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LOC127404838 H3K27ac hESC enhancer GRCh37_chr5:176449939-176450475 [ Homo sapiens (human) ]

Gene ID: 127404838, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404838
Gene description
H3K27ac hESC enhancer GRCh37_chr5:176449939-176450475
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 an accessible chromatin subregion that was validated as a silencer based on its ability to 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 LOC127404838 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177022911..177023474)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177566084..177566647)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176449912..176450475)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene unc-5 netrin receptor A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176314417-176314917 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176327167-176327668 Neighboring gene hexokinase 3 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:176370315-176371173 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:176371174-176372031 Neighboring gene ubiquitin interaction motif containing 1 Neighboring gene uncharacterized LOC124901145 Neighboring gene MPRA-validated peak5592 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16668 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176449401-176449938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16670 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176488686-176489885 Neighboring gene zinc finger protein 346 Neighboring gene FGFR4 5' regulatory region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176537235-176537734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176558105-176558658 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr5:176559765-176560316 and GRCh37_chr5:176560317-176560870 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176560871-176561422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176561423-176561976 Neighboring gene fibroblast growth factor receptor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16676 Neighboring gene nuclear receptor binding SET domain protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176692158-176693050 Neighboring gene ribosomal protein L21 pseudogene 60

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 silent region 16669

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_106783.2 

    Range
    101..664
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    177022911..177023474
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177566084..177566647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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