Cis-eQTL analysis showed that, among the risk SNPs for alcohol and nicotine co-dependence, 30 SNPs had nominal cis-acting regulatory effects on expression of HTR1A or IPO11 mRNA in the brain, PBMC or lymphoblastoid cell lines (2.3×10−13 ≤ p ≤ 0.05); among all of the 65 SNPs within this region that were genotyped for eQTL analysis, 43 (66.2%) were risk markers for alcohol and nicotine co-dependence (6.2×10−9 ≤ p ≤ 0.048) (Table S2). Cis-regulatory effects on IPO11 expression were much stronger than those on HTR1A expression. All of the risk alleles for alcohol and nicotine co-dependence increased the expression of HTR1A. However, some of the risk alleles increased the expression of IPO11 but the others decreased it.
