A curated catalogue of human genomic structural variation




Variant Details

Variant: essv9834986



Internal ID18319826
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:109746742..110608419hg38UCSC Ensembl
Innerchr2:110504319..111365996hg19UCSC Ensembl
Cytoband2q13
Allele length
AssemblyAllele length
hg38861678
hg19861678
Variant TypeCNV gain
Copy Number4
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv3575289
Supporting Variants
Samples401185LE
Known GenesLIMS3, LIMS3L, LIMS3-LOC440895, LINC00116, LINC01106, LINC01123, LOC100288570, LOC100507334, 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=116
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)essv9834986
Frequency
Sample Size873
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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