A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756917



Internal ID9632376
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:37682244..37778165hg38UCSC Ensembl
Innerchr2:37909387..38005308hg19UCSC Ensembl
Innerchr2:37762891..37858812hg18UCSC Ensembl
Innerchr2:37821038..37916959hg17UCSC Ensembl
Cytoband2p22.2
Allele length
AssemblyAllele length
hg3895922
hg1995922
hg1895922
hg1795922
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759043
Supporting Variantsessv19037, essv6407, essv19847, essv24032, essv11596, essv19810, essv19483, essv19836, essv17678, essv10711, essv20541, essv8721, essv22289, essv19335, essv1302, essv25162, essv5610, essv13820, essv20976, essv24112, essv14212, essv2140, essv20495, essv23299
SamplesNA11995, NA18508, NA18980, NA18545, NA12750, NA10835, NA07048, NA12762, NA19207, NA19200, NA10847, NA10863, NA12872, NA11839, NA12234, NA18853, NA18593, NA18978, NA12864, NA18913, NA12873, NA12874, NA12006, NA07034
Known Genes
MethodSNP array
AnalysisThe algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.
PlatformAffymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2756917
Frequency
Sample Size270
Observed Gain21
Observed Loss3
Observed Complex0
Frequencyn/a


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