A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758970



Internal ID9634429
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:152500363..152925677hg38UCSC Ensembl
Innerchr1:152472839..152898153hg19UCSC Ensembl
Innerchr1:150739463..151164777hg18UCSC Ensembl
Innerchr1:149285912..149711226hg17UCSC Ensembl
Cytoband1q21.3
Allele length
AssemblyAllele length
hg38425315
hg19425315
hg18425315
hg17425315
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756865, esv2757755
SamplesNA19142, NA18621, NA19207, NA18964, NA12154, NA19127, NA12043, NA19152, NA19194, NA18594, NA18951, NA12802, NA18561, NA12801, NA18523, NA18952, NA18975, NA07056, NA18966, NA19173, NA12752, NA18612, NA19120, NA10839, NA19003, NA12815, NA10847, NA19203, NA18529, NA18953, NA18969, NA18972, NA12005, NA18855, NA19144, NA19210, NA07348, NA18994, NA18524, NA18505, NA18506, NA18949, NA19143, NA18632, NA19140, NA11882, NA12763, NA18912, NA19211, NA18998, NA18624, NA19239, NA18854, NA18635, NA12155, NA18960, NA10846, NA12864, NA18563, NA12873, NA18991, NA12814, NA18636, NA12740, NA18592, NA18856, NA07048, NA18637, NA18973, NA18593, NA19100, NA12234, NA12144, NA12751, NA12006, NA12239, NA19153, NA18620, NA19129, NA19172, NA12892, NA19206, NA18968, NA19102, NA19119, NA18558, NA19098, NA19154, NA12057, NA10856, NA19139, NA12872, NA18504, NA18978, NA18564, NA18942, NA18540, NA18997, NA19131, NA18579, NA18974, NA19141, NA18940, NA12891, NA18999, NA12146, NA07055, NA19138, NA10860, NA19101, NA18995, NA06991, NA19193, NA18872, NA12812, NA18857, NA12156, NA19132, NA18577, NA19099, NA11992, NA18944, NA19205, NA18852, NA11993, NA19160, NA18571, NA18611, NA11829, NA12236, NA19130, NA19171, NA12717, NA12874, NA18981, NA06994, NA19200, NA18980
Known GenesC1orf68, CRCT1, IVL, KPRP, LCE1A, LCE1B, LCE1C, LCE1D, LCE1E, LCE1F, LCE2A, LCE2B, LCE2C, LCE2D, LCE3A, LCE3B, LCE3C, LCE3D, LCE3E, LCE4A, LCE5A, LCE6A, SMCP
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)esv2758970
Frequency
Sample Size270
Observed Gain58
Observed Loss80
Observed Complex0
Frequencyn/a


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