pair was considered HLC-specific if m-value ≥ 0.9 for HLCs and m-value < 0.1 for iPSCs. An eQTL-eGene pair was considered iPSC-specific if it had m-value ≥ 0.9 for iPSCs and m-value < 0.1 for HLCs. All other eQTL-eGene pairs with m-value < 0.9 and single-tissue FDR < 0.05 were considered eGenes for the relevant tissue without predicted tissue-specific effects. Due to potential biases in combining paired samples among iPSCs and HLCs with the independent set of GTEx liver samples, meta-analysis was not performed across the three datasets. However, we further assessed predicted tissue specificity of iPSC- and HLC-specific eQTL-eGene pairs by comparing to the list of GTEx liver eQTL-eGene pairs post hoc.
