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LOC110120798 VISTA enhancer hs901 [ Homo sapiens (human) ]

Gene ID: 110120798, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110120798
Gene description
VISTA enhancer hs901
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 hindbrain and midbrain of transgenic mice. A subregion associated with the OCT4 and NANOG transcription factors was also shown to be an active enhancer by ChIP-STARR-seq in naive and 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37251210..37252226)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37274886..37275902)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37251207..37252223)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28378 Neighboring gene zinc finger CCHC-type containing 7 Neighboring gene NANOG hESC enhancer GRCh37_chr9:37149770-37150271 Neighboring gene uncharacterized LOC105376033 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:37184571-37185145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28380 Neighboring gene Sharpr-MPRA regulatory region 4584 Neighboring gene ZCCHC7 intron homotypic cluster of transcription factor binding sites enhancer Neighboring gene NANOG hESC enhancer GRCh37_chr9:37226199-37226700 Neighboring gene Sharpr-MPRA regulatory region 4537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28382 Neighboring gene RNA, U6 small nuclear 677, pseudogene Neighboring gene uncharacterized LOC124902153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28387 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37385483-37385983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28389 Neighboring gene long intergenic non-protein coding RNA 1627

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
  3. 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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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 28381
  • OCT4-NANOG hESC enhancer GRCh37_chr9:37251213-37251975

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_053423.1 

    Range
    101..1117
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    37251210..37252226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    37274886..37275902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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