There are some important limitations that require consideration when using our resource for hypothesis generation. First, we limited our cis-eQTL analysis to variants within 1 Mb of the gene center, and limited our trans-eQTL analysis on variants >5 Mb from genes on the same chromosome. We acknowledge the possibility that these thresholds may have excluded distal cis-eQTLs (e.g. those caused by distal enhancers or chromatin loops), and trans-eQTLs on nearby genes. We chose these thresholds to ensure that the trans-eQTLs we observed were not driven by long-range cis-eQTLs. While our approach might have excluded long-range cis-eQTLs, we observed that for 95.6% of genes, the lead cis-eQTL SNP maps within 100kb of the gene, suggesting that long-range cis-eQTLs reflect only a small proportion of all cis-eQTLs. Second, we confined our trans-eQTL analyses to a subset of 10,317 variants previously associated with complex phenotypes. As such, a significant trans-eQTL for a trait-associated variant does not necessarily mean that the same underlying variant affects both the phenotype and gene expression. Third, PGS estimates have been shown to have variable prediction accuracy even when
