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LOC127404061 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140043900-140044566 [ Homo sapiens (human) ]

Gene ID: 127404061, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127404061
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140043900-140044566
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 naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140664315..140665038)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141189711..141190434)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene transmembrane and coiled-coil domains 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:140026953-140027488 Neighboring gene NADH:ubiquinone oxidoreductase subunit A2 Neighboring gene microRNA 3655 Neighboring gene IK cytokine Neighboring gene uncharacterized LOC124901088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140052035-140052830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140052831-140053626 Neighboring gene WD repeat domain 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23284 Neighboring gene DND microRNA-mediated repression inhibitor 1 Neighboring gene histidyl-tRNA synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23285 Neighboring gene HARS1 and HARS2 bidirectional promoter region

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 23282
  • ATAC-STARR-seq lymphoblastoid active region 23283

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_106010.2 

    Range
    101..824
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    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    140664315..140665038
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141189711..141190434
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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