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LOC127396840 H3K27ac hESC enhancer GRCh37_chr3:14989619-14990306 [ Homo sapiens (human) ]

Gene ID: 127396840, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127396840
Gene description
H3K27ac hESC enhancer GRCh37_chr3:14989619-14990306
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 an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. This locus also includes three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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, May 2023]
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Genomic context

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See LOC127396840 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (14947776..14948799)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (14950226..14951249)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (14989283..14990306)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14845672-14846414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14852491-14852991 Neighboring gene long intergenic non-protein coding RNA 2011 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:14855464-14855666 Neighboring gene FYVE, RhoGEF and PH domain containing 5 Neighboring gene Sharpr-MPRA regulatory region 8692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14905091-14905672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14920327-14920828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14941355-14942238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14942239-14943121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14955453-14956275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14956276-14957097 Neighboring gene uncharacterized LOC105376963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14962633-14963132 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:14963648-14964847 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:14965692-14965871 Neighboring gene Sharpr-MPRA regulatory region 15385 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14988241-14988930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14097 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14990307-14990994 Neighboring gene FGD5 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19523 Neighboring gene nuclear receptor subfamily 2 group C member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:15066535-15067034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19525 Neighboring gene mitochondrial ribosomal protein S25 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14100 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:15139860-15140724 Neighboring gene rabenosyn, RAB effector

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 19522
  • ATAC-STARR-seq lymphoblastoid silent region 14098
  • ATAC-STARR-seq lymphoblastoid silent region 14099

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_098810.2 

    Range
    101..1124
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    14947776..14948799
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    14950226..14951249
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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