A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756939



Internal ID9632398
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:97042874..97658064hg38UCSC Ensembl
Innerchr2:97708611..98274527hg19UCSC Ensembl
Innerchr2:97072338..97640959hg18UCSC Ensembl
Innerchr2:97130485..97733045hg17UCSC Ensembl
Cytoband2q11.2
Allele length
AssemblyAllele length
hg38615191
hg19565917
hg18568622
hg17602561
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759077
Supporting Variantsessv17999, essv17393
SamplesNA18855, NA12005
Known GenesACTR1B, ANKRD36, ANKRD36B, COX5B, FAHD2B, LOC100506076, LOC100506123
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)esv2756939
Frequency
Sample Size270
Observed Gain1
Observed Loss1
Observed Complex0
Frequencyn/a


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