Figure 2

Summary of the functional analyses for the STK3 rs7827435 locus.

(A) STK3 shows significant eQTL association with rs7827435 genotype in prostate tissues (GTEx data set). Numbers in parentheses indicate the number of cases. (B) Regulatory annotation of variants within the LD block containing STK3 rs7827435. In the LD block with the lead SNP rs7827435, ENCODE data showed evidence of enhancer elements coinciding with rs7827435 and linked variants in GM12878 B-lymphoblastoid cells, HD.CD184EC hESC-derived CD184+ endoderm cultured cells and several additional cell types. In addition, multiple regulatory motifs are predicted to be affected. (C) Expanded view of the ENCODE and GTEx data for the LD block containing the STK3 rs7827435. The H3K4Me1, H3K4Me3 and H3K27Ac tracks show the genome-wide 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, as determined by the ChIP-seq assays. These levels are thought to be associated with enhancer and promoter regions. Chromatin State Segmentation track displays chromatin state segmentations by integrating ChIP-seq data using a Hidden Markov Model for GM12878 B-lymphoblastoid cells, K562 leukemia cells, HepG2 hepatocellular carcinoma cells, HMEC normal mammary epithelial cells, NHEK epidermal keratinocytes and NHLF normal lung fibroblast cells. The chromatin state regions predicted for promoters and enhancers are highlighted. DNase clusters track shows DNase hypersensitivity areas. Tnx Factor track shows regions of transcription factor binding of DNA, as assayed by ChIP-seq experiments. The results of STK3 gene-centric eQTL analysis for prostate tissues using GTEx data are visualized as a regional plot. Closed circles highlight where rs7827435 and its linked SNPs are placed.