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LOC127817166 NANOG hESC enhancer GRCh37_chr10:6720092-6720593 [ Homo sapiens (human) ]

Gene ID: 127817166, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127817166
Gene description
NANOG hESC enhancer GRCh37_chr10:6720092-6720593
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the NANOG transcription factor. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127817166 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (6678130..6678631)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (6678365..6678866)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (6720092..6720593)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene protein kinase C theta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2109 Neighboring gene Sharpr-MPRA regulatory region 12587 Neighboring gene PRKCQ antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:6671711-6672282 Neighboring gene long intergenic non-protein coding RNA 2648 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:6690794-6691459 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:6778731-6779930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6779977-6780522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6780523-6781066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2969 Neighboring gene lncRNA in non-homologous end joining pathway 1 Neighboring gene long intergenic non-protein coding RNA 706

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, 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

  • ReSE screen-validated silencer GRCh37_chr10:6720253-6720411

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_118649.1 

    Range
    101..602
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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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    6678130..6678631
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    6678365..6678866
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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