A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757162



Internal ID9632621
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:31385552..31574531hg38UCSC Ensembl
Innerchr6:31353329..31542308hg19UCSC Ensembl
Innerchr6:31461308..31650287hg18UCSC Ensembl
Innerchr6:31461308..31650287hg17UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg38188980
hg19188980
hg18188980
hg17188980
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759414
Supporting Variantsessv3592, essv7685, essv6210, essv13266, essv13301, essv6851
SamplesNA18969, NA18563, NA19201, NA18558, NA19202, NA18620
Known GenesATP6V1G2, ATP6V1G2-DDX39B, DDX39B, HCG26, HCP5, LTA, MCCD1, MICA, MICB, NFKBIL1, SNORD117, SNORD84
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)esv2757162
Frequency
Sample Size270
Observed Gain0
Observed Loss6
Observed Complex0
Frequencyn/a


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