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LOC127266842 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1590308-1591030 [ Homo sapiens (human) ]

Gene ID: 127266842, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127266842
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1590308-1591030
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 was validated as an active enhancer 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 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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See LOC127266842 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 (1658847..1659569)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1093309..1094031)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1590308..1591030)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MIB E3 ubiquitin protein ligase 2 Neighboring gene uncharacterized LOC124903821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1565596-1566158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1568259-1569070 Neighboring gene matrix metallopeptidase 23B Neighboring gene cyclin dependent kinase 11B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30 Neighboring gene solute carrier family 35 member E2B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1601211-1601711 Neighboring gene ribosomal protein S7 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 31 Neighboring gene Sharpr-MPRA regulatory region 10763 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1618619-1618776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1619919-1620419 Neighboring gene Sharpr-MPRA regulatory region 15043 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 88 Neighboring gene matrix metallopeptidase 23A (pseudogene)

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 28
  • ATAC-STARR-seq lymphoblastoid active region 29

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_088717.1 

    Range
    101..823
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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
    1658847..1659569
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1093309..1094031
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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