Three HLA region CNVs, namely CNVR2841.20, CNVR2845.14, and CNVR2845.46, were recently shown to be associated with Crohn's disease, rheumatoid arthritis, and type 1diabetes, respectively [8]. Our expression study confirms that the last two of these (tagged at r2>0.90) are eQTLs that regulate the expression of multiple genes in this region; in contrast, the first CNV shows no evidence for being an eQTL. A previously identified Crohn's disease associated locus CNVR2647.1 [5] on chromosome 5, 22 kb upstream of the IRGM gene, is a trans eQTL for SHISA4 (p = 3e-05). Two replicated SNPs associated with HDL cholesterol are tagging (r2≥0.99) nearby CNVs, CNVR3814.1 (chrom8:19898924–19899800) and CNVR5165.1 (chrom11:48557432–48560877). Our study shows that both CNVs are eQTLs, with CNVR5165.1 targeting, distally, the olfactory receptor gene OR6J1. The CNV CNVR3814.1 is also well-tagged (r2 = 0.913) by a SNP reproducibly associated with triglycerides and is an eQTL targeting ARF4, which has been shown, in mice, to be involved in metabolic disorders [13].
