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. Author manuscript; available in PMC: 2022 Dec 6.
Published in final edited form as: Science. 2022 Mar 17;375(6586):1247–1254. doi: 10.1126/science.abj5117

Figure 3 -. Integrative non-coding variant effect prediction.

Figure 3 -

(A) Empirical cumulative probability distribution of the first through fourth principal component (PC) scores from Enformer for allelic MPRA hits and other tested variants significant and non-significant MPRA allelic hits; genome-wide percentiles computed across all common variants in 1000 Genomes Phase 3. Inset shows a blow up of lower genome-wide percentile curves (B) Significance of a Kolgomorov-Smirnov (K-S) test comparing the empirical distributions of Enformer scores for significant and non-significant allelic MPRA hits v; magenta horizontal line indicates significance by K-S test (p-value < 0.05). (C) Same as in (A) except showing annotation principle components from FAVOR; genome-wide percentiles computed across all variants in TOPMed Freeze5. (D) Same as in B, except testing FAVOR aPCs.