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. 2023 May 30;24:130. doi: 10.1186/s13059-023-02959-0

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — Biological and technical features predicting causality. a Percent variance in gene expression explained by chromatin accessibility (r²(Y,M)) in X-M-Y triplets supporting causal forward model versus independence in progenitors (upper, purple) and neurons (lower, green). Unpaired t-test p-value is shown. b Absolute distance of variants relative to TSS of the genes for X-M-Y triplets supporting causal forward model versus independence in progenitors (upper, purple) and neurons (lower, green). Unpaired t-test p-value is shown. c Distribution of variants located within gene promoter (within + / − 2 kb window from gene TSS) within X-M-Y triplets supporting causal forward model versus independence in progenitors (upper, purple) and neurons (lower, green). Chi-square test p-value is shown. d Number of testable variants detected to disrupt TF binding motifs via motifbreakR in X-M-Y triplets supporting causal forward model versus independence in progenitors (upper, purple) and neurons (lower, green). Chi-square test p-value is shown. e Number of testable variants (either variant itself or LD proxy) showed allele-specific chromatin accessibility (ASCA) in X-M-Y triplets supporting causal forward model versus independence in progenitors (upper, purple) and neurons (lower, green). Chi-square test p-value is shown