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LOC111674470 DNase I hypersensitive region 15.6 kb downstream of CFTR [ Homo sapiens (human) ]

Gene ID: 111674470, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111674470
Gene description
DNase I hypersensitive region 15.6 kb downstream of CFTR
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, enhancer_blocking_element, silencer, 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
Also known as
DHS+15.6kb
Summary
This genomic sequence represents a DNase I hypersensitive region located approximately 15 kb downstream of the CFTR (cystic fibrosis transmembrane conductance regulator) gene. This region can interact physically with the CFTR promoter and other elements in a larger topologically associating domain (TAD), and multiple transcription factor binding sites have been identified. A sub-region, IVc, was shown to enhance basal CFTR promoter expression in reporter assays in transfected HepG2 and Caco2 cells, while two sub-regions, PQ and RS, were defined as enhancer-blocking elements that could block activation of a human gamma-globin promoter by the mouse HS2 beta-globin enhancer when positioned between the enhancer and promoter in transfected K562 cells. Another sub-region was shown to cooperate with the DHS1 and DHS11 regulatory elements to augment expression of a basal CFTR promoter in transfected Caco2 cells. In addition, a nonconserved sub-region, NR10, represents a silencer that was shown to strongly repress an SV40 promoter coupled to the HS2 beta-globin enhancer in transfected K562 and HeLa cells. [provided by RefSeq, Nov 2018]
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Genomic context

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Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117682135..117684043)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (118997496..118999404)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117322189..117324097)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375468 Neighboring gene DNase I hypersensitive site -20.9 kb upstream of CFTR Neighboring gene greater CFTR locus negative regulatory element NR9 Neighboring gene CFTR promoter region Neighboring gene CFTR intron 1 enhancer Neighboring gene CFTR intron 2 DNase I hypersensitive site Neighboring gene CFTR intron 3 DNase I hypersensitive site Neighboring gene greater CFTR locus negative regulatory element CR19 Neighboring gene CF transmembrane conductance regulator Neighboring gene greater CFTR locus negative regulatory element CR20 Neighboring gene DNase I hypersensitive sites in intron 10ab of CFTR Neighboring gene DNase I hypersensitive site in intron 10c of CFTR Neighboring gene CFTR antisense RNA 1 Neighboring gene CFTR intron 11 enhancer Neighboring gene DNase I hypersensitive sites in introns 16 and 17a of CFTR Neighboring gene CFTR intron 18a DNase I hypersensitive site Neighboring gene DNase I hypersensitive site in intron 18 of CFTR Neighboring gene CFTR intron 18b DNase I hypersensitive site Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:117270281-117271480 Neighboring gene CFTR intron 19 DNase I hypersensitive site Neighboring gene CFTR intron 20 enhancer Neighboring gene CFTR intron 21 enhancer Neighboring gene CFTR intron 23 enhancer Neighboring gene DNase I hypersensitive region 5.4 to 7.4 kb downstream of CFTR Neighboring gene CFTR +21.5 kb DNase I hypersensitive site Neighboring gene CFTR +36.6 kb downstream enhancer Neighboring gene greater CFTR locus negative regulatory element NR11 Neighboring gene CTTNBP2 intron enhancer-blocking element 7-1-1 Neighboring gene uncharacterized LOC105375469 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:117372591-117372808 Neighboring gene greater CFTR locus negative regulatory element NR12 Neighboring gene DNase I hypersensitive site 83.7 kb downstream of CFTR Neighboring gene cortactin binding protein 2 Neighboring gene greater CFTR locus negative regulatory element CR27 Neighboring gene greater CFTR locus negative regulatory element NR13 Neighboring gene greater CFTR locus negative regulatory element CR28 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:117449968-117450716 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:117450717-117451463 Neighboring gene greater CFTR locus negative regulatory element NR14 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:117499510-117499710 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:117590690-117591889 Neighboring gene greater CFTR locus negative regulatory element NR19 Neighboring gene uncharacterized LOC105375470

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. DNA polymorphisms in potential regulatory elements of the CFTR gene alter transcription factor binding. Rowntree R, et al. Hum Genet, 2002 Jul. PMID 12136238
  2. The role of CTCF in coordinating the expression of single gene loci. Gillen AE, et al. Biochem Cell Biol, 2011 Oct. PMID 21916612
  3. Analysis of DNase-I-hypersensitive sites at the 3' end of the cystic fibrosis transmembrane conductance regulator gene (CFTR). Nuthall HN, et al. Biochem J, 1999 Aug 1. PMID 10417323, Free PMC Article
  4. Genomic approaches to studying CFTR transcriptional regulation. Ott CJ, et al. Methods Mol Biol, 2011. PMID 21594786
  5. Novel regulatory mechanisms for the CFTR gene. Ott CJ, et al. Biochem Soc Trans, 2009 Aug. PMID 19614605, Free PMC Article

See all (30) 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • CFTR +15.6 kb DNase I hypersensitive site
  • CFTR +15.6 kb enhancer-blocking insulator elements
  • CFTR 3' insulators
  • CFTR looping element IV
  • greater CFTR locus negative regulatory element NR10
  • greater CFTR locus silencer NR10

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_056126.2 

    Range
    101..2009
    Download
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    117682135..117684043
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    118997496..118999404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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