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LOC127406568 NANOG hESC enhancer GRCh37_chr6:70623798-70624319 [ Homo sapiens (human) ]

Gene ID: 127406568, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127406568
Gene description
NANOG hESC enhancer GRCh37_chr6:70623798-70624319
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 in naive human embryonic stem cells, where it associates with the NANOG transcription factor. An overlapping 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 K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127406568 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (69913906..69914429)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71094031..71094554)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70623798..70624321)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5886 silencer Neighboring gene LMBR1 domain containing 1 Neighboring gene uncharacterized LOC124901337 Neighboring gene nucleophosmin 1 pseudogene 37 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70505853-70506409 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70506410-70506965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17315 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:70597939-70598122 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:70627263-70628462 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:70845103-70845604 Neighboring gene collagen type IX alpha 1 chain Neighboring gene MPRA-validated peak5887 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24730

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_chr6:70624123-70624321

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_108539.2 

    Range
    101..624
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    69913906..69914429
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    71094031..71094554
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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