We examined whether the regulatory effects of eQTL SNPs were caused by mutations in transcription factor-binding sites (TFBSs), splicing-affecting sites, or microRNA (miRNA)-binding sites. The proportion of SNPs in LD (r2>0.8) with a SNP predicted to be located on such sites was compared between the 37 eQTL SNPs affecting expression levels in both whole blood and lymphoblastoid cell lines; 49 eQTL SNPs affecting only whole blood expression levels; and 5,681 non-eQTL SNPs located within 100 kB of the 107 genes that were regulated by the eQTL SNPs identified in the current study. A web-based tool (FuncPred; http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm) was used to predict the functional properties of the SNPs. As shown in Table 1, eQTL SNPs were more likely to be in LD with SNPs located on TFBSs, splicing-affecting sites, and miRNA-binding sites.
