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LOC124174268 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68280925-68281630 [ Homo sapiens (human) ]

Gene ID: 124174268, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124174268
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68280925-68281630
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 in primed 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 a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (67368690..67369395)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (67795182..67795887)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (68281129..68281423)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene centrosome and spindle pole associated protein 1 Neighboring gene uncharacterized LOC124901956 Neighboring gene ADP ribosylation factor guanine nucleotide exchange factor 1 Neighboring gene nucleophosmin 1 pseudogene 44 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:68153855-68154652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68221915-68222570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68222571-68223225 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:68255030-68255710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19262 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:68261316-68261816 Neighboring gene ARFGEF1 divergent transcript Neighboring gene CRISPRi-validated cis-regulatory element chr8.1934 Neighboring gene Sharpr-MPRA regulatory region 12286 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68281631-68282336 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:68293145-68293756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27499 Neighboring gene ribosomal protein L17 pseudogene 31 Neighboring gene carboxypeptidase A6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:68424545-68425147 Neighboring gene uncharacterized LOC105375886 Neighboring gene NACA pseudogene 10

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. 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

  • Sharpr-MPRA regulatory region 8634

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_078567.2 

    Range
    101..806
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    67368690..67369395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    67795182..67795887
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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