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. 2024 May 6;15:3786. doi: 10.1038/s41467-024-48244-x

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© The Author(s) 2024

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 — In each subfigure, the top three panels show the -log10 nominal p-values (<0.01), in a region of 500 kb around the top cis-QTL (x-axis), for cis-QTL associations with exon levels (dark blue), intron levels (blue) and exon–intron-ratios (orange), and the fourth panel shows the −log10 p-values for the GWAS trait associations (red) in the same region. The rsID of the top cis-QTL(s) are indicated (in black, if colocalized with the GWAS trait variants, or in grey if not). The p value of the RTC (regulatory trait concordance) colocalization analysis is indicated inside each cis-QTL panel, in case colocalization was testable, i.e. QTLs and GWAS variants are within the same genomic region between recombination hotspots. The bottom panel shows examples for RNA-Seq read distributions at the associated gene from two homozygous individuals, one with reference (Ref/Ref; blue) and one with alternative (Alt/Alt; red) genotype, for the top cis-QTL variant. The positions of the top cis-QTL as well as QTLs sharing the cis-QTL signal are indicated with thick or thin lines, respectively. A A cis-QTL from cluster 1, associated with TMEM156 and colocalizing with a GWAS variant for monocyte count. B A cis-QTL from cluster 2, associated with SMAD3 and colocalizing with a GWAS variant for FVC, a trait related to lung function. C A cis-QTL from cluster 3, associated with SDF4 and colocalizing with a GWAS variant for systemic lupus erythematosus. D A cis-QTL from cluster 4, associated with FAR2 and colocalizing with a GWAS variant for interleukin-27 levels. E A cis-QTL from cluster 5, associated with GBAP1 and colocalizing with a GWAS variant for mean corpuscular haemoglobin concentration. F A cis-QTL from cluster 6, associated with SUMO2 and colocalizing with a GWAS variant for sex hormone binding globulin levels.