A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756896



Internal ID9632355
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:248432380..248654081hg38UCSC Ensembl
Innerchr1:248595681..248817382hg19UCSC Ensembl
Innerchr1:246662304..246884005hg18UCSC Ensembl
Innerchr1:244921722..245143423hg17UCSC Ensembl
Cytoband1q44
Allele length
AssemblyAllele length
hg38221702
hg19221702
hg18221702
hg17221702
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759015
Supporting Variantsessv3335, essv12021
SamplesNA19141, NA18948
Known GenesOR2G6, OR2T10, OR2T11, OR2T2, OR2T27, OR2T29, OR2T3, OR2T34, OR2T35, OR2T5
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)esv2756896
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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