trans-eQTL analysis was restricted to protein-coding genes and to GTEx tissues that are composed of at least one Roadmap Epigenomics cell type (26 tissues), which included 85 eVariants and 23 eGenes (10% FDR). We quantified enrichment of the trans variants relative to random variants in both enhancer and promoter elements in the GTEx discovery tissue’s matched Roadmap cell type (Extended Data Table 4). We then performed the same analysis with randomly matched cis-eGenes. Matching cis-eGenes were selected as follows: for each of the 23 trans-eGenes g, each having Ng associated eVariants (10% FDR), we randomly selected a cis-eGene that also had at least Ng associated variants (10% FDR). We then selected the top Ng variants associated with this gene based on P value. We then performed the same analysis using random sets of the strongest cis-eGenes, rather than random eGenes. Matching the strongest cis-eGenes was performed as follows: for each of the 23 trans-eGenes g, each having Ng associated eVariants (10% FDR), we randomly selected a cis-eGene amongst the ten strongest cis-eGenes in that tissue, based on the P value
