To enable a comparison of gene expression levels between the HapMap B cell line samples and the celiac peripheral blood samples, we limited our analysis to 12,401 transcripts that map to identical exons. The expression levels for these transcripts were quantile normalized. cis-eQTLs that have only been significantly detected in the celiac peripheral blood dataset, reflect probes that on average show higher expression in the celiac peripheral blood samples compared to HapMap B cell line samples (Wilcoxon Signed-Ranks test, P = 7.6 × 10-7) (see Figure 3). Conversely, probes that comprised HapMap B cell line specific cis-eQTLs were higher expressed than within the celiac peripheral blood dataset (P = 2.0 × 10-4). As expected, probes that comprised cis-eQTLs that were common to both data sets did not show differences in expression (P = 0.30). Noteworthy is that IL18RAP and CCR3, both recently identified as being genetically associated with celiac disease [21], exhibited significant cis-regulation in the celiac peripheral blood dataset but not in the HapMap B cell line dataset. Cis-effects for these two genes could be detected as these two
