A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759258



Internal ID9634717
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:68304361..69548454hg38UCSC Ensembl
Innerchr4:69170079..70414172hg19UCSC Ensembl
Innerchr4:68852674..70448761hg18UCSC Ensembl
Innerchr4:68998845..70594932hg17UCSC Ensembl
Cytoband4q13.2
Allele length
AssemblyAllele length
hg381244094
hg191244094
hg181596088
hg171596088
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757064, esv2757063, esv2757061, esv2757940, esv2757065, esv2757062
SamplesNA10859, NA18503, NA19012, NA11881, NA18621, NA19207, NA18870, NA18964, NA12154, NA18863, NA19127, NA12043, NA19152, NA19194, NA12249, NA18861, NA18605, NA12750, NA18594, NA18951, NA19192, NA18914, NA18871, NA12802, NA19222, NA18561, NA12801, NA18523, NA18952, NA18975, NA07056, NA18966, NA19173, NA12752, NA12875, NA18612, NA19209, NA18501, NA19093, NA19120, NA18500, NA18526, NA10839, NA18550, NA18570, NA19003, NA18859, NA19223, NA12815, NA10847, NA18545, NA18603, NA18948, NA18516, NA12707, NA12813, NA06993, NA19203, NA18521, NA18529, NA18953, NA18969, NA18972, NA18517, NA18947, NA18573, NA18542, NA07019, NA12005, NA18855, NA19144, NA19210, NA07348, NA18507, NA10855, NA18860, NA18994, NA07029, NA18524, NA18965, NA18505, NA12044, NA19208, NA18506, NA18862, NA18943, NA18949, NA19143, NA10863, NA18632, NA12865, NA19140, NA11882, NA12763, NA18912, NA19211, NA18998, NA18624, NA18508, NA18967, NA19239, NA12056, NA18992, NA11839, NA11840, NA12753, NA07034, NA12004, NA18854, NA11994, NA18635, NA12155, NA18576, NA18622, NA18960, NA10846, NA12864, NA18563, NA07345, NA07357, NA18623, NA12762, NA12873, NA18990, NA18991, NA12814, NA18636, NA12740, NA18592, NA18856, NA07048, NA12761, NA18959, NA18609, NA18547, NA11831, NA18637, NA18973, NA11995, NA18593, NA19100, NA12234, NA12144, NA18970, NA12751, NA12006, NA19000, NA12239, NA12145, NA19153, NA12716, NA18537, NA18620, NA18515, NA19129, NA19172, NA12892, NA18633, NA18572, NA19094, NA19103, NA06985, NA19206, NA18968, NA19102, NA18522, NA19238, NA19005, NA18502, NA19119, NA18558, NA19098, NA19154, NA12057, NA10856, NA19139, NA12872, NA18504, NA18978, NA18564, NA18858, NA18942, NA18961, NA18997, NA19221, NA18562, NA19131, NA19159, NA18974, NA18945, NA19141, NA18940, NA19145, NA11832, NA12891, NA18987, NA10851, NA18582, NA18999, NA10857, NA12146, NA07055, NA18552, NA19138, NA10860, NA19101, NA19201, NA18995, NA06991, NA19193, NA18872, NA19128, NA12812, NA18857, NA12156, NA19116, NA10835, NA18971, NA19132, NA10830, NA18577, NA19099, NA07022, NA12878, NA11830, NA11992, NA12003, NA18944, NA19205, NA10838, NA18852, NA11993, NA19160, NA12248, NA18571, NA18611, NA11829, NA12236, NA19130, NA19171, NA19240, NA12717, NA12874, NA18532, NA18853, NA19204, NA18981, NA06994, NA18913, NA12760, NA19092, NA18555, NA19200, NA19007, NA19202, NA07000, NA18980, NA10854, NA10861, NA19142, NA19137, NA10831
Known GenesTMPRSS11E, UGT2A3, UGT2B10, UGT2B11, UGT2B15, UGT2B17, UGT2B28, UGT2B4, UGT2B7, YTHDC1
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)esv2759258
Frequency
Sample Size270
Observed Gain240
Observed Loss81
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer