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LOC127824458 H3K27ac hESC enhancer GRCh37_chr12:65019275-65019991 [ Homo sapiens (human) ]

Gene ID: 127824458, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127824458
Gene description
H3K27ac hESC enhancer GRCh37_chr12:65019275-65019991
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 liver carcinoma cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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 LOC127824458 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (64625495..64626211)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (64604322..64605038)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Ras association domain family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4624 Neighboring gene RASSF3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6597 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:65035223-65035726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65041527-65042250 Neighboring gene microRNA 548z Neighboring gene microRNA 548c Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65046125-65046302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6600 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65066263-65066452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65068096-65068875 Neighboring gene Sharpr-MPRA regulatory region 4654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65151732-65152612 Neighboring gene glucosamine (N-acetyl)-6-sulfatase Neighboring gene small nucleolar RNA U13 Neighboring gene TBC1 domain family member 30

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6598
  • ReSE screen-validated silencer GRCh37_chr12:65019389-65019578

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_125975.1 

    Range
    101..817
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    64625495..64626211
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    64604322..64605038
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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