A curated catalogue of human genomic structural variation




Variant Details

Variant: essv18917



Internal ID2930578
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:9570783..9762940hg38UCSC Ensembl
Outerchr4:9519966..9789088hg38UCSC Ensembl
Innerchr4:9572407..9764564hg19UCSC Ensembl
Outerchr4:9521611..9790712hg19UCSC Ensembl
Innerchr4:9181505..9373662hg18UCSC Ensembl
Outerchr4:9130709..9399810hg18UCSC Ensembl
Innerchr4:9248676..9440833hg17UCSC Ensembl
Outerchr4:9197880..9466981hg17UCSC Ensembl
Cytoband4p16.1
Allele length
AssemblyAllele length
hg38269123
hg19269102
hg18269102
hg17269102
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757034
Supporting Variants
SamplesNA12717
Known GenesDRD5, MIR548I2
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)essv18917
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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