A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757065



Internal ID9632524
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:69154215..69433003hg38UCSC Ensembl
Innerchr4:70019933..70298721hg19UCSC Ensembl
Innerchr4:70054522..70333310hg18UCSC Ensembl
Innerchr4:70200693..70479481hg17UCSC Ensembl
Cytoband4q13.2
Allele length
AssemblyAllele length
hg38278789
hg19278789
hg18278789
hg17278789
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759258
Supporting Variantsessv7058, essv18800, essv2941, essv18564, essv14933, essv19721, essv14680, essv2710, essv18789, essv2550, essv2750, essv948, essv17361, essv13281, essv22735, essv13243, essv24362, essv25079, essv6553, essv629, essv5980, essv12915, essv1692, essv3334, essv24445, essv593, essv13960, essv2115, essv14829, essv992, essv8687, essv18689, essv3907, essv8662, essv20535, essv945, essv8261, essv13207, essv518, essv19348, essv5615, essv14926, essv16609, essv8392
SamplesNA18998, NA18947, NA11995, NA10851, NA12236, NA19145, NA12248, NA18959, NA12865, NA18944, NA19201, NA19119, NA12891, NA19131, NA18960, NA18964, NA18949, NA10839, NA19120, NA18948, NA18981, NA19208, NA12056, NA18912, NA12892, NA12239, NA19101, NA06985, NA19160, NA19132, NA18593, NA18974, NA19094, NA18952, NA18517, NA19093, NA18972, NA18552, NA19129, NA18968, NA18624, NA18612, NA19153, NA18965
Known GenesUGT2B11, UGT2B28
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)esv2757065
Frequency
Sample Size270
Observed Gain2
Observed Loss42
Observed Complex0
Frequencyn/a


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