Paralog-specific regulation at the CHRNA7 locus (Chr 15q13.3). A 143 kb region (Chr 15: 32,153,206–32,460,660; GRCh38) is shown. Segmental duplications (SDs) are colored orange for >99% sequence identity and gray for <98% identity. No ENCODE candidate cis-regulatory elements (cCREs) are annotated in this locus. The MPRA data are visualized as activity relative to the human ancestral locus and plotted on these coordinates. Each point represents a 200-mer tile, and tiles are colored by which homolog they correspond to (teal: chimpanzee CHRNA7; orange: human-specific CHRFAM7A; gray: identical in both) and filled in if they scored as differentially active. Two 1 kb regions are highlighted in the insets; the left panel shows a zoomed in plot of the MPRA measurements per tile, and the right shows a relative luciferase activity of the entire sequence, as assayed in the corresponding cell type. Asterisks on the box plots mark significantly different activity with respect to the human ancestral sequence. See also Supplemental Table S13.