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. 2023 Nov 18;14:7501. doi: 10.1038/s41467-023-43077-6

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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/.

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Fig. 5 — a Variants with high DAF are enriched for cis-regulatory variants. All variants and lead variants of cis-eQTLs were divided into different DAF intervals. The bar plot represents the proportion of all variants (cyan) or lead variants of cis-eQTLs (sky blue) in each DAF interval (left y-axis). The line indicates the relative ratio of the proportion of cis-eQTLs to the proportion of all variants in each DAF interval (right y-axis). A total of 13,877 lead variants were used in this analysis. Derived alleles were identified based on wild rice data (“Methods”). b High-frequency derived alleles at cis-eQTLs of SPP TWAS-significant genes tend to have a positive effect on SPP. The cis-eQTLs of SPP PAGs (left panel) and NAGs (right panel) are divided into different intervals (x-axis) according to DAF, and the y-axis represents the proportion of cis-eQTLs whose derived allele is up-regulating gene expression (red) or down-regulating gene expression (blue). The numbers at the top of the bars indicate the number of TWAS significant genes containing cis-eQTL in each interval. Source data are provided as a Source Data file.