Finally, in a case study applying eQTL data to a specific disease, expression traits and eSNPs pertinent to IBD were identified. In a first-step analysis, previously reported associations rs2298428/UBE2L3 and rs1050152/SLC22A4 were confirmed and the novel eQTL rs1050152/SLC22A5 was also identified. Conversely, the previously reported eSNP, rs2927488/BCL3, was not replicated and rs2631372/SLC22A5 could not be confirmed because the SNP was not measured in this study. An additional analysis encompassing 142 subjects for which ImmunoChip data were available was performed to evaluate 155 IBD-associated SNPs that passed the same quality control measures as the OmniExpress data. Of these 155 SNPs, 24 (15%) exhibited cis effects in 27 eQTL pairs at an α level of 5% and windows size of 50 kb (Table 2). Alternatively, using windows of size 1 mb and an α level of 10%, the number of significant cis-acting eSNPs was also 24 (15%) (Supplementary Table 5). After correction for multiple testing, 2 eQTL reached significance in trans.
