A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759412



Internal ID9634871
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:29824657..30007367hg38UCSC Ensembl
Innerchr6:29792434..29975144hg19UCSC Ensembl
Innerchr6:29900413..30083123hg18UCSC Ensembl
Innerchr6:29900413..30083123hg17UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg38182711
hg19182711
hg18182711
hg17182711
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757159, esv2758040
SamplesNA19012, NA18621, NA18863, NA19194, NA12750, NA18951, NA12802, NA19222, NA18561, NA18952, NA19173, NA12752, NA12875, NA19093, NA19120, NA18526, NA19223, NA12815, NA18545, NA18603, NA12813, NA19203, NA18529, NA18969, NA18972, NA18947, NA18608, NA18855, NA07348, NA18994, NA18506, NA18862, NA18949, NA19143, NA12865, NA19211, NA18998, NA18508, NA18967, NA12056, NA18992, NA11839, NA07034, NA12004, NA11994, NA18622, NA18960, NA12864, NA07357, NA18623, NA12762, NA12873, NA18990, NA18991, NA12814, NA18636, NA18592, NA07048, NA12761, NA18959, NA18976, NA18973, NA18593, NA12144, NA18970, NA19000, NA19129, NA18572, NA19094, NA18502, NA19119, NA12057, NA19139, NA18942, NA18961, NA18997, NA19159, NA18945, NA18940, NA12891, NA10851, NA18582, NA18999, NA19138, NA18995, NA06991, NA19128, NA19116, NA10835, NA18971, NA19132, NA19099, NA12003, NA18944, NA12248, NA18571, NA19171, NA12874, NA18981, NA12760, NA19200, NA19202
Known GenesHCG4B, HCG9, HLA-A, HLA-G, HLA-H, HLA-J, ZNRD1-AS1
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)esv2759412
Frequency
Sample Size270
Observed Gain18
Observed Loss84
Observed Complex0
Frequencyn/a


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