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LOC122847297 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:153309665-153310256 [ Homo sapiens (human) ]

Gene ID: 122847297, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122847297
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:153309665-153310256
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 and primed 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 non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122847297 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (152453151..152453742)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (152905563..152906154)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (153309929..153310223)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373689 Neighboring gene uncharacterized LOC105373688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:153183153-153183652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:153258063-153258564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:153258565-153259064 Neighboring gene formin like 2 Neighboring gene Sharpr-MPRA regulatory region 2662 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:153280187-153280913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:153280914-153281639 Neighboring gene nuclear distribution C pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 469 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:153310257-153310847 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:153312623-153313213 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:153357706-153358281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16649 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:153474731-153475930 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:153502126-153503325 Neighboring gene NANOG hESC enhancer GRCh37_chr2:153508427-153509132 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:153519134-153520333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16650 Neighboring gene pre-mRNA processing factor 40 homolog A Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:153557503-153558702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:153558975-153559476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16655 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:153574523-153575228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12013 Neighboring gene ADP ribosylation factor like GTPase 6 interacting protein 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:153661367-153661578 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:153702825-153704024 Neighboring gene ubiquilin 4 pseudogene 2

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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 8392

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_077032.2 

    Range
    101..692
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    152453151..152453742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    152905563..152906154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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