Fig. 3

Putative functional variants and association of rs11049453 with gene expression in breast tumor tissues. a Epigenetic signals of five potential functional variants. From top to bottom, lanes showing that those variants mapped to transcription factors predicted binding motifs, DNase I hypersensitivity sites and transcription factor ChIP-Seq binding peaks in the Encyclopedia of DNA Elements (ENCODE) cell lines and MCF7. The corresponding location of each variant is indicated by a dashed line. b Epigenetic landscape at the 12p11 locus for breast cancer risk. From top to bottom, RefSeq genes (PTHLH and CCDC91), layered H3K4Me1, H3K4Me3 and H3K27Ac histone modifications and annotation using chromatin states on 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). Red and orange in the chromatin states represent the active promoter and strong enhancer regions, respectively (the detailed color scheme of the chromatin states was described in the previous study [45]). c rs11049453 and the expression of coiled-coil domain containing 91 (CCDC91) and parathyroid hormone-like hormone (PTHLH). The association of the genotypes and the expression level of each gene was evaluated by residual linear regression [29]. bp base pairs, C/EBP CCAAT/enhancer-binding protein, E2F3 E2F transcription factor 3, HNF1B HNF1 homeobox B, PPARG peroxisome proliferator-activated receptor gamma, PAX paired box