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LOC110120880 VISTA enhancer hs486 [ Homo sapiens (human) ]

Gene ID: 110120880, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110120880
Gene description
VISTA enhancer hs486
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 embryonic heart of transgenic mice. A subregion was also validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37998338..37999192)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38459961..38460815)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (38394345..38395199)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene RNA polymerase II, I and III subunit F Neighboring gene MPRA-validated peak4487 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38378831-38379668 Neighboring gene SRY-box transcription factor 10 Neighboring gene VISTA enhancer hs564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38392633-38393194 Neighboring gene microRNA 4534 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:38424434-38424934 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:38427029-38428228 Neighboring gene VISTA enhancer hs491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38438297-38438796 Neighboring gene VISTA enhancer hs492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38446442-38446942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38446943-38447443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18990 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:38452863-38453488 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:38453489-38454112 Neighboring gene protein interacting with PRKCA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38470967-38471468 Neighboring gene uncharacterized LOC105373027 Neighboring gene solute carrier family 16 member 8

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • Sharpr-MPRA regulatory region 3171

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_053503.1 

    Range
    101..955
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    37998338..37999192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    38459961..38460815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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