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. 2020 Sep 11;21:234. doi: 10.1186/s13059-020-02122-z

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© The Author(s) 2020

Open AccessThis 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. 2 — The GTEx v8 haplotype-level allelic expression resource. a Number of genes per tissue with haplotype-level AE data (AE genes) in at least 1 individual versus the median number of samples with data per gene. b Percentage of AE genes with significant allelic imbalance (binomial test, gene-level FDR < 5%) in at least n samples per gene using all samples (blue) or excluding samples heterozygous for any top (FDR < 5%) or independent GTEx eQTL (permutation p < 1e−4) (red). Faded points are values for individual tissues, and solid points are the median across tissues. Proportions above data points indicate the reduction in percentage of AE genes with imbalance after removing eQTL heterozygotes. A full summary of these statistics across tissues and sample thresholds is available in Additional file 3: Table S2. c The effect of the number of heterozygous variants in or proximal to gene promoters (< 10 kb upstream of TSS) on allelic imbalance stratified by minor allele frequency. Plotted values are effect estimates and 95% confidence intervals (see the “Promoter variant effect modeling” section in the “Methods” section)