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LOC110121280 VISTA enhancer hs2204 [ Homo sapiens (human) ]

Gene ID: 110121280, updated on 17-Sep-2024

Summary

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Gene symbol
LOC110121280
Gene description
VISTA enhancer hs2204
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 heart tissue of transgenic mouse embryos. A subregion was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region). The same subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, May 2021]
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Genomic context

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See LOC110121280 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (11699806..11703497)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (8036781..8040468, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11557315..11561006)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 208 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11456947-11457783 Neighboring gene MPRA-validated peak6905 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11478375-11478875 Neighboring gene Sharpr-MPRA regulatory region 10445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11487938-11488828 Neighboring gene uncharacterized LOC105379242 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:11530424-11530618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:11532437-11532959 Neighboring gene GATA binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18936 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11566565-11567490 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11567491-11568414 Neighboring gene small nucleolar RNA, H/ACA box 99 Neighboring gene HNF4 motif-containing MPRA enhancer 121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:11584607-11585590 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11593264-11593764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27031 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11594517-11595018 Neighboring gene VISTA enhancer hs2205 Neighboring gene VISTA enhancer hs508 Neighboring gene long intergenic non-protein coding RNA 2905

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 9827

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_053895.1 

    Range
    101..3792
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    11699806..11703497
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    1644589..1648275 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    8036781..8040468 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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