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LOC114827848 VISTA enhancer hs1656 [ Homo sapiens (human) ]

Gene ID: 114827848, updated on 15-Mar-2024

Summary

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Gene symbol
LOC114827848
Gene description
VISTA enhancer hs1656
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 locus represents a conserved genomic element that can function as an enhancer. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic heart of transgenic mice. A subregion was also validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. Another subregion marked by the H3K27ac histone modification was also shown to be an active enhancer by ChIP-STARR-seq in primed human embryonic stem cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Orthologs
mouse all
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (59837210..59839588)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60705964..60708342)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57914612..57916949)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8782 Neighboring gene clathrin heavy chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:57760547-57761746 Neighboring gene Sharpr-MPRA regulatory region 12460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57780642-57781146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57781147-57781650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57784605-57785260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57794547-57795046 Neighboring gene peptidyl-tRNA hydrolase 2 Neighboring gene vacuole membrane protein 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:57831571-57832770 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57845677-57846178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57860713-57861526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57911971-57912470 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:57917673-57918402 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:57919688-57919882 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57923900-57924888 Neighboring gene RNA, U6 small nuclear 450, pseudogene Neighboring gene microRNA 21

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. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  4. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

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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Homology

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 12517
  • BRD4-independent group 4 enhancer GRCh37_chr17:57914776-57915975
  • H3K27ac hESC enhancer GRCh37_chr17:57915481-57916210

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_065204.2 

    Range
    101..2479
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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
    59837210..59839588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    60705964..60708342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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