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LOC121725216 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114880021-114880787 [ Homo sapiens (human) ]

Gene ID: 121725216, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725216
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114880021-114880787
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive and primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes three 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, May 2023]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (115544324..115545090)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (116057126..116057892)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (114880329..114880623)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene COX assembly mitochondrial protein homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22932 Neighboring gene chaperonin containing TCP1 subunit 5 pseudogene 1 Neighboring gene fem-1 homolog C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22934 Neighboring gene TMED7-TICAM2 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16252 Neighboring gene TIR domain containing adaptor molecule 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114937526-114938048 Neighboring gene TICAM2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22936 Neighboring gene transmembrane p24 trafficking protein 7

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 16249
  • ATAC-STARR-seq lymphoblastoid silent region 16250
  • ATAC-STARR-seq lymphoblastoid silent region 16251
  • Sharpr-MPRA regulatory region 5951

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_075690.2 

    Range
    101..867
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    115544324..115545090
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    116057126..116057892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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