A curated catalogue of human genomic structural variation




Variant Details

Variant: essv12093



Internal ID9609329
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:143538619..143765385hg38UCSC Ensembl
Innerchr1:149028045..149260033hg19UCSC Ensembl
Outerchr1:148000850..149711434hg19UCSC Ensembl
Innerchr1:147294669..147526657hg18UCSC Ensembl
Outerchr1:146467474..147978058hg18UCSC Ensembl
Innerchr1:145807637..146039625hg17UCSC Ensembl
Outerchr1:145115762..146524507hg17UCSC Ensembl
Cytoband1q21.1
Allele length
AssemblyAllele length
hg38226767
hg191710585
hg181510585
hg171408746
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2756863
Supporting Variants
SamplesNA19099
Known GenesFCGR1C, LINC00623, LINC00869, LOC101929780, LOC388692, LOC645166, NBPF10, NBPF14, NBPF15, NBPF16, NBPF23, NBPF8, NBPF9, PPIAL4A, PPIAL4B, PPIAL4C, PPIAL4D, PPIAL4E, PPIAL4F
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)essv12093
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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