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. 2023 Aug 21;14:5062. doi: 10.1038/s41467-023-40569-3

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — A The DIRECT consortium derived genetic, transcriptomic, proteomic and metabolite data from blood and plasma samples from 3029 individuals. Significant genetic associations (FDR < 0.05) after linear regression between the molecular phenotypes and SNPs in cis (cis-QTLs) and trans (trans-QTLs or GWAS) were used to build a network of genetic perturbations affecting molecular phenotypes. Partially created with BioRender.com. B Location of the lead eSNP with respect to the TSS of the significantly associated genes (FDR < 0.05) for cis-eQTL. The most associated eSNP per gene (primary) is shown in black (n = 15,305). Secondary cis-eQTL are shown in orange (n = 44,667). Data shows the -log10 P values of the linear regressions between gene expression and SNPs, n = 3029. C Number of cis-eQTLs per gene, ranging from 1 to 38. D The location of the SNPs acting as cis-pQTLs (pSNPs) centred around the TSS of the coding gene. The most associated pSNP per protein (primary) is shown in black (n = 373). Secondary cis-pQTL are shown in orange (n = 1217). Stronger cis-pQTLs were significantly closer to the canonical TSS of the gene coding the protein than secondary signals (Wilcoxon test = 9.54e-25). Data shows the -log10 P values of the linear regressions between proteins abundance and SNPs, n = 3027. E Number of cis-pQTLs per protein, ranging from 1 to 19. F Integration of cis-eQTLs identified the largest cis-network of local regulatory genetic effects for genes around POLR2J2. The lower lollipop plot shows the genomic location of the genes (boxes) and SNPs (lollipops), coloured by the associated genes. G Abundance of genes sharing the lead cis-eSNPs ordered by the distance between the TSS of the pair of genes in Mb. H Pairs of genes with the same lead eSNP (n = 583). Data show the -log10 P values of the linear regressions between gene expression and the common SNPs, adjusted by the direction of the effect of the eSNP.