We conducted simulations to evaluate enrichment for eQTLs among the tCNVs included in our study. To empirically generate the null distribution of no enrichment, we randomly generated sets of SNPs of matching minor allele frequency as the original list of SNPs tagging the tCNVs, as previously described [10]. To enable us to perform simulations conditional on MAF, we constructed non-overlapping MAF bins, each of width 0.05, using the MAFs of the SNPs in the HapMap CEU samples. The null sets were drawn from the combined platform SNPs (Affymetrix 6.0 and Illumina 1M) as well as from the entire set of HapMap CEU SNPs. The observed count is then compared to the empirically generated distribution to get an empirical p value for the enrichment.
