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LOC127403798 H3K4me1 hESC enhancer GRCh37_chr5:131801783-131802284 [ Homo sapiens (human) ]

Gene ID: 127403798, updated on 27-Aug-2024

Summary

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Gene symbol
LOC127403798
Gene description
H3K4me1 hESC enhancer GRCh37_chr5:131801783-131802284
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. 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, May 2023]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132466091..132466881)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132985910..132986700)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MIR3936 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131712295-131712796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23070 Neighboring gene solute carrier family 22 member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16319 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131751322-131751510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763030-131763616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763617-131764201 Neighboring gene long intergenic non-protein coding RNA 2863 Neighboring gene colitis associated IRF1 antisense regulator of intestinal homeostasis Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131780806-131781485 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:131786393-131787031 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131791634-131791826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792105-131792775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792776-131793445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131799668-131800632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131800633-131801597 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23080 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:131821689-131822888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131825338-131825985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131827280-131827925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131832117-131833091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23085 Neighboring gene interferon regulatory factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131892292-131892952 Neighboring gene interleukin 5

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23078

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_105747.2 

    Range
    101..891
    Download
    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
    132466091..132466881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132985910..132986700
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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