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. 2019 Jun 14;10:2632. doi: 10.1038/s41467-019-10602-5

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© The Author(s) 2019

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. 4 — Regulation of eQTLs to their associated genes mediated by chromatin interactions. a Distribution of SNPs in promoter proximal regions, distal elements, gene bodies, and intergenic regions. b The numbers of overlapped interactions between ChIA-PET loops and eQTL SNP-eTrait pairs. The distance distribution of the simulated loops is similar to that from the ChIA-PET loops. ****P < 0.0001 from T-test. Values represent numbers of loops and eQTLs. c eQTL gene, genes that are associated with eQTL and not linked to eQTL by ChIA-PET loops; Looped gene, genes that are associated with eQTL and also linked to eQTL by ChIA-PET loops; QTL interacting gene, genes that are not associated with eQTL, but linked to an eQTL by ChIA-PET loops. Random gene, genes which are not associated with eQTL and not linked to eQTL by ChIA-PET loops. d The expression Pearson correlation coefficient of looped genes and random genes, eQTL interacting genes or eQTL genes. eQTL:eQTL represents the pairs of eQTL genes. eQTL:Loop represents the pairs of eQTL genes and Loop genes. eQTL_interacting:Loop represents the pairs of eQTL interacting genes and Loop genes. Random:Loop, the pairs of random genes and Loop genes. Random:eQTL_interacting, the pairs of random genes and eQTL interacting genes, random genes, the same distance distribution as the eQTL interacting genes and Loop genes. ****P < 0.0001, **P < 0.05, ns—P > 0.1 from Wilcoxon test. Boxplots show the median, and third and first quartiles. The whiskers are defined as 0.25–1.5 IQR/0.75 + 1.5 IQR, IQR is interquartile range. e A SNP in a distal element that affects the expression of multiple genes. f Interactions between genes potentially affected by distal elements SNP and other genes identified as expression QTLs in (e), PPI interaction means promoter proximal interaction. g A SNP in a promoter proximal region that affects the expression of multiple genes. h Interactions between genes potentially affected by a SNP in a promoter and other genes identified as expression QTLs in (g). i A proposed model based on chromatin interactions for eQTL regulation of gene expression. Source Data underlying (b, c) are provided in a Source Data file