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LOC112067720 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3400077-3400640 [ Homo sapiens (human) ]

Gene ID: 112067720, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112067720
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3400077-3400640
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. It 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. 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 unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). 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 LOC112067720 in Genome Data Viewer
Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (3378847..3379410)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (3424240..3424803)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (3400329..3400623)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit A5 pseudogene 1 Neighboring gene vomeronasal 1 receptor 56 pseudogene Neighboring gene zinc finger protein 195 Neighboring gene tumor suppressing subtransferable candidate 2 (pseudogene) Neighboring gene olfactory receptor family 7 subfamily E member 12 pseudogene Neighboring gene Sharpr-MPRA regulatory region 4578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3425235-3426069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:3426070-3426903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3427261-3427774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3427775-3428286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3430516-3431016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:3431017-3431517 Neighboring gene family with sequence similarity 86, member A pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3078

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. 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
  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

  • ATAC-STARR-seq lymphoblastoid silent region 3076
  • Sharpr-MPRA regulatory region 5988

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_056451.2 

    Range
    101..664
    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
    3378847..3379410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    3424240..3424803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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