A curated catalogue of human genomic structural variation




Variant Details

Variant: essv9834979



Internal ID18339303
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:109746742..110225841hg38UCSC Ensembl
Innerchr2:110504319..110983418hg19UCSC Ensembl
Cytoband2q13
Allele length
AssemblyAllele length
hg38479100
hg19479100
Variant TypeCNV loss
Copy Number1
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv3584010
Supporting Variants
Samples401783BD
Known GenesLIMS3, LIMS3L, LIMS3-LOC440895, LINC00116, LINC01123, LOC100288570, LOC440895, MALL, MIR4267, MIR4436B1, MIR4436B2, NPHP1, RGPD5, RGPD6
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
CommentsNumber of probes=115
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)essv9834979
Frequency
Sample Size873
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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