To evaluate the significance of the observed number of joint cis eQTLs-mQTLs (for the same target gene) among the top Bipolar Disorder associated SNPs, we conducted simulations (see Materials and Methods for details of the simulation procedure to empirically generate the null distribution to test the significance of the observed count of such joint cis eQTLs-mQTLs). The results of the simulation analysis on joint cis eQTLs-mQTLs show that such SNPs altering expression level and DNA methylation of the same proximal transcript constitute a small proportion of either cis mQTLs or cis eQTLs, and that the count of such joint eQTLs-mQTLs falls well within the range (enrichment p = 0.75) that can occur by chance based on our simulation analysis. 75% of all simulated sets matched or exceeded the actual count of joint (cis) eQTLs-mQTLs.
