Fig. 3

PCHi-C Peaky fine-mapping prioritizes CCVs at 10q14 and 6p22.3. a Chromatin interactions at 9q33.1 in MCF7 breast cancer cells. Topologically associating domains (TADs; Additional file 2: Table S16) are shown as horizontal gray bars above GENCODE-annotated coding (blue) and non-coding (green) genes. The PCHi-C bait is depicted as a black box. CCVs are shown as red vertical lines. The ATAC-seq track is shown as a dark blue histogram. Peaky-defined MPPC values (from PCHi-C BaitID: 479054) are plotted with the prioritized CCV overlaid as a red vertical line. CHiCAGO-scored interactions are shown as black arcs. The dashed red outline highlights the prioritized CCV rs811688 and the dashed gray outline the target gene (PAPPA). b Chromatin interactions at 10q14 in T47D breast cancer cells. Topologically associating domains (TADs) are shown as horizontal gray bars above GENCODE-annotated coding (blue) and non-coding (green) genes. The PCHi-C bait is depicted as a black box. CCVs are shown as red vertical lines. The ATAC-seq track is shown as a dark blue histogram. Peaky-defined MPPC values (from PCHi-C BaitID: 486406) are plotted with the prioritized CCVs overlaid as red vertical lines. CHiCAGO-scored interactions are shown as black arcs. The dashed red outline highlights the prioritized CCVs and the dashed gray outline the target gene (GATA3). c Zoomed in view of prioritized CCVs at 10q14. HindIII fragments are shown as gray bars with their fragment IDs. CCVs are shown as red vertical lines. Black histograms denote ChIP-seq data from T47D cells for H3K27ac, GATA3, and estrogen receptor (ER; cells treated with DMSO or 17 beta-estradiol (EST)). The dashed gray outline highlights CCV rs12765282. d Position weight matrix of the GATA3 binding site from JASPAR (red arrowhead indicates the CCV position in the motif), with homology to the risk (t) and protective (g) alleles of rs12765282 colored below