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LOC110121469 VISTA enhancer hs1971 [ Homo sapiens (human) ]

Gene ID: 110121469, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121469
Gene description
VISTA enhancer hs1971
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are marked by H3K4me1 histone modification and one is additionally marked by H3K27ac. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (57439654..57444237)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59217477..59222060)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56014710..56019293)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RBM38 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55966169-55966670 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55966671-55967170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55970944-55971905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55973481-55973980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55975022-55975885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18148 Neighboring gene RNA binding motif protein 38 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55984023-55984528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18149 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:55985201-55985370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55988977-55989746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55989747-55990514 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:55990515-55991283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18154 Neighboring gene uncharacterized LOC124904939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18155 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:56012611-56012842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56014209-56014710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18156 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr20:56026537-56027036 and GRCh37_chr20:56027096-56027596 Neighboring gene uncharacterized LOC105372688 Neighboring gene Sharpr-MPRA regulatory region 5175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56039390-56040220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56042501-56043002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56045653-56046391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56048063-56048564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56048565-56049064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56051358-56051858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13063 Neighboring gene high mobility group box 1 pseudogene 1

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. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56016245-56017104
  • H3K4me1 hESC enhancer GRCh37_chr20:56014711-56015210

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_054082.1 

    Range
    101..4684
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    57439654..57444237
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    59217477..59222060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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