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LOC121832841 NANOG-H3K4me1 hESC enhancer GRCh37_chr12:66285256-66286168 [ Homo sapiens (human) ]

Gene ID: 121832841, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121832841
Gene description
NANOG-H3K4me1 hESC enhancer GRCh37_chr12:66285256-66286168
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC121832841 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (65891476..65892388)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (65870999..65871911)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (66285809..66286103)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:66155026-66155586 Neighboring gene Sharpr-MPRA regulatory region 15140 Neighboring gene ribosomal protein SA pseudogene 52 Neighboring gene NANOG hESC enhancer GRCh37_chr12:66172695-66173196 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:66175547-66176083 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:66192736-66193237 Neighboring gene Sharpr-MPRA regulatory region 869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:66219383-66219990 Neighboring gene high mobility group AT-hook 2 Neighboring gene MPRA-validated peak1769 silencer Neighboring gene HMGA2 antisense RNA 1 Neighboring gene MPRA-validated peak1770 silencer Neighboring gene hESC enhancers GRCh37_chr12:66289853-66290620 and GRCh37_chr12:66290621-66291388 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:66291389-66292155 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:66320206-66320716 Neighboring gene HNF4 motif-containing MPRA enhancer 102 Neighboring gene uncharacterized LOC124902955 Neighboring gene negCOR silencer S1 Neighboring gene microRNA 6074

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. 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

  • Sharpr-MPRA regulatory region 11590

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_075916.2 

    Range
    101..1013
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    65891476..65892388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    65870999..65871911
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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