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LOC127399371 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185655136-185655863 [ Homo sapiens (human) ]

Gene ID: 127399371, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127399371
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185655136-185655863
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 an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive 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 two accessible chromatin subregions that were validated as enhancers based on their ability to activate 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 LOC127399371 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (185937236..185938075)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (188753025..188753864)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (185655024..185655863)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene insulin like growth factor 2 mRNA binding protein 2 Neighboring gene uncharacterized LOC124906313 Neighboring gene Sharpr-MPRA regulatory region 9603 Neighboring gene Sharpr-MPRA regulatory region 5696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185487094-185487594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185487595-185488095 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185491440-185492292 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:185496875-185497772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185497860-185498360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185501879-185502772 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185504559-185505450 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185507237-185508130 Neighboring gene microRNA 548aq Neighboring gene VISTA enhancer hs1976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185516757-185517258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185517259-185517758 Neighboring gene NANOG hESC enhancer GRCh37_chr3:185520396-185520897 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:185525354-185525896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:185540833-185541696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14977 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185542636-185542866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14978 Neighboring gene Sharpr-MPRA regulatory region 6530 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185623478-185623669 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185667767-185668709 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:185666824-185667766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185670624-185671147 Neighboring gene transformer 2 beta homolog Neighboring gene Sharpr-MPRA regulatory region 2251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:185701333-185701854 Neighboring gene NmrA like redox sensor 2, pseudogene Neighboring gene uncharacterized LOC124909470 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:185795356-185795551 Neighboring gene ETS variant transcription factor 5 Neighboring gene ETV5 antisense RNA 1

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 active region 20929
  • ATAC-STARR-seq lymphoblastoid active region 20930

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_101337.2 

    Range
    101..940
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    185937236..185938075
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    188753025..188753864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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