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. 2019 Feb 25;9:2695. doi: 10.1038/s41598-019-39633-0

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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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Multi-layered evidence for candidate functional AS-SNPs in LD with two eQTL SNPs. AS-SNP rs1257573 is in LD with two eQTL SNPs (rs2182909 and rs568515) associated to the expression of CR2. The SNPs are located in a genomic region with a multi loop TAD architecture defined by HiC data (purple interactions) that narrows the possible target genes to few candidates. HiCap data (green interaction) showed an interaction between the promoter of CD55 and the regulatory element harboring the AS-SNP rs1257573. The distal probe region (~5 kb) is highlighted in gray. Histone modifications tracks for H3K4me1, H3K4me3 and H3K27ac were retrieved from the ENCODE project for the B cell line GM12878 (scaled using vertical viewing range settings) as well as the DNaseI hypersensitive clusters (DHS).The PMM tracks show the networks of intra-motif dependencies at each position using PMMs with defined parameters. The sequence logo for the TF binding motif of PRD14 has been computed from putative BSs predicted by PMMs.