A curated catalogue of human genomic structural variation

Variant Details

Variant: essv18027

Internal ID9615922
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:269563..275926hg38UCSC Ensembl
Outerchr12:248849..323985hg38UCSC Ensembl
Innerchr12:378729..385092hg19UCSC Ensembl
Outerchr12:358015..433151hg19UCSC Ensembl
Innerchr12:248990..255353hg18UCSC Ensembl
Outerchr12:228276..303412hg18UCSC Ensembl
Innerchr12:248990..255353hg17UCSC Ensembl
Outerchr12:228276..303412hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757484
Supporting Variants
Known GenesKDM5A, SLC6A13
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)
Pubmed ID17122850
Accession Number(s)essv18027
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0

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