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LOC128667231 RFX6 prostate cancer risk allelic enhancer [ Homo sapiens (human) ]

Gene ID: 128667231, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128667231
Gene description
RFX6 prostate cancer risk allelic enhancer
Gene type
biological region
Feature type(s)
protein_bind
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region, which is located in an intron of the RFX6 (regulatory factor X6) gene, represents an enhancer with differential allelic activity. It includes a single nucleotide polymorphism (SNP), rs339331, for which the T allele is associated with prostate cancer susceptibility. This region was validated as a T allele-preferred enhancer that can activate the RFX6 promoter by reporter gene assays in LNCaP and VCaP prostate cancer cells. This enhancer also exhibits increased activity in response to androgen, especially for the T allele. The rs339331 SNP is located in a binding site for the HOXB13 transcription factor, which preferentially binds the T allele. The HOXB13 binding site was shown to be important for RFX6 gene expression in prostate cancer cells by both TALEN-mediated genome editing and reporter gene assays. [provided by RefSeq, Feb 2023]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116888439..116889340)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (118072225..118073126)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377963 Neighboring gene G protein-coupled receptor class C group 6 member A Neighboring gene RFX6 promoter region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:117198416-117199374 Neighboring gene regulatory factor X6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:117246147-117247346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25000 Neighboring gene ribosomal protein S29 pseudogene 13 Neighboring gene RNA, 5S ribosomal pseudogene 214

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The Role of HOX Transcription Factors in Cancer Predisposition and Progression. Li B, et al. Cancers (Basel), 2019 Apr 12. PMID 31013831, Free PMC Article
  2. Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants. Dadaev T, et al. Nat Commun, 2018 Jun 11. PMID 29892050, Free PMC Article
  3. Prostate Cancer Germline Variations and Implications for Screening and Treatment. Dias A, et al. Cold Spring Harb Perspect Med, 2018 Sep 4. PMID 29101112, Free PMC Article
  4. Interactions Between Genome-Wide Significant Genetic Variants and Circulating Concentrations of 25-Hydroxyvitamin D in Relation to Prostate Cancer Risk in the National Cancer Institute BPC3. Dimitrakopoulou VI, et al. Am J Epidemiol, 2017 Mar 15. PMID 28399564, Free PMC Article
  5. Systematic meta-analyses of gene-specific genetic association studies in prostate cancer. Hao Q, et al. Oncotarget, 2016 Apr 19. PMID 26967244, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

General gene information

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Other Names

  • CAUSEL-validated RFX6 intronic cis-regulatory element

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_149640.1 

    Range
    101..1002
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    116888439..116889340
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    118072225..118073126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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