A curated catalogue of human genomic structural variation

Variant Details

Variant: essv9497

Internal ID9631636
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:725908..855385hg38UCSC Ensembl
Outerchr12:677072..855385hg38UCSC Ensembl
Innerchr12:835074..964551hg19UCSC Ensembl
Outerchr12:786238..964551hg19UCSC Ensembl
Innerchr12:705335..834812hg18UCSC Ensembl
Outerchr12:656499..834812hg18UCSC Ensembl
Innerchr12:705335..834812hg17UCSC Ensembl
Outerchr12:656499..834812hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757485
Supporting Variants
Known GenesWNK1
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)
Pubmed ID17122850
Accession Number(s)essv9497
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0

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