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LOC108004546 enhancer upstream of SOX9 [ Homo sapiens (human) ]

Gene ID: 108004546, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108004546
Gene description
enhancer upstream of SOX9
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region contains an enhancer that is thought to regulate expression of the SRY-box 9 (SOX9) gene, located approximately 1 Mb downstream. Chromatin conformation capture evidence suggests that this sequence associates directly with the promoter of SOX9. Naturally-occurring polymorphisms in this region affect association by androgen receptor and forkhead box A1, which act to regulate the activity of this sequence. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC108004546 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (71111474..71112664)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (71984171..71985361)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (69107615..69108805)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904104 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:68983705-68984206 Neighboring gene VISTA enhancer hs1467 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:69028546-69029302 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:69029303-69030057 Neighboring gene SOX9 enhancer cre1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:69067578-69068777 Neighboring gene cancer susceptibility 17 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:69297407-69297907 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:69300220-69300720 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:69300721-69301221 Neighboring gene U6 spliceosomal RNA Neighboring gene RNA, U7 small nuclear 155 pseudogene

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. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Smyk M, et al. Am J Med Genet A, 2015 Aug. PMID 26059046
  2. Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Zhang X, et al. Genome Res, 2012 Aug. PMID 22665440, Free PMC Article
  3. Chromosome conformation capture-on-chip analysis of long-range cis-interactions of the SOX9 promoter. Smyk M, et al. Chromosome Res, 2013 Dec. PMID 24254229

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

See Variation Viewer (GRCh37.p13)

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_050864.1 

    Range
    101..1291
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    71111474..71112664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    71984171..71985361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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