U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC127403256 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79950324-79951092 [ Homo sapiens (human) ]

Gene ID: 127403256, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC127403256
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79950324-79951092
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 an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC127403256 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 (80654478..80655273)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (81139378..81140182)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79950297..79951092)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1337 Neighboring gene Sharpr-MPRA regulatory region 2279 Neighboring gene Sharpr-MPRA regulatory regions 13584 and 3862 Neighboring gene dihydrofolate reductase Neighboring gene MT-RNR2 like 2 (pseudogene) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79963410-79963977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79963978-79964546 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:79968379-79969578 Neighboring gene MPRA-validated peak5310 silencer Neighboring gene mutS homolog 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:80040756-80040944 Neighboring gene S-phase kinase-associated protein 1-like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:80043670-80044230 Neighboring gene MPRA-validated peak5311 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:80142431-80142931 Neighboring gene ribosomal protein S26 pseudogene 27

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 16140

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_105205.2 

    Range
    101..896
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    80654478..80655273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    81139378..81140182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases