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LOC127824871 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104350309-104350822 [ Homo sapiens (human) ]

Gene ID: 127824871, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127824871
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104350309-104350822
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 naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its 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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See LOC127824871 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 (103956531..103957083)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (103918246..103918798)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (104350309..104350861)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat domain 41, pseudogene Neighboring gene uncharacterized LOC124903001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6900 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23563 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104321935-104322117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6902 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23584 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23591 Neighboring gene microRNA 3652 Neighboring gene heat shock protein 90 beta family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6905 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 6 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23620 Neighboring gene thymine DNA glycosylase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23681 Neighboring gene glycosyltransferase 8 domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104408145-104408367 Neighboring gene phosphoglycerate mutase 1 (brain) 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. 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
  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

  • ATAC-STARR-seq lymphoblastoid silent region 4783

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_126386.2 

    Range
    101..653
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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
    103956531..103957083
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    103918246..103918798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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