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LOC110121481 VISTA enhancer hs2084 [ Homo sapiens (human) ]

Gene ID: 110121481, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121481
Gene description
VISTA enhancer hs2084
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 transgenic mice embryos. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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: 21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (34543666..34547364)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (32926232..32929930)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (35915964..35919662)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene salivary glue protein Sgs-3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:35788990-35790189 Neighboring gene NANOG hESC enhancer GRCh37_chr21:35802003-35802504 Neighboring gene small integral membrane protein 34 Neighboring gene NANOG hESC enhancer GRCh37_chr21:35825641-35826142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35827602-35828102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35828103-35828603 Neighboring gene small nucleolar RNA SNORA11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35831243-35832104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35832105-35832965 Neighboring gene potassium voltage-gated channel subfamily E regulatory subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18395 Neighboring gene regulator of calcineurin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35954416-35954916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35954917-35955417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13273 Neighboring gene chloride intracellular channel 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36095588-36096365 Neighboring gene uncharacterized LOC107985515 Neighboring gene long intergenic non-protein coding RNA 160

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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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 13268

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_054094.1 

    Range
    101..3799
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    34543666..34547364
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    32926232..32929930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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