We compared the identified cis-eQTLs in the celiac peripheral blood dataset to a published human genetical genomics dataset [3]. We reanalyzed expression data from EBV-transformed B cell lines (further described as HapMap B cell line dataset) for 90 CEU HapMap samples [3]. Analyses were performed as described for the celiac disease samples. To enable a comparison between the celiac peripheral blood dataset and the HapMap B cell line dataset, only SNPs were tested that had been successfully called within HapMap and that were present on the Illumina HumanHap300 platform (257,013 SNPs). Although this is only a subset of all the SNPs that have been called for these HapMap samples, this subset of SNPs is known to capture most genetic Caucasian variation well [26].
