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Fig. 1 | Breast Cancer Research

Fig. 1

From: Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

Fig. 1

Genetic mapping and epigenetic landscape of the 12p11 locus (a). Regional association plot of the genotyped and imputed Illumina iSelect genotyping array of the Collaborative Oncological Gene-environment Study (iCOGS) genotype data. Three independent signals were identified, marked as signal 1, 2 and 3. b Functional annotations using data from the Encyclopedia of DNA Elements (ENCODE) project. From top to bottom, the epigenetic signals evaluated include histone modifications, DNase clusters, transcription factor ChIP-seq clusters, and ENCODE chromatin states (ChromHMM) in the ENCODE cell lines. The signals of different layered histone modifications from the same ENCODE cell line are shown in the same color (the detailed color scheme for each ENCODE cell line is described in the UCSC genome browser; http://genome.ucsc.edu). Red and orange in chromatin states represent active promoter and strong enhancer regions, respectively (the detailed color scheme of the chromatin states was described in the previous study [45]). All tracks were generated by the UCSC genome browser (hg 19). c Long-range chromatin interactions. From top to bottom, genome conformation capture (Hi-C), chromatin interaction analysis by paired end tag (ChIA-PET) and RNA-Seq data from K562 cell lines, Hi-C and RNA-Seq from human mammary epithelial cells (HMEC), ChIA-PET and RNA-Seq from MCF7 cell lines, gene annotations and single nucleotide polymorphism (SNP) annotations. Black lines represent interactions with the promoter region (-1500/+500) of Parathyroid hormone-like hormone (PTHLH), and gray lines represent chromatin interaction that did not involve the PTHLH promoter region. The value of the RNA-Seq analysis corresponds to the mean reads per million (RPM) value for PTHLH from 65 K562, 4 HMEC and 19 MCF7 datasets, respectively. The annotation has been obtained through the Bioconductor annotation package TxDb.Hsapiens.UCSC.hg19.knownGene. The Hi-C and ChIA-PET raw data, available in the Gene Expression Omnibus (GEO) [GSE63525.K56, GSE33664, GSE39495], were processed using the GenomicRanges package. The tracks have been generated using ggplot2 and ggbio libraries in R

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