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LOC127828463 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:96968616-96969211 [ Homo sapiens (human) ]

Gene ID: 127828463, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127828463
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:96968616-96969211
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 primed 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 subregion, 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, Jun 2023]
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Genomic context

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See LOC127828463 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (96502196..96502874)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (90733799..90734477)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (96968533..96969211)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8986 Neighboring gene adenylate kinase 7 Neighboring gene phosphatidylethanolamine binding protein 1 pseudogene 1 Neighboring gene ribosomal protein L23a pseudogene 10 Neighboring gene MPRA-validated peak2245 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:96967424-96968020 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:96968021-96968615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:96970367-96970868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:96970869-96971368 Neighboring gene PAPOLA divergent transcript Neighboring gene poly(A) polymerase alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8988 Neighboring gene RN7SK pseudogene 108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8989 Neighboring gene uncharacterized LOC105370645 Neighboring gene NANOG hESC enhancer GRCh37_chr14:97142464-97143129

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 8987
  • ATAC-STARR-seq lymphoblastoid silent region 6055

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_129962.2 

    Range
    101..779
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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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    96502196..96502874
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    90733799..90734477
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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