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LOC114827852 VISTA enhancer hs2289 [ Homo sapiens (human) ]

Gene ID: 114827852, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114827852
Gene description
VISTA enhancer hs2289
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 forebrain of transgenic mice. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in naive and primed human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac histone modification, and one is additionally marked by H3K4me1. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (10351197..10353153)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (10435727..10437684)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (10372744..10374700)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene SET binding factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4428 Neighboring gene G protein subunit gamma 10 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3147 Neighboring gene Sharpr-MPRA regulatory region 210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3149 Neighboring gene Sharpr-MPRA regulatory region 6386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10361539-10362039 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10361038-10361538 Neighboring gene uncharacterized LOC100130460 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10375005-10375536 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10375537-10376067 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:10388109-10388608 Neighboring gene Sharpr-MPRA regulatory region 7754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10413861-10414740 Neighboring gene adrenomedullin Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10430364-10430864 Neighboring gene RNA, U6atac small nuclear 33, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10430865-10431365 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:10437608-10437821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:10500293-10500792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10509586-10510490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10521616-10522209 Neighboring gene adenosine monophosphate deaminase 3

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. 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

  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:10373942-10374473
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10373411-10373941

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_065208.1 

    Range
    101..2057
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    10351197..10353153
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    10435727..10437684
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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