As reported before [21]–[25] we also observed that eQTLs are strongly enriched for trait-associated SNPs (SNPs associated with a trait or disease phenotype, as reported in the Catalog of Published Genome-Wide Association Studies [1]): We therefore concentrated on these variants and imputed (Impute v2.0 [26]) additional genotype data permitting us to test 1,167 trait-associated SNPs. After removing false-positive eQTLs due to primer-polymorphisms and cross-hybridization 472 (40.4%) of these SNPs were cis-eQTLs, affecting the expression of 679 different transcripts, representing 538 genes (Figure 1, Table 1, Figure S2, Table S3). 67 (5.7%) SNPs were trans-acting on 130 different transcripts, representing 113 genes (Table S4). Results on the number of detected eQTLs per complex trait are provided in Table S5 and Figure S3. For nearly all significant trans-eQTLs the effect was present in each of the seven individual patient and controls cohorts, making up the total dataset (Table S6).
