,587 eGenes in the iPSCs, 2,392 eGenes in the HLCs, and 1,511 eGenes in the GTEx livers at a false discovery rate (FDR) < 5% (Table S3). The HLCs and livers shared a total of 477 eGenes, 176 of which were not associated in the iPSCs at FDR < 5% (Figure 1B). The eQTLs were primarily associated with protein coding genes (83%), and the majority of eGenes were nominally associated (P < 0.05) in more than one cell type.
