Fig. 5

mencRNAs linked to distal CCVs at 6q25. a WashU genome browser showing annotated GENCODE genes (blue) and mencRNAs (black) within the 6q25 risk region. mencRNAs whose promoters participate in chromatin interactions with CCVs are highlighted in blue, green, and red. CCVs are shown as colored vertical lines. The ATAC-seq data is shown as a blue histogram, histone modification ChIP-seq data is shown as black histograms, and CHi-C chromatin interactions are shown as arcs from the MCF7 breast cancer cell line. Colored arcs depict chromatin looping between CCVs and color-matched mencRNA promoter regions. b Correlation between expression of the three captured transcripts and ESR1 in the TCGA cohort. Each dot in the scatterplots represents a breast cancer individual with gene expression values being plotted as log2 (FPKM) on the x- and y-axes. c Boxplot showing absolute correlation coefficient values compared between looped and non-looped pairs of mencRNAs and nearby protein-coding genes (within 1 Mb up- and downstream)