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LOC114827857 VISTA enhancer hs2509 [ Homo sapiens (human) ]

Gene ID: 114827857, updated on 15-Mar-2024

Summary

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Gene symbol
LOC114827857
Gene description
VISTA enhancer hs2509
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. It can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic limb of transgenic mice. This locus also includes three accessible chromatin subregions that were validated as enhancers based on their 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Orthologs
mouse all
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Genomic context

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See LOC114827857 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (44260653..44262837)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (45141498..45143682)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (44756101..44758285)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2659 Neighboring gene long intergenic non-protein coding RNA 841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44475579-44476080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44476081-44476580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44501255-44501828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44510639-44511138 Neighboring gene NANOG hESC enhancer GRCh37_chr10:44537391-44537911 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12630 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12643 Neighboring gene uncharacterized LOC124902543 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:44607592-44608157 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12798 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12804 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:44664362-44665561 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44688953-44689454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44689455-44689954 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44703238-44703811 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44728896-44729550 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:44730206-44730859 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44729551-44730205 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3311 Neighboring gene uncharacterized LOC124902544 Neighboring gene NANOG hESC enhancer GRCh37_chr10:44793368-44793869 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:44796158-44797357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3312 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:44805333-44805502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44806263-44806765 Neighboring gene long intergenic non-protein coding RNA 2881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2339 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:44821405-44821620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:44833715-44834216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44852471-44853402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44859545-44860046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:44860047-44860546 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:44866272-44866820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44873825-44874771 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44878101-44878794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44878795-44879488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:44879489-44880180 Neighboring gene C-X-C motif chemokine ligand 12

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. 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

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 3308
  • ATAC-STARR-seq lymphoblastoid active region 3309
  • ATAC-STARR-seq lymphoblastoid active region 3310

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_065213.1 

    Range
    101..2285
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    44260653..44262837
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    45141498..45143682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
Molecular Biology Databases