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LOC127884564 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75467440-75468007 [ Homo sapiens (human) ]

Gene ID: 127884564, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127884564
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75467440-75468007
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 includes an enhancer that was validated 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 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 LOC127884564 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75433489..75434109)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81479363..81479984)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75467387..75468007)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 758, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:75339050-75340249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75341536-75342036 Neighboring gene craniofacial development protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11128 Neighboring gene CFDP1 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11129 Neighboring gene small nucleolar RNA SNORA76 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75465381-75465580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7719 Neighboring gene tigger transposable element-derived protein 1-like Neighboring gene transmembrane protein 170A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75490353-75490854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11131 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75498257-75498757

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 11130

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_134342.2 

    Range
    101..721
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    75433489..75434109
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    81479363..81479984
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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