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LOC127273388 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55276593-55277405 [ Homo sapiens (human) ]

Gene ID: 127273388, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127273388
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55276593-55277405
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 (MPRA) in primed 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 three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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 LOC127273388 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55049457..55050281)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55046671..55047495)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (55276593..55277417)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene EMAP like 6 Neighboring gene RNA, U7 small nuclear 81 pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:55130773-55131972 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:55177255-55178454 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55194629-55195622 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:55201598-55201799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11493 Neighboring gene reticulon 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15772 Neighboring gene RNA, U6 small nuclear 433, pseudogene Neighboring gene uncharacterized LOC105374662 Neighboring gene Sharpr-MPRA regulatory region 4359 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:55360796-55361708 Neighboring gene CRISPRi-validated cis-regulatory element chr2.2087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11496 Neighboring gene clathrin heavy chain linker domain containing 1 Neighboring gene CDPF1 pseudogene 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 15773
  • ATAC-STARR-seq lymphoblastoid silent region 11494
  • ATAC-STARR-seq lymphoblastoid silent region 11495

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_095239.2 

    Range
    101..925
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    55049457..55050281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    55046671..55047495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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