A curated catalogue of human genomic structural variation




Variant Details

Variant: essv13365



Internal ID9610742
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:1322056..1325358hg38UCSC Ensembl
Outerchr3:1322056..1326792hg38UCSC Ensembl
Innerchr3:1363740..1367042hg19UCSC Ensembl
Outerchr3:1363740..1368476hg19UCSC Ensembl
Innerchr3:1338740..1342042hg18UCSC Ensembl
Outerchr3:1338740..1343476hg18UCSC Ensembl
Innerchr3:1338740..1342042hg17UCSC Ensembl
Outerchr3:1338740..1343476hg17UCSC Ensembl
Cytoband3p26.3
Allele length
AssemblyAllele length
hg384737
hg194737
hg184737
hg174737
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2756970
Supporting Variants
SamplesNA19159
Known GenesCNTN6
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)essv13365
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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