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LOC112695098 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41908781-41909388 [ Homo sapiens (human) ]

Gene ID: 112695098, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112695098
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41908781-41909388
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 in primed 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 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC112695098 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41512777..41513384)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (41991613..41992220)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (41908849..41909143)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41842575-41843270 Neighboring gene uncharacterized LOC105373043 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41843271-41843966 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41864665-41865226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41865227-41865788 Neighboring gene PHD finger protein 5A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13791 Neighboring gene aconitase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:41906728-41906890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41909996-41910602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41910603-41911209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19118 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:41922291-41922505 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41927905-41928713 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41928714-41929522 Neighboring gene Sharpr-MPRA regulatory region 5669 Neighboring gene RNA polymerase III subunit H Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41939835-41940672 Neighboring gene uncharacterized LOC105373044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41951599-41952098 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:41952629-41952876

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. 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

  • Sharpr-MPRA regulatory region 731

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_060876.2 

    Range
    101..708
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    41512777..41513384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    41991613..41992220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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