We considered two types of validation for the results of the multiple-tissue analysis of gene expression described above: validation at the system level and validation at the tissue/cell-type level. For validation at the system level, we classified the top tissue or cell type for each trait with a significant enrichment into one of nine systems (Online Methods), and we considered an enrichment to be validated if a tissue or cell type from the same system passed FDR < 5% for the same phenotype in the chromatin analysis. For validation at the tissue/cell-type level, we only analyzed the 27 tissues present in both GTEx and EN-TEx, and we considered an enrichment of a tissue in GTEx to be validated if any mark in the same tissue in EN-TEx passed FDR < 5% for the same phenotype. The top enrichment from our multi-tissue analysis of gene expression was validated at the system level for 33 out of 34 phenotypes (Figure 3a, Table S5), and the top enrichment of a tissue or cell type shared between GTEx and EN-TEx was validated at the
