In this study, tissue-specific eQTLs were defined as eQTL effects not replicating in any of the 44 tissues analysed by the GTEx Project 24. Replication was tested on the level of individual eQTL variants between all pairs of tissues. For this analysis, we considered full cis eQTL output of iPSC eQTLs from HipSci and 44 tissues from GTEx (V6p results; 2,025 tissue pairs). The included tissues and cell lines are detailed in Supplementary Table 5a. For each discovery tissue, we tested for the replication of all lead eQTL effects (lead eQTL variant - target eGene; hereon referred to as ‘ePair’) originally reported (FDR 5% in both HipSci and GTEx; Supplementary Table 5a). Ideally, the exact same ePair would have been tested across all tissues. However, due to differences in genotyping methods and allele-frequency due to sample size it was not always possible to query the exact same ePair in all tissues. To account for this, if the original lead variant was not available to test in the query tissue, a proxy variant was tested instead. We note that the selected proxy may differ across the replication tissues. The approach to define the proxy variant is summarized in the Supplementary Information.
