4,681 Illumina expression probes had oligonucleotide sequences that are shared between the two different oligonucleotide arrays used (Human Ref8 v2 & Human WG-1 v1). By limiting the analysis to a window size of 250 kb and only to SNPs that had been successfully genotyped in both studies, 576 different SNP-probe effects in the celiac peripheral blood data at a FDR = 0.05 (338 at an FDR = 0.01) were detected. These reflect 573 different SNPs and 197 different probes. In the HapMap B cell line data, 573 different SNP-probe effects were identified at an FDR = 0.05 (290 at an FDR = 0.01), reflecting 573 different SNPs and 189 different probes. A combined meta-analysis of both cohorts (weighted-Z method) identified 1,133 different SNP-probe associations at an FDR = 0.05 (428 at an FDR = 0.01) (see Figure 2). These reflect 1,120 SNPs and 328 unique probes. 440 SNP-probe pairs, reflecting 217 different probes and 439 different SNPs (FDR = 0.05) were not detected when either dataset was analyzed separately.
