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LOC127824749 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95007851-95008440 [ Homo sapiens (human) ]

Gene ID: 127824749, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127824749
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95007851-95008440
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 in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. An overlapping 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 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127824749 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (94613916..94614664)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (94594730..94595478)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (95007692..95008440)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene microRNA 7844 Neighboring gene transmembrane and coiled-coil domain family 3 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:95010515-95011014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6788 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6790 Neighboring gene uncharacterized LOC105369914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:95043785-95044500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6795 Neighboring gene uncharacterized LOC124902989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6796

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. 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

  • ReSE screen-validated silencer GRCh37_chr12:95007692-95007922

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_126265.2 

    Range
    101..849
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    94613916..94614664
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    94594730..94595478
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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