Fig. 2
From: Epigenome-wide association studies identify DNA methylation associated with kidney function
Regional association plot and genomic annotation surrounding the index cg19942083 CpG site on chromosome 12p13. Y-axis: -log10(P-values) for association between methylation and eGFR from a combined analysis of ARIC and FHS; x-axis: chromosomal position. Each dot represents an evaluated CpG, the color-coding reflects the degree of correlation of methylation values at all other CpGs with that of the index site (red: positive correlation, blue: negative correlation). The index probe cg19942083 is represented as a black dot and included in a red box to facilitate mapping across annotation tracks. Chromatin annotation from various tissues and histone modification marks from kidney cells (black tracks) show that the index probe maps into an active enhancer in kidney tissues. H3K4me1 marks represent poised enhancer elements, H3K4me3 marks represent transcription start sites for actively transcribed genes, and H3K27ac marks represent active enhancer elements. Chromatin annotation track color-code: dark red: active promoter, light red: weak promoter, dark green: transcriptional transition/elongation, light green: weak transcribed, yellow: weak/poised enhancer, orange: strong enhancer, blue: insulator, gray: repressed polycomb, light gray: heterochromatin;low signal;repetitive/CNV. Chromatin annotation tracks were evaluated from 9 different cell lines from the ENCODE Project: B-lymphoblastoid cells (GM12878), embryonic stem cells (H1 hESC), erythrocytic leukemia cells (K562), hepatocellular carcinoma cells (HepG2), umbilical vein endothelial cells (HUVEC), mammary epithelial cells (HMEC), skeletal muscle myoblasts (HSMM), normal epidermal keratinocytes (NHEK), and normal lung fibroblasts (NHLF)
