Multi-tissue cis-eQTL analyses have been shown to increase power by explicitly modelling sharing patterns across tissues15,18,20. We did not observe an improvement in power for trans-eQTL discovery, consistent with the limited sharing observed across tissues (Extended Data Table 3). However, we did observe improvements for cis-eQTL discovery, particularly among tissues with smaller sample sizes (Extended Data Fig. 10). To ensure that these findings did not depend on the modelling assumptions of Meta-Tissue, we analysed the P values for all genes and all tissues with treeQTL, which controls the FDR of eGene discoveries across tissues17. This procedure identified 17,411 cis-eGenes at 5% FDR, 2,314 fewer eGenes than with the single-tissue analysis. Although this analysis is more conservative overall than the tissue-by-tissue analysis, we observed an increase in the number of eGenes detected in the tissues with the smallest sample sizes, including several brain regions, as well as an increase in the average number of tissues in which an eGene was detected (from 7.8 for single-tissue analysis to 8.3; Extended Data Fig. 10). Additional cis-eGenes identified through meta-analysis were more likely to
