genes that had large discrepancies in correlation measurements between the UW and UC studies that did not overlap a known SNP (9 probes with strong UW correlation but low UC correlation, 6 of the converse; Table S2). We found that none of these 15 probes harbored SNPs in the 60 UW liver samples or a panel of 35 CEU HapMap samples. Collectively, our data suggest future array designs/eQTL studies would benefit from more aggressive avoidance of known SNPs, but current SNP annotations are sufficiently comprehensive that unknown variants are of little concern to eQTL analyses.
