not among the set of per-gene lowest association P-values, this eQTL was assigned the higher FDR value corresponding to the next eQTL available among the set of lead variants per gene. We refer to this procedure as ‘gene-level’ FDR, but note that the FDR estimates should be evaluated as ‘analysis-wide’, since the ultimate distribution of permuted P-values used to calculate our FDR estimates was derived for all tested genes, rather than per-gene. Cis-eQTLs with a gene-level FDR<0.05 (corresponding to P<2.02×10−5) that were tested in more than one cohort were deemed significant.
