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LOC127404865 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176830685-176831542 [ Homo sapiens (human) ]

Gene ID: 127404865, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404865
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176830685-176831542
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 and H3K4me1 histone modifications. This locus also includes three accessible chromatin subregions that were validated as silencers based on their 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, May 2023]
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Genomic context

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See LOC127404865 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 (177403684..177404636)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177946902..177947854)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176830685..176831637)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176814616-176815116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176815117-176815617 Neighboring gene VISTA enhancer hs2229 Neighboring gene solute carrier family 34 member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176823005-176823660 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:176824881-176825056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176828971-176829828 Neighboring gene profilin 3 Neighboring gene coagulation factor XII Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176853351-176853890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23719 Neighboring gene G protein-coupled receptor kinase 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176867639-176868335 Neighboring gene PRR7 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176874472-176875100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876138-176876638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876639-176877139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16688 Neighboring gene proline rich 7, synaptic Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176881361-176882061 Neighboring gene Sharpr-MPRA regulatory region 1974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16691

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 16683
  • ATAC-STARR-seq lymphoblastoid silent region 16684
  • ATAC-STARR-seq lymphoblastoid silent region 16685

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_106810.2 

    Range
    101..1053
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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
    177403684..177404636
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177946902..177947854
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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