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Fig. 2 | Cancer Cell International

Fig. 2

From: Genetic variants in the circadian rhythm pathway as indicators of prostate cancer progression

Fig. 2

a ENCODE data for the linkage disequilibrium (LD) block containing NPAS2 rs6542993. H3K4Me1, H3K4Me3, and H3K27Ac tracks show the levels of enrichment of the mono-methylation of lysine 4, tri-methylation of lysine 4, and acetylation of lysine 27 of the H3 histone protein, respectively, across the genome as determined by chromatin immunoprecipitation sequencing (ChIP-seq) assays. These marks are thought to be associated with enhancer and promoter regions. Chromatin State Segmentation track displays chromatin state segmentations by integrating the ChIP-seq data using a Hidden Markov Model for HepG2 hepatocellular carcinoma cells, HMEC normal mammary epithelial cells, and NHLF normal lung fibroblast cells. The chromatin state regions predicted for promoters and enhancers are highlighted. The DNase clusters track shows DNase hypersensitivity areas. The Tnx factor track shows regions of transcription factor binding to DNA as assayed by ChIP-seq experiments. b Regulatory annotation of variants within the LD block containing NPAS2 rs6542993. In the LD block with the tagSNP rs6542993, there are strong enrichments of promoter and enhancer marks among the several different cell types tested. In addition, multiple regulatory motifs are predicted to be affected by the linked variants

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