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LOC127888986 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:22006613-22007527 [ Homo sapiens (human) ]

Gene ID: 127888986, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127888986
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:22006613-22007527
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. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in both phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) and untreated K562 erythroleukemia cells. This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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, Jun 2023]
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Genomic context

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See LOC127888986 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (24426594..24427563)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (24620905..24621874)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (22006558..22007527)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene oxysterol binding protein like 1A Neighboring gene uncharacterized LOC124904267 Neighboring gene uncharacterized LOC124904268 Neighboring gene Sharpr-MPRA regulatory region 8214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:21964078-21964578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:21964579-21965079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9364 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:22005698-22006612 Neighboring gene MPRA-validated peak3074 silencer Neighboring gene impact RWD domain protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:22052464-22052964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13172 Neighboring gene histamine receptor H4 Neighboring gene uncharacterized LOC105372026 Neighboring gene zinc finger protein 470 pseudogene

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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
  3. 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 silent region 9365
  • ATAC-STARR-seq lymphoblastoid silent region 9366
  • ReSE screen-validated silencer GRCh37_chr18:22006750-22006937

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_138543.2 

    Range
    101..1070
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    24426594..24427563
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    24620905..24621874
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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