U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC110121459 VISTA enhancer hs1903 [ Homo sapiens (human) ]

Gene ID: 110121459, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC110121459
Gene description
VISTA enhancer hs1903
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 melanocytes and somite of transgenic mice. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where one subregion is marked by the H3K27ac and H3K4me1 histone modifications and the other is associated with the NANOG transcription factor. 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77040521..77045067)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71250274..71254817)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77506871..77511353)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77496104-77496624 Neighboring gene interferon regulatory factor 2 binding protein like Neighboring gene uncharacterized LOC105370579 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77499197-77499746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5964 Neighboring gene long intergenic non-protein coding RNA 2288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77519369-77519932 Neighboring gene Sharpr-MPRA regulatory region 7445 Neighboring gene long intergenic non-protein coding RNA 2289 Neighboring gene Sharpr-MPRA regulatory region 8378 Neighboring gene uncharacterized LOC124903350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77564243-77565072

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 8787
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:77506864-77507595
  • NANOG hESC enhancer GRCh37_chr14:77510900-77511410

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_054072.2 

    Range
    101..4647
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    77040521..77045067
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71250274..71254817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases