It is attractive to assume most of the observed cis-eQTLs reflect overall gene expression level alterations. However, we did observe 14 genes (Table 2) where different probes showed significant opposite allelic effects. For at least five out of the 14 genes (POFUT2, PTER, MYOM2, ADI1 and HLA-DRB5) polymorphisms within the probe are known to exist in dbSNP. For each of these genes, it may be that one cis-eQTL for instance reflects a real expression difference, whereas the other reflects a hybridization effect due to the presence of these SNPs within the probe. However, recently Kwan et al [39] provided another potential explanation, as they showed for three of the 14 genes (IRF5, MRPL43 and PTER), using Affymetrix GeneChip Human Exon 1.0 ST Arrays, that different genetic variants can result in premature 3' termination events. The SNPs that make up these cis-eQTLs are all in strong linkage disequilibrium with the SNPs Kwan et al described (IRF5: rs7808907 and rs6969930: D' = 1, R2 = 0.74 rs2863095, MRPL43: rs2863095 and rs12241232: D' = 0.89, R2 = 0.75, PTER: rs7909832 and rs1055340: D'
