A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757009



Internal ID9632468
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:129990804..130220530hg38UCSC Ensembl
Innerchr3:129709647..129939373hg19UCSC Ensembl
Innerchr3:131192337..131422063hg18UCSC Ensembl
Innerchr3:131192345..131422071hg17UCSC Ensembl
Cytoband3q21.3
Allele length
AssemblyAllele length
hg38229727
hg19229727
hg18229727
hg17229727
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759177
Supporting Variantsessv7913, essv7247, essv13981, essv3933, essv15447, essv13351, essv24021, essv17683, essv24211, essv16594, essv21911, essv4536, essv14244, essv1817, essv25059, essv8676, essv6075, essv20534, essv15175, essv22029, essv12031, essv7657, essv597, essv1695, essv5778, essv17382, essv18901, essv3261, essv23703, essv6200, essv13289, essv14822, essv5608, essv8698, essv101, essv5882, essv13949, essv20809, essv630, essv14010, essv8054, essv13360, essv4349, essv21634, essv4512, essv6465, essv9563, essv11360, essv20690, essv1085, essv8975, essv2718, essv10603, essv18544, essv6066, essv21084, essv22608, essv11322, essv5681, essv24091, essv22707, essv21502, essv8413, essv8987, essv5886, essv3321, essv3683, essv14951, essv14842, essv7504, essv991, essv14213, essv20488, essv8083, essv1577, essv6786, essv15196, essv1053, essv18796, essv25040, essv8250, essv23744, essv11595, essv2772, essv9495, essv12071, essv19152, essv4322, essv2143, essv18878, essv19802, essv23323, essv12930, essv13507, essv19844, essv7460, essv17355, essv21607, essv6504, essv3833, essv1317, essv20848, essv5961, essv8906, essv18467, essv944, essv10508, essv20708, essv24448, essv3439, essv502, essv21479, essv11396, essv14676, essv25170, essv22252, essv11062, essv12871, essv7956, essv12119, essv21568, essv5836, essv1640, essv10981, essv7926, essv1303, essv13320, essv2118, essv15962, essv21656, essv7681, essv23640, essv8490, essv12146, essv2907, essv13230, essv13263, essv2427, essv6422, essv3593, essv4116, essv6556, essv7441, essv9307, essv1983, essv3496, essv5700, essv13223, essv21937, essv6844, essv968, essv12892, essv21745, essv2726, essv8574, essv14914, essv18011, essv20457, essv5629, essv7989, essv18522, essv195, essv5006, essv2569, essv5429, essv744, essv10, essv20472, essv20985, essv7490, essv19714, essv6112, essv12087, essv7623, essv983, essv7984, essv9279
SamplesNA19142, NA19137, NA18621, NA19207, NA18870, NA18964, NA12154, NA19194, NA12249, NA18861, NA18605, NA18594, NA18951, NA19192, NA18914, NA12802, NA19222, NA18561, NA12801, NA18952, NA18975, NA19173, NA12752, NA19209, NA19093, NA19120, NA18500, NA18550, NA19003, NA12264, NA12815, NA18545, NA18603, NA18948, NA12813, NA19203, NA18529, NA18953, NA18969, NA18517, NA18947, NA18573, NA18542, NA18855, NA19210, NA07348, NA18507, NA10855, NA18860, NA18994, NA07029, NA18524, NA18965, NA18505, NA18943, NA18949, NA19143, NA10863, NA18632, NA12865, NA19161, NA12763, NA18912, NA19211, NA18998, NA18624, NA18967, NA19239, NA11840, NA12004, NA18854, NA18566, NA18635, NA12155, NA18576, NA18622, NA12864, NA18563, NA18623, NA12873, NA18990, NA12740, NA07048, NA12761, NA18956, NA18959, NA18547, NA18637, NA18973, NA11995, NA18593, NA19100, NA12234, NA12144, NA18970, NA19000, NA19153, NA18620, NA19129, NA12892, NA18633, NA18572, NA19094, NA19103, NA19206, NA18968, NA18522, NA19238, NA19005, NA18502, NA19119, NA18558, NA19098, NA19154, NA12057, NA19139, NA18504, NA18978, NA18564, NA18858, NA18942, NA18961, NA18540, NA18997, NA19221, NA18562, NA19131, NA19159, NA18579, NA18974, NA18945, NA19145, NA11832, NA18582, NA18999, NA12146, NA07055, NA19138, NA19101, NA19201, NA19128, NA12812, NA19116, NA10835, NA18971, NA19132, NA10830, NA18577, NA19099, NA12878, NA11992, NA12003, NA18944, NA10838, NA18852, NA11993, NA19160, NA12248, NA18571, NA11829, NA12236, NA19130, NA19171, NA19240, NA12717, NA12874, NA18532, NA18981, NA06994, NA18913, NA19092, NA19007, NA19202, NA18980, NA10854, NA10861
Known GenesALG1L2, COL6A4P2, FAM86HP
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)esv2757009
Frequency
Sample Size270
Observed Gain148
Observed Loss29
Observed Complex0
Frequencyn/a


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