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LOC125316820 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80334527-80335396 [ Homo sapiens (human) ]

Gene ID: 125316820, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125316820
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80334527-80335396
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125316820 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82376651..82377520)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83245817..83246685)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80334527..80335396)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80282821-80283426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80283427-80284032 Neighboring gene secreted and transmembrane 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80290146-80290948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80302606-80303141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13005 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:80309262-80309440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80309821-80310697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80313765-80314700 Neighboring gene Sharpr-MPRA regulatory region 9771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80320818-80321596 Neighboring gene testis expressed 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80337379-80337880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80337881-80338380 Neighboring gene urotensin 2 receptor Neighboring gene uncharacterized LOC124904092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80343201-80343886 Neighboring gene uncharacterized LOC124904090 Neighboring gene 2-oxoglutarate and iron dependent oxygenase domain containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80357274-80357880

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • Sharpr-MPRA regulatory region 5835

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_080638.2 

    Range
    101..970
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    82376651..82377520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    83245817..83246685
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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