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LOC112939936 Sharpr-MPRA regulatory region 9855 [ Homo sapiens (human) ]

Gene ID: 112939936, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112939936
Gene description
Sharpr-MPRA regulatory region 9855
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 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Aug 2018]
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Genomic context

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See LOC112939936 in Genome Data Viewer
Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (4259522..4259816)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (4228958..4229252)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (4261249..4261543)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene otopetrin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4227786-4228406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4229028-4229648 Neighboring gene transmembrane protein 128 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:4249292-4249918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4258767-4259267 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:4271128-4271305 Neighboring gene Ly1 antibody reactive Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4289830-4290368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4290369-4290906 Neighboring gene zinc finger and BTB domain containing 49

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_061514.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    4259522..4259816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    4228958..4229252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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