Impact of CNVs on gene regulation. (a) There are multiple ways in which CNVs can impact transcription by overlapping coding regions of the genes. (b) Blekhman et al. (2010) used RNA-seq data to determine whether specific genes are differentially expressed between human, chimpanzee, and macaque . Based on their results, we plotted the proportion of human CNVs (H) and hotspot CNVs (HCR) that are differentially expressed between species. In particular, 3,423 of the Ensembl genes analyzed by Blekhman et al. (2010) overlap with human CNVs. Based on these data, here we plot the proportion of the genes that are differentially expressed between two or all three species, evolved under directional selection in the human lineage (Directional Human) or under stabilizing selection (that is, no expression differences between species). (c) At least three HCR CNVs overlap with regions with clear enhancer and/or promoter signals in the genome. To visualize the enhancer and promoter activity, we used the H3K4Me3 track generated by the ENCODE consortium  from the UCSC Genome Browser.