However, common variants have been identified that might exert their function by altering gene expression rather than by altering protein structure [2], [12]–[16] (expression quantitative trait loci, eQTLs). Comprehensive eQTL mapping (or genetical genomics [17]) will enable us to assess for every known disease-associated variant if it significantly affects gene expression. Genetic variants that affect expression of genes that map in their vicinity (cis-eQTLs) can potentially pinpoint the true disease gene from an associated locus. In addition, genetic variants may also affect expression of genes that reside further away or are on different chromosomes (trans-eQTLs) [18]. These trans-eQTLs are especially interesting, since they allow us to identify downstream affected disease genes which were not implicated by GWAS studies at all, and thereby potentially having the ability to reveal previously unknown (disease) pathways.
