The mixed sets consisted of CNEs found in the vicinity of 154 heart-specific genes. Nine sets were constructed. All mixed sets contained CNEs within 10 kbp upstream and 10 kbp downstream of the transcription start sites (TSSs). We expanded the mixed sets by including n CNEs that are closest to the TSSs, if they were not already included, n = 0, 10, 20, 30, 40, 60, 80, 100, ∞. A control set included five times as many sequences as its mixed set counterpart. We controlled for sequence length while assembling the control sets.