135 identical SNP-Probe effects (reflecting 135 different SNPs and 51 different probes) had been identified in both the 110 celiac disease samples and in the 90 HapMap B cell line samples (FDR = 0.05). In all cases, the combined meta-P-Value for each of these shared cis-eQTLs was more significant due to the larger sample size, indicating allelic effects in the same direction. A comparison between cis-eQTLs that had been detected in a large scale linkage based genetical genomics study using RNA obtained from peripheral blood mononuclear cells [2], and the cis-eQTLs we detected, indicates that 57.3% (distance 250 kb, 0.05FDR) of probes, displaying a genotypic effect in the celiac peripheral blood dataset, also show a linkage cis-eQTL signal. Of note is that CCR3 and IL18RAP are both identified as cis-eQTLs in both these datasets.
