A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756945



Internal ID9632404
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:130016945..130727062hg38UCSC Ensembl
Innerchr2:130774518..131484635hg19UCSC Ensembl
Innerchr2:130490988..131201105hg18UCSC Ensembl
Innerchr2:130490748..131318354hg17UCSC Ensembl
Cytoband2q21.1
Allele length
AssemblyAllele length
hg38710118
hg19710118
hg18710118
hg17827607
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759092
Supporting Variantsessv2399, essv5707
SamplesNA18550, NA18976
Known GenesCCDC115, CCDC74B, CFC1, CFC1B, CYP4F30P, CYP4F62P, FAR2P1, FAR2P2, IMP4, LOC646743, MED15P9, MZT2B, POTEF, POTEI, POTEJ, PTPN18, SMPD4, TISP43, TUBA3E
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)esv2756945
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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