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LOC127400780 H3K27ac hESC enhancers GRCh37_chr4:52917119-52917620 and GRCh37_chr4:52917621-52918120 [ Homo sapiens (human) ]

Gene ID: 127400780, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127400780
Gene description
H3K27ac hESC enhancers GRCh37_chr4:52917119-52917620 and GRCh37_chr4:52917621-52918120
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 genomic region includes two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in human embryonic stem cells, where they are marked by the H3K27ac histone modification. 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, Jun 2023]
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Genomic context

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See LOC127400780 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (52050953..52052096)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (55536893..55538036)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (52917119..52918262)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15421 Neighboring gene long intergenic non-protein coding RNA 2480 Neighboring gene sarcoglycan beta Neighboring gene spermatogenesis associated 18 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:53068243-53068918 Neighboring gene NANOG hESC enhancer GRCh37_chr4:53135291-53135887 Neighboring gene uncharacterized LOC107986279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53243316-53243864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53243865-53244412 Neighboring gene metallophosphoesterase 1 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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 21553
  • ATAC-STARR-seq lymphoblastoid silent region 15422
  • H3K27ac hESC enhancer GRCh37_chr4:52917119-52917620
  • H3K27ac hESC enhancer GRCh37_chr4:52917621-52918120

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_102743.2 

    Range
    101..1244
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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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    52050953..52052096
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    55536893..55538036
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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