A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756999



Internal ID9632458
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:75342927..75953885hg38UCSC Ensembl
Innerchr3:75392078..76003036hg19UCSC Ensembl
Innerchr3:75474768..76085726hg18UCSC Ensembl
Innerchr3:75474768..76085726hg17UCSC Ensembl
Cytoband3p12.3
Allele length
AssemblyAllele length
hg38610959
hg19610959
hg18610959
hg17610959
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759157
Supporting Variantsessv25118, essv23098, essv16189, essv16595, essv19331, essv5675, essv18483, essv5628, essv23314, essv24549, essv15966, essv7885, essv20508, essv24203, essv19813, essv24012
SamplesNA18860, NA12156, NA11831, NA18605, NA12872, NA18579, NA19142, NA12264, NA12144, NA10856, NA12043, NA12716, NA12864, NA19140, NA12873, NA18506
Known GenesFAM86DP, FLJ20518, FRG2C, LINC00960, MIR1324, MIR4273, ZNF717
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)esv2756999
Frequency
Sample Size270
Observed Gain3
Observed Loss13
Observed Complex0
Frequencyn/a


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