We quantified the tissue-specificity and tissue-sharing of cis- and trans-eQTLs using Meta-Tissue15. This tool extends Metasoft74, a meta-analysis package, by using a mixed effects model for eQTL sharing that accounts for correlation of expression between tissues driven by overlapping donors. All genotypes and gene expression quantification estimates were adjusted for covariates in accordance to the single tissue analysis as described in the previous sections. For each variant–gene pair, we calculated mixed model effect size estimates in each expressed tissue, thereby adjusting for partial sharing of signal between tissues. These effect size estimates were used in meta-analysis using Metasoft74 to assess the tissue-specificity of each variant–gene pair. For each variant–gene pair tested, Meta-Tissue estimates a global P value of association and the posterior probability that an effect exists in a tissue (m value). For computational feasibility, the Markov chain Monte Carlo (MCMC) method was used to approximate the exact solution.
