For IRF8, a novel treatment-specific cis-eQTL is seen, maximal after induction of gene expression by LPS for 2 hours (P = 9.9 × 10−19), for which the peak SNP, rs17445836, is also a lead GWAS SNP for multiple sclerosis (MS) and associated with up-regulation of interferon response gene sets in peripheral blood mononuclear cells (PBMCs) from MS patients (41). For the chemokine receptor 3 gene (CCR3), we also find evidence of a stimulus-specific cis-eQTL, after 24-hour LPS (P = 2.3 × 10−14), for which the lead eSNP was recently reported as the peak GWAS SNP for Behçet’s disease, a multisystem inflammatory disorder involving severe vasculitis (42). Other observations include an eQTL to IRF1 with the peak SNP (PLPS2 = 6.9 × 10−17) overlapping with a Crohn’s locus (43) and an eQTL observed to the gene LILRA5 only after 24-hour LPS intersecting with a prostate cancer locus (44).
