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LOC127896240 OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39415894-39416734 [ Homo sapiens (human) ]

Gene ID: 127896240, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127896240
Gene description
OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39415894-39416734
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 two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in human embryonic stem cells, where both are marked by the H3K27ac and H3K4me1 histone modifications and one additionally associates with the OCT4 transcription factor. 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 LOC127896240 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39019889..39021568)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39490309..39491988)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39415894..39417573)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39370179-39370956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13737 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:39380734-39381933 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39382500-39382695 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3B Neighboring gene APOBEC3B antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:39394090-39394730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39406643-39407144 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr22:39409474-39410092 and GRCh37_chr22:39410093-39410710 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39417574-39418413 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39423978-39424906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39426361-39427157 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:39432783-39433673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39437791-39438568 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39439415-39439645 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3F Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:39445317-39446516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39448525-39449459 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39458436-39458615 Neighboring gene uncharacterized LOC107985563 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39465577-39466080

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 19026
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39416735-39417573
  • hESC enhancers GRCh37_chr22:39415894-39416734 and GRCh37_chr22:39416735-39417573

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_148301.2 

    Range
    101..1780
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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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39019889..39021568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39490309..39491988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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