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LOC123864065 NANOG hESC enhancer GRCh37_chr6:129761748-129762353 [ Homo sapiens (human) ]

Gene ID: 123864065, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123864065
Gene description
NANOG hESC enhancer GRCh37_chr6:129761748-129762353
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC123864065 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (129440603..129441208)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (130634310..130634915)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (129761889..129762183)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene laminin subunit alpha 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:129493212-129493926 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:129493927-129494640 Neighboring gene bone morphogenetic protein receptor type 1A pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:129561118-129561327 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:129572793-129572997 Neighboring gene NANOG hESC enhancer GRCh37_chr6:129691636-129692145 Neighboring gene RNA, U6 small nuclear 861, pseudogene Neighboring gene uncharacterized LOC124901401 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:129811717-129812916 Neighboring gene uncharacterized LOC102723409 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:129822854-129824053

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 661

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_078197.2 

    Range
    101..706
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    129440603..129441208
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    130634310..130634915
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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