We assessed tissue specificity of HLC and iPSC eGenes by selecting SNP-eGene pairs (the most significant single-tissue SNP per gene) (Table S5). Among 2,392 HLC eGenes, we found 267 HLC-specific eGenes (HLC m-value ≥ 0.9; iPSC m-value < 0.1) and 1,051 eGenes with evidence of tissue specificity in both HLCs and iPSCs (HLC m-value ≥ 0.9; iPSC m-value ≥ 0.9). Among 3,587 iPSC eGenes, we found 474 iPSC-specific eGenes (HLC m-value < 0.1; iPSC m-value ≥ 0.9) and 1,279 eGenes with evidence of effects in both HLCs and iPSCs (HLC m-value ≥ 0.9; iPSC m-value ≥ 0.9). We also indirectly assessed potential HLC and iPSC specificity of GTEx liver eGenes by comparing GTEx liver eGenes to m-values estimated from our data. We found 24 GTEx liver eGenes (HLC m-value ≥ 0.9; iPSC m-value < 0.1) and 10 GTEx liver eGenes (HLC m-value < 0.1; iPSC m-value ≥ 0.9) that potentially share HLC or iPSC tissue specificity, respectively.
