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LOC127887705 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66031597-66032144 [ Homo sapiens (human) ]

Gene ID: 127887705, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127887705
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66031597-66032144
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 region includes an enhancer that was validated 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 a silencer based on its ability to repress 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 LOC127887705 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (68035468..68036028)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (68911283..68911804)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (66031584..66032144)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8883 Neighboring gene chromosome 17 open reading frame 58 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66016003-66016576 Neighboring gene tRNA-Arg (anticodon CCG) 2-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12635 Neighboring gene MPRA-validated peak2956 silencer Neighboring gene karyopherin subunit alpha 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66076452-66076952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66076953-66077453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:66083143-66083718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12636 Neighboring gene uncharacterized LOC124904048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66097037-66097816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66097817-66098595 Neighboring gene F-box protein 36 pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 674 Neighboring gene leucine rich repeat containing 37 member A16, pseudogene Neighboring gene SH3 domain containing GRB2 like 1, endophilin A2 pseudogene 3

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 silent region 8885

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_137340.2 

    Range
    101..661
    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
    68035468..68036028
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    68911283..68911804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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