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LOC123477746 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57773523-57774452 [ Homo sapiens (human) ]

Gene ID: 123477746, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477746
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57773523-57774452
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). 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, May 2023]
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Genomic context

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See LOC123477746 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (56907357..56908286)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (60398785..60399710)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (57773549..57773843)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 357, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15455 Neighboring gene serine peptidase inhibitor Kazal type 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57710833-57711338 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57711339-57711844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:57714899-57715398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:57775383-57776312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:57780934-57781434 Neighboring gene RE1 silencing transcription factor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:57802865-57804064 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:57831417-57831519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21588 Neighboring gene nitric oxide associated 1 Neighboring gene uncharacterized LOC124900913 Neighboring gene RNA polymerase II subunit B

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 15456
  • Sharpr-MPRA regulatory region 6073

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_077549.2 

    Range
    101..1030
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    56907357..56908286
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    60398785..60399710
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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