A curated catalogue of human genomic structural variation




Variant Details

Variant: esv25966



Internal ID11043199
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:29686177..29961064hg38UCSC Ensembl
Innerchr6:29653954..29928841hg19UCSC Ensembl
Innerchr6:29761933..30036820hg18UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg38274888
hg19274888
hg18274888
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv20940, esv15726, esv18554, esv12140, esv15856, esv17468, esv11180, esv20324, esv20595, esv13518, esv15908, esv10151, esv10073
SamplesNA12489, NA18861, NA07037, NA18523, NA19114, NA18511, NA11931, NA12828, NA18517, NA12776, NA19257, NA19108, NA15510, NA18505, NA12044, NA12287, NA19147, NA12414, NA18508, NA11995, NA18916, NA19190, NA12006, NA07045, NA12239, NA06985, NA18502, NA18858, NA18907, NA18909, NA12749, NA12156, NA19099, NA12878, NA19225, NA11993, NA19240
Known GenesHCG4, HCG4B, HLA-A, HLA-F, HLA-F-AS1, HLA-G, HLA-H, IFITM4P, LOC554223
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)esv25966
Frequency
Sample Size40
Observed Gain35
Observed Loss10
Observed Complex0
Frequencyn/a


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