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LOC112272578 H3K27ac hESC enhancers GRCh37_chr15:25017418-25018314 and GRCh37_chr15:25018315-25019210 [ Homo sapiens (human) ]

Gene ID: 112272578, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112272578
Gene description
H3K27ac hESC enhancers GRCh37_chr15:25017418-25018314 and GRCh37_chr15:25018315-25019210
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. Two subregions marked by the H3K27ac histone modification were validated as active enhancers by ChIP-STARR-seq in naive and primed human embryonic stem cells. An overlapping subregion was also validated as a functional 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 non-DNase unmatched - State 3:PromF, promoter flanking). This locus also includes a subregion containing a Neanderthal adaptively introgressed genetic variant. That subregion was validated as an enhancer by massively parallel reporter assays (MPRAs) in K562 cells, with activity observed for both the introgressed and non-introgressed 15:25018251 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC112272578 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (24772271..24774063)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (22508906..22510698)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (25017418..25019210)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr15:24877390-24877896 Neighboring gene Prader-Willi region non-protein coding RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:24932126-24932730 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:24941505-24942052 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:24942053-24942599 Neighboring gene nuclear pore associated protein 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:25101506-25102019 Neighboring gene Sharpr-MPRA regulatory region 849 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:25103559-25104072 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:25104073-25104585 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:25107499-25108228 Neighboring gene small nucleolar RNA U13 Neighboring gene small nucleolar RNA host gene 14 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:25143773-25144405 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:25145037-25145537 Neighboring gene small nuclear ribonucleoprotein polypeptide N Neighboring gene ribosomal protein L5 pseudogene 1

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, Free PMC Article
  2. 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
  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

  • H3K27ac hESC enhancer GRCh37_chr15:25017418-25018314
  • H3K27ac hESC enhancer GRCh37_chr15:25018315-25019210
  • Neanderthal introgressed variant-containing enhancer experimental_39217
  • Sharpr-MPRA regulatory region 9168

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_056715.2 

    Range
    101..1893
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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    24772271..24774063
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    22508906..22510698
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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