A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758763



Internal ID9634222
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:42538595..43394901hg38UCSC Ensembl
Innerchr19:43042747..43899053hg19UCSC Ensembl
Innerchr19:47734587..48590893hg18UCSC Ensembl
Innerchr19:47734587..48590893hg17UCSC Ensembl
Cytoband19q13.2
Allele length
AssemblyAllele length
hg38856307
hg19856307
hg18856307
hg17856307
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757697, esv2758501
SamplesNA10859, NA18503, NA19142, NA19012, NA19137, NA10831, NA11881, NA18621, NA19207, NA18870, NA18964, NA12154, NA19127, NA12043, NA19152, NA12249, NA18861, NA18605, NA12750, NA18594, NA19192, NA18914, NA12802, NA18561, NA12801, NA18523, NA18975, NA07056, NA18966, NA19173, NA12752, NA12875, NA18612, NA19209, NA18501, NA19093, NA18500, NA10839, NA19003, NA12264, NA12815, NA10847, NA18516, NA06993, NA19203, NA18521, NA18953, NA18969, NA18972, NA18517, NA18947, NA07019, NA12005, NA18855, NA19144, NA19210, NA10855, NA18860, NA18994, NA07029, NA18524, NA12044, NA19208, NA18506, NA18862, NA18949, NA19143, NA10863, NA12865, NA11882, NA19161, NA12763, NA18912, NA19211, NA18998, NA19239, NA18992, NA11839, NA11840, NA12753, NA07034, NA12004, NA18566, NA11994, NA18635, NA12155, NA18576, NA18622, NA10846, NA18563, NA07357, NA12762, NA18990, NA18991, NA12814, NA18636, NA12740, NA18856, NA07048, NA12761, NA18956, NA18959, NA18609, NA11831, NA18976, NA18973, NA11995, NA12234, NA12144, NA12751, NA12006, NA12239, NA12145, NA19153, NA12716, NA18537, NA18515, NA19129, NA12892, NA18633, NA18572, NA19103, NA06985, NA18968, NA19102, NA18522, NA18502, NA19119, NA18558, NA19154, NA12057, NA10856, NA19139, NA18504, NA18978, NA18961, NA18540, NA18997, NA19159, NA19141, NA19145, NA11832, NA18999, NA10857, NA12146, NA07055, NA19138, NA10860, NA19101, NA06991, NA19128, NA12812, NA12156, NA19116, NA10835, NA10830, NA18577, NA19099, NA07022, NA12878, NA11830, NA18944, NA19205, NA10838, NA11993, NA19160, NA12248, NA11829, NA12236, NA19130, NA19171, NA12717, NA12874, NA18981, NA06994, NA18913, NA18555, NA19007, NA07000, NA18980, NA10854
Known GenesCD177, CEACAM8, LIPE-AS1, LOC100289650, LOC284344, PRG1, PSG1, PSG10P, PSG11, PSG2, PSG3, PSG4, PSG5, PSG6, PSG7, PSG8, PSG9, TEX101
MethodBAC aCGH
SNP array
AnalysisArray images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
The 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)
Agilent
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2758763
Frequency
Sample Size270
Observed Gain151
Observed Loss33
Observed Complex0
Frequencyn/a


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