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LOC127896280 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506 [ Homo sapiens (human) ]

Gene ID: 127896280, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127896280
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506
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 an accessible chromatin subregion that was validated as an enhancer based on its 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 LOC127896280 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39318612..39319501)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39789264..39790153)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39714617..39715506)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39712838-39713726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39715507-39716396 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39716397-39717285 Neighboring gene small nucleolar RNA, C/D box 83A Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene ribosomal protein L3 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene Sharpr-MPRA regulatory region 3662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39753396-39753924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39755840-39756638 Neighboring gene synaptogyrin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39757867-39758453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39758454-39759039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39769919-39770434 Neighboring gene Sharpr-MPRA regulatory region 1576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13751 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811177-39811678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811679-39812178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39824885-39825527 Neighboring gene uncharacterized LOC100506472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39829518-39830236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39830237-39830954

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 19043

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_145814.1 

    Range
    101..990
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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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39318612..39319501
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39789264..39790153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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