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LOC112268482 Sharpr-MPRA regulatory region 9489 [ Homo sapiens (human) ]

Gene ID: 112268482, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112268482
Gene description
Sharpr-MPRA regulatory region 9489
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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Mar 2018]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (53306251..53306545)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (47514155..47514449)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (53772969..53773263)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5752 Neighboring gene uncharacterized LOC105370502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8402 Neighboring gene DDHD1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5753 Neighboring gene NANOG hESC enhancer GRCh37_chr14:53726964-53727525 Neighboring gene uncharacterized LOC105370504 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:53822218-53822978 Neighboring gene VISTA enhancer hs1151 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:53858219-53859418 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:53924665-53925864 Neighboring gene VISTA enhancer hs1629 Neighboring gene uncharacterized LOC124903316 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:54074633-54075832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8404 Neighboring gene RPS3A pseudogene 46

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_056679.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    53306251..53306545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    47514155..47514449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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