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LOC110121271 VISTA enhancer hs2181 [ Homo sapiens (human) ]

Gene ID: 110121271, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121271
Gene description
VISTA enhancer hs2181
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 blood vessels of transgenic mice. A subregion was also identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (137694278..137697238)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (138220130..138223088)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (137029967..137032927)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 Neighboring gene uncharacterized LOC105379192 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:136481153-136482352 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:136536474-136537125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16381 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:136570305-136571504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:136655443-136655942 Neighboring gene MPRA-validated peak5485 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:136965897-136966647 Neighboring gene Sharpr-MPRA regulatory region 15161 Neighboring gene MPRA-validated peak5486 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr5:137020129-137020374 Neighboring gene Sharpr-MPRA regulatory region 14679 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137023227-137023961 Neighboring gene kelch like family member 3 Neighboring gene microRNA 874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:137071377-137072045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137088711-137089402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23186 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:137090093-137090784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23187 Neighboring gene heterogeneous nuclear ribonucleoprotein A0 Neighboring gene neuropeptide Y receptor Y6 (pseudogene)

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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

  • MPRA-validated peak5487 silencer

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_053886.1 

    Range
    101..3061
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    137694278..137697238
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    138220130..138223088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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