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. 2019 Sep 30;9:14011. doi: 10.1038/s41598-019-50586-2

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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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rs11121615 affects enhancer activity within a topologically associated domain (TAD) containing CASZ1. (A) UCSC snapshot showing the following tracks: UCSC genes, 100 vertebrates basewise conservation by PhyloP, ENCODE layered ChIP-Seq data for H3K27ac and H3K4me1 from seven cell lines (NHEK cells in purple), ENCODE DNase I hypersensitivity data, and 15-state chromatin state Segmentation by HMM (ChromHMM) for nine cell lines. hg19 chromosome 1 coordinates are shown. (B) Allele-specific enhancer activity for rs11121615 was assessed using a luciferase reporter assay in HEK293 cells. The rs11121615 T variant (major allele) did not harbour enhancer activity whereas the C variant (minor allele) did. The average of five biological replicates+/− the standard error of the mean is shown. Statistical significance was determined by a one-way ANOVA followed by a Tukey’s multiple comparisons test (*P < 0.0001). (C) Hi-C contact map in NHEK cells (normal human epidermal keratinocyte) at chr1:10140000-11450000 (hg19), obtained from the 3D genome browser (http://www.3dgenome.org). TADs, calculated using the directional bias method¹³, are indicated by alternating orange and blue bars. NCBI reference genes are annotated below.