A curated catalogue of human genomic structural variation

Variant Details

Variant: esv11880

Internal ID11029114
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:3299096..3300546hg38UCSC Ensembl
Innerchr1:3215660..3217110hg19UCSC Ensembl
Innerchr1:3205520..3206970hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv22281
Supporting Variantsessv44690, essv76497, essv66312, essv47309, essv37405, essv34614, essv62523, essv40713, essv52452, essv74973, essv69175
SamplesNA12489, NA18861, NA18511, NA15510, NA12044, NA12004, NA11894, NA12006, NA18502, NA12878, NA19240
Known GenesPRDM16
MethodOligo aCGH
AnalysisSegment log2 ratios from each sample. This was done running the GADA algorithm (Pique-Regi et al., 2008) using the options "-M 10 -T 10 -a 2.5". Filter non-CNV segments using intensity thresholds. Merge remaining CNV "calls" within each sample. Adjacent calls of the same direction (gain or loss) are merged if both: the distance between calls is less than 10kb, and the distance between calls is less than 10% of the size of the largest of the two calls.
PlatformSanger H. Sapiens 42mCGH Array 5781_53 726K v1
Pubmed ID19812545
Accession Number(s)esv11880
Sample Size40
Observed Gain0
Observed Loss11
Observed Complex0

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