U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC127892542 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5100059-5100939 [ Homo sapiens (human) ]

Gene ID: 127892542, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC127892542
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5100059-5100939
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 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 three accessible chromatin subregions, two of which were validated as enhancers and one as a silencer based on their ability to activate or 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 LOC127892542 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (5119413..5120491)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (5158836..5159914)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (5100059..5101137)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S21 pseudogene 7 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:5008813-5009342 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:5013735-5013892 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:5025885-5026104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17505 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:5041439-5042638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5046523-5047023 Neighboring gene transmembrane protein 230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5053633-5054152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5054153-5054671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5062418-5062918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17509 Neighboring gene RNA, 5S ribosomal pseudogene 474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17510 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:5099178-5100058 Neighboring gene small nucleolar RNA SNORA26 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:5107325-5107826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17514 Neighboring gene PCNA antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5113215-5113716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5113717-5114216 Neighboring gene proliferating cell nuclear antigen Neighboring gene CDP-diacylglycerol synthase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5150939-5151438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17515 Neighboring gene Sharpr-MPRA regulatory region 2649 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:5156307-5156942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17517

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 active region 17512
  • ATAC-STARR-seq lymphoblastoid active region 17513
  • ATAC-STARR-seq lymphoblastoid silent region 12653

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_142345.2 

    Range
    101..1179
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    5119413..5120491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    5158836..5159914
    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