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. 2020 Jun 8;21:135. doi: 10.1186/s13059-020-02049-5

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© The Author(s) 2020

Open AccessThis 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/. 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 in a credit line to the data.

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Fig. 3 — SMC relevant transcription factors are colocalized with QTLs. Results from HOMER reference motif scanning on ± 50-bp windows surrounding a bQTLs and b caQTLs. Allele-specific motif scanning with flipped SNPs in ± 20-bp windows surrounding c bound-vs-less-bound bQTLs, d open-vs-closed caQTLs, and e closed-vs-open caQTLs. f Heatmaps show the bQTL, caQTL, and clQTL densities at TCF21 peaks, ATAC peaks, JUN peaks, SRF peaks, and AHR:ARNT binding motifs. ***P < 10⁻⁸; **P < 10⁻⁴; *P < 10⁻²; ^n.sP > 0.01. g Heatmaps show the ATACseq open chromatin (ATAC), histone H3K27ac (K27ac), and H3K4me1(K4me1) mark enrichment at bQTLs, caQTLs, and clQTLs in ± 5-kb windows. h Density plot showing open chromatin, H3K27ac, and H3K4me1 enrichment at chromosomal loop anchors (yellow area within dashed lines). i Boxplots show differences between the enrichments of open chromatin, H3K27ac, and H3K4me1, on chromosomal loop anchors with and without clQTLs