A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757227



Internal ID9979304
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr7:65233863..65908864hg38UCSC Ensembl
Innerchr7:64694241..65373851hg19UCSC Ensembl
Innerchr7:64331676..65011286hg18UCSC Ensembl
Innerchr7:64138391..64818001hg17UCSC Ensembl
Cytoband7q11.21
Allele length
AssemblyAllele length
hg38675002
hg19679611
hg18679611
hg17679611
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759534
Supporting Variantsessv25184
SamplesNA11840
Known GenesCCT6P1, INTS4L2, LOC441242, SNORA22, VKORC1L1, ZNF92
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)esv2757227
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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