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LOC127821685 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67888828-67889593 [ Homo sapiens (human) ]

Gene ID: 127821685, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127821685
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67888828-67889593
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 was validated as an active enhancer 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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Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (68121361..68122126)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68125005..68125771)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67805851-67806472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67817396-67818388 Neighboring gene microRNA 4691 Neighboring gene NADH:ubiquinone oxidoreductase core subunit S8 Neighboring gene T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 Neighboring gene microRNA 6753 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67834020-67834520 Neighboring gene choline kinase alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67850572-67850749 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67861600-67861729 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67870988-67871188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67886638-67887154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5132 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67889594-67890360 Neighboring gene CHKA divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67907579-67907779 Neighboring gene lysine methyltransferase 5B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67981441-67982143 Neighboring gene Sharpr-MPRA regulatory region 2086 Neighboring gene MPRA-validated peak1319 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:68034746-68035945 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68039550-68040404 Neighboring gene chromosome 11 open reading frame 24

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 3659

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_123130.1 

    Range
    101..866
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    68121361..68122126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    68125005..68125771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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