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. 2020 Sep 11;21:232. doi: 10.1186/s13059-020-02026-y

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© The Author(s) 2020

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. 8 — Examples of identified violations of exclusion restrictions. All three examples are identified from the PTWAS scan procedure; the corresponding tissues represent the tissues where the minimum p values are achieved. Each SNP-level estimate and its corresponding 95% confidence interval are plotted. Data points with the same color represent the SNPs within the same signal cluster and in LD. The size of the point reflects the relative magnitude of SNP-level PIP. In all examples, within cluster estimates are highly consistent; estimates by different clusters are qualitatively different, which is a clear indication of violation of the exclusion restriction. The I² statistics computed for the three cases are 0.94 (GUCY1A1), 0.96 (CTB-171A8.1), and 0.98 (HLA-DQB2), respectively