The observed concordance in allelic direction for the 135 significant SNP-probe effects, detected in both the 110 celiac peripheral blood and the 90 HapMap B cell line samples was perfect when probe sequences were identical. We also assessed whether the allelic directions for cis-eQTLs probes was the same when multiple significant cis-eQTL probes mapped within the same genes. We identified 14 genes (see Table 2) where this was not the case: significant cis-eQTL probes with different oligonucleotide sequences mapped to the same genes but showed opposite allelic directions. For three of the genes, MRPL43, OAS1 and TIPRL, we re-sequenced the probe regions in four, four and three individuals with different genotypes, respectively, and did not discover any polymorphisms, confirming that these cis-eQTLs do not result from artificial hybridization differences.
