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LOC127408509 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:10979917-10980837 [ Homo sapiens (human) ]

Gene ID: 127408509, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127408509
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:10979917-10980837
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 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, 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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See LOC127408509 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (10940136..10941210)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (11070726..11071800)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (10979763..10980837)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC79150 Neighboring gene uncharacterized LOC107986766 Neighboring gene VISTA enhancer hs793 Neighboring gene MPRA-validated peak6384 silencer Neighboring gene uncharacterized LOC124900231 Neighboring gene MPRA-validated peak6385 silencer Neighboring gene uncharacterized LOC100131472 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:10763070-10763266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:10781799-10782298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:10948792-10949324 Neighboring gene uncharacterized LOC107986767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17973 Neighboring gene Sharpr-MPRA regulatory region 7861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17975 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:11022338-11022514 Neighboring gene NDUFA4 mitochondrial complex associated Neighboring gene ribosomal protein L23a pseudogene 52 Neighboring gene PHD finger protein 14 Neighboring gene MPRA-validated peak6386 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:11224740-11225283 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:11232333-11233080 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:11233081-11233827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25661 Neighboring gene nucleophosmin 1 pseudogene 11

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 25659
  • ATAC-STARR-seq lymphoblastoid silent region 17972

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_110477.2 

    Range
    101..1175
    Download
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    10940136..10941210
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    11070726..11071800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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