257,013 autosomal SNPs were tested for association with expression levels in the 110 celiac disease samples that met analysis criteria of minor allele frequency (MAF) > 0.1, exact Hardy-Weinberg equilibrium P-Value > 0.0001 and call-rate > 0.95. Analyses were confined to those probe-SNP pairs for which the distance from probe genomic midpoint to SNP genomic location was less than 250 kb or 500 kb, depending on the analysis performed. To prevent spurious associations due to outliers, a non-parametric Spearman's rank correlation analysis was performed. In order to correct for multiple testing we controlled the false discovery rate (FDR) [25]. The distribution of all the observed p-values was used to calculate the FDR, by comparing this distribution to a null-distribution, obtained from an identical analysis where the expression phenotypes, relative to the genotypes had been permuted. Through 1,000 permutations the Spearman's rank correlation P-value threshold could be determined that corresponded to an FDR of 0.01 or 0.05.
