A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756863



Internal ID9632322
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:147802277..149995979hg19UCSC Ensembl
Innerchr1:146268901..148262603hg18UCSC Ensembl
Innerchr1:144917189..146809052hg17UCSC Ensembl
Cytoband1q21.1
Allele length
AssemblyAllele length
hg192193703
hg181993703
hg171891864
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758968
Supporting Variantsessv6431, essv6462, essv1563, essv6936, essv22616, essv8654, essv8055, essv21103, essv1300, essv12093, essv11482, essv19038, essv2771, essv5887, essv14239, essv2131, essv19302, essv703, essv19728, essv15960, essv13497, essv21364, essv22727, essv18916, essv21927, essv25169, essv23307, essv25167, essv5854, essv5662, essv19130, essv16169, essv7239, essv18551, essv24338, essv2935, essv8706, essv18578, essv23641, essv20523, essv20532, essv5618, essv19885, essv6416, essv21892, essv19363, essv1715, essv91, essv6084, essv6845, essv7932, essv14225, essv17872, essv2387, essv22691, essv20464, essv10704, essv6535, essv20734, essv12952, essv6790, essv21629, essv21474, essv19350, essv24181, essv942
SamplesNA12717, NA18621, NA11995, NA18592, NA18508, NA10851, NA18980, NA18545, NA12004, NA10857, NA18526, NA07357, NA19005, NA18940, NA10854, NA18635, NA18558, NA18949, NA18611, NA07019, NA12044, NA19209, NA19200, NA11993, NA19007, NA07022, NA18637, NA19103, NA18976, NA11839, NA19142, NA19000, NA11840, NA10830, NA18856, NA12239, NA12264, NA19099, NA19101, NA18555, NA06985, NA18593, NA18576, NA18608, NA18978, NA18914, NA11882, NA06991, NA12716, NA11881, NA12057, NA10859, NA18913, NA19100, NA07348, NA07055, NA18594, NA06994, NA10860, NA18506, NA19102, NA07056, NA18968, NA12154, NA07034, NA18997
Known GenesBOLA1, FCGR1A, FCGR1C, HIST2H2AA3, HIST2H2AA4, HIST2H2AB, HIST2H2AC, HIST2H2BC, HIST2H2BE, HIST2H2BF, HIST2H3A, HIST2H3C, HIST2H3D, HIST2H4A, HIST2H4B, LINC00623, LINC00869, LINC01138, LOC100130000, LOC101929780, LOC388692, LOC645166, MIR5087, MIR6077-1, MIR6077-2, MTMR11, NBPF10, NBPF14, NBPF15, NBPF16, NBPF23, NBPF8, NBPF9, OTUD7B, PPIAL4A, PPIAL4B, PPIAL4C, PPIAL4D, PPIAL4E, PPIAL4F, SF3B4, SV2A
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)esv2756863
Frequency
Sample Size270
Observed Gain6
Observed Loss60
Observed Complex0
Frequencyn/a


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