To complement the eQTL analyses, and to assess the effects of cis-regulatory variants at lower frequencies that eQTL analyses are underpowered to detect, we quantified allele-specific expression (ASE) in iPSCs and HLCs (individual-level data not provided in the manuscript due to privacy concerns). Genome-wide, we identified 1,721 independent SNPs in 494 genes that exhibited significant ASE in iPSCs (FDR < 5%) and 2,137 independent SNPs in 631 genes that exhibited significant ASE in HLCs. Furthermore, 876 independent SNPs in 541 genes exhibited differential ASE (FDR < 5%) between iPSCs and HLCs (Table S4), indicating cell-type-specific regulatory effects. Genes exhibiting differential ASE were significantly enriched for cell-type-specific eGenes (odds ratio = 3.3, P < 1.8 × 10−13), independently confirming the cell-type-specific regulatory effects identified with the two methodologies.
