To further refine cell-type-specific effects of cis-eQTLs between iPSCs and HLCs, we conducted a mixed model meta-analysis. Considering our paired sample design we used METASOFT (Han and Eskin, 2012) and Meta-Tissue (Sul et al., 2013) to estimate effect sizes of each variant-gene pair accounting for covariates used in single-tissue analyses as well as tissue sharing among individuals. All SNPs within 100 kb of 20,488 genes expressed in either iPSCs or HLCs were used for meta-analysis. The probability of tissue specificity was estimated using m-values (Han and Eskin, 2012). Briefly, m-values indicate the posterior probability that the effect exists in each study or cell type. We considered m-values ≥ 0.9 as indicating a particular variant had a molecular effect in each cell type. The most significant HLC eGenes with respect to meta-analysis P-values were AMDHD1, FA2H, and ACAA2 (Table S5).
