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. Author manuscript; available in PMC: 2021 Jan 27.
Published in final edited form as: Nat Ecol Evol. 2020 Jul 27;4(10):1332–1341. doi: 10.1038/s41559-020-1261-z

Figure 5. Hundreds of RAs have regulatory activity independent of NDAs.

Figure 5.

The number and fraction of RAs and NDAs by population with significant differential gene regulatory activity in MPRAs. Among introgressed variants identified in each Eurasian population, RAs are significantly more likely than NDAs to have independent regulatory activity (odds ratios: 1.46–1.65, P < 1e−3 for all populations). RAs have similar levels of activity compared to non-introgressed variants (odds ratios: ~1.0, P > 0.01), while NDAs are significantly depleted for activity compared to non-introgressed variants (odds ratios: 0.65–0.68; P < 1e−6 for each population). Introgressed variants were required to have significantly different activity from the non-introgressed allele (controlling the FDR at 5%) in at least one of the two cell lines assayed (K562, HepG2; Methods). The odds ratio is the ratio of differentially active RA:NDA over the ratio of all RA:NDA tested (Supplementary Table 8). The enrichment for activity among RAs compared to NDAs held across a range of activity thresholds and when comparing only to sites with activity (Supplementary Table 9). Significance of the differences between variant sets was evaluated with Fisher’s exact test; * indicates P < 1e–3, ** indicates P < 1e–6, *** indicates P < 1e−9.