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LOC121466699 NANOG-H3K4me1 hESC enhancers GRCh37_chr12:50338782-50339658 and GRCh37_chr12:50339659-50340534 [ Homo sapiens (human) ]

Gene ID: 121466699, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121466699
Gene description
NANOG-H3K4me1 hESC enhancers GRCh37_chr12:50338782-50339658 and GRCh37_chr12:50339659-50340534
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. Two subregions were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K4me1 histone modification. An overlapping subregion was also validated as a functional 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). 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 K562 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (49944999..49946751)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (49907990..49909742)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50339389..50339683)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2396 Neighboring gene long intergenic non-protein coding RNA 2395 Neighboring gene uncharacterized LOC124902930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50335615-50336600 Neighboring gene uncharacterized LOC105369763 Neighboring gene AQP5 and AQP2 antisense RNA 2 Neighboring gene aquaporin 2 Neighboring gene uncharacterized LOC105369764 Neighboring gene aquaporin 5

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. 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
  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

  • NANOG-H3K4me1 hESC enhancer GRCh37_chr12:50338782-50339658
  • NANOG-H3K4me1 hESC enhancer GRCh37_chr12:50339659-50340534
  • ReSE screen-validated silencer GRCh37_chr12:50339322-50339562
  • Sharpr-MPRA regulatory region 197

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_074631.2 

    Range
    101..1853
    Download
    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
    49944999..49946751
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    49907990..49909742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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