The cis and trans eQTLs identified from the first pass analysis provide a significantly reduced set of SNPs on which to focus (∼3,700 versus 782,476). The set of SNPs associated with expression (eSNPs) can be considered a functionally validated set, given that the SNPs in this set have been found to associate with biologically relevant control of gene expression. In fact, many of the gene expression traits associated with eSNPs correspond to genes that have previously been associated with many different human diseases (Table S3). For example, BRCA1, a well-known susceptibility gene for breast cancer, and CFH, a susceptibility gene for age-related macular degeneration identified in one of the first published GWASs, are each strongly associated with an eSNP (p = 9.73 × 10−17 for BRCA1 and p = 6.94 × 10−22 for CFH) that falls within 1Mb of the corresponding structural gene (Table S3). Genes associated with drug response are also represented in this set. For example, VKORC1, a gene recently associated with warfarin dosing [24], has liver gene expression values that are significantly associated with an eSNP near the 3′ end of the gene (p = 1.66 × 10−23).
