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LOC112529900 Sharpr-MPRA regulatory region 2370 [ Homo sapiens (human) ]

Gene ID: 112529900, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112529900
Gene description
Sharpr-MPRA regulatory region 2370
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 a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2018]
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Genomic context

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Location:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (18746616..18746910)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (18692770..18693064)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (18649929..18650223)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 286B (pseudogene) Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:18585117-18585622 Neighboring gene forkhead box O3B Neighboring gene ubiquitin conjugating enzyme E2 S pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18601479-18602036 Neighboring gene tripartite motif containing 16 like (pseudogene) Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:18621593-18622463 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:18622464-18623334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18624898-18625462 Neighboring gene F-box and WD repeat domain containing 10 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:18673855-18674355 Neighboring gene trans-golgi network vesicle protein 23 homolog B Neighboring gene NANOG hESC enhancer GRCh37_chr17:18706781-18707432 Neighboring gene coiled-coil domain-containing protein 144A-like Neighboring gene RNA, 7SL, cytoplasmic 627, 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. 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

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)

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_056890.1 

    Range
    101..395
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    18746616..18746910
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    18692770..18693064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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