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. 2018 Jun 25;19:494. doi: 10.1186/s12864-018-4859-7

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© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.

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Fig. 1 — Simulated GWAS pairs with overlapping samples. Data was simulated for two quantitative trait GWAS with no genetic effects but overlap in samples (each with n=12,500 including 5000 overlapping samples). d=100,000 SNPs were simulated under the null model (phenotype is simulated independent from genotype). Panel a: the p-value distribution for trait 1; Panel b: the p-value distribution for trait 2; Panel c: The p-value distribution for trait 2 given that the p-value in study 1 was less than 0.1; Panel d: quantile-quantile plot for the p-values in study 2, stratified by the p-value in study 1