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LOC110121236 VISTA enhancer hs1968 [ Homo sapiens (human) ]

Gene ID: 110121236, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121236
Gene description
VISTA enhancer hs1968
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 dorsal root ganglion of transgenic mice. A subregion marked by the H3K27ac and H3K4me1 histone modifications was also shown to be an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive 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]
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (237894726..237898972)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (238384732..238388982)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (238803368..238807597)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 44 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238766078-238766866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238766867-238767653 Neighboring gene small nucleolar RNA SNORD55/SNORD39 Neighboring gene receptor activity modifying protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238791275-238791776 Neighboring gene MPRA-validated peak4098 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17378 Neighboring gene MPRA-validated peak4100 silencer Neighboring gene uncharacterized LOC105373960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12482 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:238850021-238850520 Neighboring gene uncharacterized LOC124908001

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 17377
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238803635-238804513

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_053851.2 

    Range
    101..4347
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    237894726..237898972
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    238384732..238388982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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