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LOC112840906 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:227514829-227515742 [ Homo sapiens (human) ]

Gene ID: 112840906, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112840906
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:227514829-227515742
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 human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (226650113..226651026)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (227131725..227132638)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (227514849..227515143)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2716 Neighboring gene uncharacterized LOC646736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17192 Neighboring gene uncharacterized LOC105373915 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:227342641-227343191 Neighboring gene NANOG hESC enhancer GRCh37_chr2:227348646-227349147 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:227513913-227514828 Neighboring gene MPRA-validated peak4063 silencer Neighboring gene MPRA-validated peak4064 silencer Neighboring gene MPRA-validated peak4065 silencer Neighboring gene microRNA 5702 Neighboring gene Sharpr-MPRA regulatory region 3334 Neighboring gene MPRA-validated peak4066 silencer Neighboring gene Sharpr-MPRA regulatory region 11623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12389 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:227661675-227662624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12391 Neighboring gene insulin receptor substrate 1

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 active region 17193
  • ATAC-STARR-seq lymphoblastoid silent region 12388
  • Sharpr-MPRA regulatory region 2633

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_060941.2 

    Range
    101..1014
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    226650113..226651026
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    227131725..227132638
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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