10-11). Numbers within brackets in table 1 denote the number of cis-eQTLs, probes or genes that are potentially due to these primer polymorphisms. If these primer polymorphisms are responsible for different hybridization efficacies, these SNPs should be in LD with the SNPs that make up the cis-eQTLs. We could assess this for those cis-eQTLs where genotype data was available within HapMap Phase II for both the SNP that makes up the eQTL and for the SNPs that map within the probe that constitutes this particular eQTL. We compared the resulting distribution of r2 values to a null distribution, generated by calculating the LD between the SNP that makes up an eQTL and the SNP that mapped immediately adjacent to the primer polymorphism SNP. While the mean LD (mean r2 = 0.27) in the celiac peripheral blood was not significantly higher than the mean LD in the null distribution (mean r2 = 0.25, Wilcoxon Mann-Whitney P-Value = 0.86), this was observed for the HapMap B cell line dataset (mean r2 = 0.46, mean r2 of null distribution = 0.30, Wilcoxon Mann-Whitney P-Value = 6.3 × 10-8).
