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LOC127405537 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24721651-24722444 [ Homo sapiens (human) ]

Gene ID: 127405537, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127405537
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24721651-24722444
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 three 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: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (24720928..24722216)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (24592061..24593348)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (24721156..24722444)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene acyl-CoA thioesterase 13 Neighboring gene uncharacterized LOC124901278 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:24699525-24699689 Neighboring gene chromosome 6 open reading frame 62 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24720063-24720856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24157 Neighboring gene long intergenic non-protein coding RNA 2828 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:24754099-24754309 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:24758062-24758263 Neighboring gene AP3S1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24158 Neighboring gene geminin DNA replication inhibitor

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 24154
  • ATAC-STARR-seq lymphoblastoid active region 24155
  • ATAC-STARR-seq lymphoblastoid active region 24156

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_107508.2 

    Range
    101..1389
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    24720928..24722216
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    24592061..24593348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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