A curated catalogue of human genomic structural variation




Variant Details

Variant: esv3570588



Internal ID18698786
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:178380083..178391804hg38UCSC Ensembl
Innerchr5:177807084..177818805hg19UCSC Ensembl
Cytoband5q35.3
Allele length
AssemblyAllele length
hg3811722
hg1911722
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsdgv1680e212
Supporting Variantsessv9776969, essv9776972, essv9776975, essv9776973, essv9776970, essv9776971, essv9776974, essv9776976, essv9776979
Samples400739SS, 400821FE, 400340CD, 401566DD, 401646MC, 401977ES, 401210PB, 400845ML, 400238BB
Known GenesCOL23A1
MethodSNP array
AnalysisWe used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
PlatformAffymetrix CytoScan HD 2.7M array
Comments
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)esv3570588
Frequency
Sample Size873
Observed Gain0
Observed Loss9
Observed Complex0
Frequencyn/a


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