To ascertain whether these SNPs are more often constituting an eQTL than expected, we used a methodology that is not affected by the following potential confounders: non-even distribution of SNP markers and expression probe markers across the genome, differences in MAF between SNPs and LD structure within the genotype date and correlation between probes in the expression data. Additionally, this methodology is also not confounded by the fact that for certain traits different SNPs in strong LD can have been reported, due to differences in the platforms that were used to identify these loci.
