A curated catalogue of human genomic structural variation




Variant Details

Variant: esv25563



Internal ID4356464
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:31269247..31272540hg38UCSC Ensembl
Innerchr6:31237024..31240317hg19UCSC Ensembl
Innerchr6:31345003..31348296hg18UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg383294
hg193294
hg183294
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv20367, esv12719
SamplesNA19108, NA12414, NA19190, NA12006
Known GenesHLA-C
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
Comments
ReferenceConrad_et_al_2009
Pubmed ID19812545
Accession Number(s)esv25563
Frequency
Sample Size40
Observed Gain0
Observed Loss4
Observed Complex0
Frequencyn/a


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