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LOC127404336 NANOG-H3K4me1 hESC enhancers GRCh37_chr5:150804400-150804900 and GRCh37_chr5:150804901-150805401 [ Homo sapiens (human) ]

Gene ID: 127404336, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404336
Gene description
NANOG-H3K4me1 hESC enhancers GRCh37_chr5:150804400-150804900 and GRCh37_chr5:150804901-150805401
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 two adjacent enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where they associate with the NANOG transcription factor and are marked by the H3K4me1 histone modification. An overlapping subregion containing a Neanderthal adaptively introgressed genetic variant was also validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 5:150804897 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC127404336 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (151424839..151425840)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (151963807..151964808)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (150804400..150805401)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378234 Neighboring gene solute carrier family 36 member 1 Neighboring gene mediator complex subunit 13 pseudogene Neighboring gene RUN domain containing 1 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150767117-150768055 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:150816347-150816517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82502 Neighboring gene RNA, 5S ribosomal pseudogene 197 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82529 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:150875552-150876101 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150877439-150878100 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82543 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82555 Neighboring gene FAT atypical cadherin 2 Neighboring gene microRNA 6499

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, 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

  • NANOG-H3K4me1 hESC enhancer GRCh37_chr5:150804400-150804900
  • NANOG-H3K4me1 hESC enhancer GRCh37_chr5:150804901-150805401
  • Neanderthal introgressed variant-containing enhancer experimental_82492

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_106285.2 

    Range
    101..1102
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    151424839..151425840
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    151963807..151964808
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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