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LOC110121222 VISTA enhancer hs1909 [ Homo sapiens (human) ]

Gene ID: 110121222, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121222
Gene description
VISTA enhancer hs1909
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, limb and somite of transgenic mice. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (43217582..43220159)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (43222953..43225526)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (43444721..43447298)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43360411-43361174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43361175-43361936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43367134-43367705 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43367706-43368276 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43379975-43380123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43384913-43385431 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43385646-43385841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43394830-43395476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43396769-43397414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43397590-43398275 Neighboring gene uncharacterized LOC124907755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43404972-43405498 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1717 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:43407075-43407600 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:43411165-43412364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43412481-43413214 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43413949-43414682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43414683-43415416 Neighboring gene CRISPRi-validated cis-regulatory element chr2.1723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:43421149-43422068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43437212-43437806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43441787-43442553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11423 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:43453393-43454356 Neighboring gene ZFP36 ring finger protein like 2 Neighboring gene long intergenic non-protein coding RNA 1126

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
  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

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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 active region 15663
  • ATAC-STARR-seq lymphoblastoid silent region 11420
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43445617-43446146
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:43446147-43446676

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_053837.1 

    Range
    101..2678
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    43217582..43220159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    43222953..43225526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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