Fig. 6
Genomic context of the CpGs associated with rs3934834. a The entire investigated region. b Zoom on the region surrounding rs3934834. Genomic positions of RefSeq genes and rs3934834 are displayed in the top panel. Within the two vertical red dotted lines, the LD r2 > 0.8. The positions of the tested CpGs are displayed. Long-range interactions as defined by ChIA-PET libraries from five cell lines using chromatin immunoprecipitation with antibodies targeting three transcription factors (Additional file 5) are displayed as arcs. For clarity of visualization, we chose to display only the long-range interactions of genomic regions containing associated CpGs. Two interacting genomic regions are represented by an arc that links them, and the thickness of the arc line is proportional to the strength of this interaction. The color of the arc corresponds to the target transcription factor and the shade of the color corresponds to the cell line: red for RNA polymerase II, blue for ERα, and green for CTCF. In the bottom panel, chromatin states in 11 tissues are displayed. Chromatin states were obtained using chromHMM prediction using data on seven histone marks (see “Methods”). The color of each band corresponds to a particular state. AN adipose nuclei, BrainAC brain anterior caudate, BrainAG brain angular gyrus, BrainCG brain cingulate gyrus, BrainHIPPO brain hippocampus, BrainITL brain inferior temporal lobe, BrainSN brain substantia nigra, PBMC peripheral blood mononuclear primary cells, PI pancreatic islets, SM skeletal muscle