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LOC127269625 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:84543332-84543857 [ Homo sapiens (human) ]

Gene ID: 127269625, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127269625
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:84543332-84543857
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 was validated as an active enhancer 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 an accessible chromatin subregion that was validated as a silencer based on its ability to 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 LOC127269625 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (84077649..84078174)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (83918104..83918629)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (84543332..84543857)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tubulin tyrosine ligase like 7 Neighboring gene TTLL7 intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1013 Neighboring gene uncharacterized LOC124904205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1246 Neighboring gene protein kinase cAMP-activated catalytic subunit beta Neighboring gene TXN2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1016 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:84621187-84622386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:84689847-84690648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:84690649-84691448 Neighboring gene NEDD8 pseudogene 1

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 silent region 1014

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_091486.1 

    Range
    101..626
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    84077649..84078174
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    83918104..83918629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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