A curated catalogue of human genomic structural variation

Variant Details

Variant: esv2759046

Internal ID9634505
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:46305673..46647012hg38UCSC Ensembl
Innerchr2:46532812..46874151hg19UCSC Ensembl
Innerchr2:46386316..46727655hg18UCSC Ensembl
Innerchr2:46444463..46785802hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756919, esv2757795
SamplesNA10847, NA12146
Known GenesATP6V1E2, CRIPT, EPAS1, LOC100506142, LOC101805491, PIGF, RHOQ, TMEM247
MethodBAC aCGH
SNP array
AnalysisArray images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
The 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)esv2759046
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0

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