Figure 1.

Statistically significant CHi-C interaction peaks at the 2q35 locus. The number of statistically significant interaction peaks mapping to each HindIII fragment (y-axis) is plotted against the genomic location of the HindIII fragment (x-axis) for a 1.6-Mb region (217.2–218.8 Mb) of chromosome 2q35 including the 0.8-Mb genomic region (217,609,776–218,362,744 bp) that was targeted in the sequence capture step of our CHi-C protocol. All coordinates are based on hg19. The capture region is denoted by a double-headed red arrow; the “bait end” of the interaction peaks (i.e., the end that maps to the capture region) is indicated in red, the target end (i.e., the region that maps outside the capture region) is indicated in green. The interaction peaks are aligned with (1) GENCODE genes (v19) with protein-coding transcripts colored blue and noncoding transcripts colored green; and (2) CTCF and RAD21 binding sites, active (H3K27ac, H3K4me1 and H3K4me3) and repressive (H3K27me3) histone modification marks (in black), and ESR1 and FOXA1 binding sites (in blue) generated in the breast cancer cell line MCF7 by the ENCODE Project, Frietze et al. (2012), and Hurtado et al. (2011). The location of the breast cancer risk SNP rs13387042 is also shown.