A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756838



Internal ID9632297
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:16482199..16981663hg38UCSC Ensembl
Innerchr1:16808694..17308158hg19UCSC Ensembl
Innerchr1:16681281..17180745hg18UCSC Ensembl
Innerchr1:16554000..17053464hg17UCSC Ensembl
Cytoband1p36.13
Allele length
AssemblyAllele length
hg38499465
hg19499465
hg18499465
hg17499465
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758925
Supporting Variantsessv17368, essv15449, essv19315, essv1654, essv7452, essv9844, essv12038, essv7649, essv15972, essv8984, essv1297, essv4337, essv6477, essv18520, essv192, essv1047, essv24438, essv13968, essv2144, essv5761, essv1690, essv3658, essv995, essv17392, essv13252, essv1975, essv11309, essv9483, essv14021, essv11603, essv1545, essv18576, essv20753, essv12447, essv23162, essv14835, essv19066, essv19470, essv8586, essv19867, essv8565, essv635, essv14216, essv18043, essv12117, essv25036, essv25159, essv12088, essv22714, essv2364, essv24554, essv2114, essv5427, essv5953, essv3943, essv4527, essv5657, essv5646, essv6935, essv10959, essv19114, essv19372, essv934, essv1070, essv3913, essv13406, essv1312, essv7246, essv5077, essv10595, essv7960, essv2, essv25180, essv2727, essv24180, essv747, essv6079, essv23764, essv2946, essv507, essv18806, essv7481, essv13308, essv19296, essv21752, essv14673, essv3252, essv22267, essv8527, essv1573, essv19814, essv4325, essv7670, essv11467, essv12895, essv19889, essv7638, essv20981, essv15194, essv24605, essv8890, essv5003, essv17409, essv6418, essv6464, essv7051, essv24221, essv13992, essv98, essv13338, essv22697, essv9528, essv23321, essv7936, essv16559, essv15917, essv14928, essv19145, essv3853, essv20548, essv613, essv10181, essv3489, essv9511, essv11327, essv12074, essv14801, essv3684, essv7886, essv14917, essv2922, essv6855, essv13813, essv5680, essv19835, essv8061, essv949, essv2391, essv8050, essv12873, essv18478, essv3575, essv7990, essv1669, essv20473, essv2412, essv1807, essv18898, essv3327, essv8675, essv23097, essv15156, essv5622, essv722, essv10512, essv8991, essv23713, essv8266, essv15944, essv21893, essv20819, essv21496, essv21574, essv3440, essv21960, essv2702, essv24019, essv9970, essv4106, essv19712, essv2566, essv6198, essv14235, essv5863, essv8718, essv8492, essv9267, essv18690, essv22785, essv6793
SamplesNA18503, NA19142, NA19012, NA19137, NA10831, NA11881, NA18621, NA19207, NA18870, NA18964, NA18863, NA12043, NA19152, NA19194, NA12249, NA18605, NA12750, NA18594, NA18951, NA19222, NA18561, NA12801, NA18523, NA18952, NA18975, NA19173, NA12875, NA18612, NA19209, NA18500, NA18526, NA18570, NA19003, NA12264, NA19223, NA10847, NA18545, NA18948, NA18516, NA06993, NA19203, NA18521, NA18529, NA18953, NA18972, NA18517, NA18947, NA18608, NA18542, NA07019, NA18855, NA19144, NA19210, NA10855, NA18994, NA18965, NA12044, NA18943, NA18949, NA19143, NA10863, NA18632, NA12865, NA19140, NA19161, NA12763, NA19211, NA18998, NA18967, NA12056, NA18992, NA11839, NA11840, NA12753, NA12004, NA18854, NA11994, NA18635, NA18622, NA18960, NA12864, NA18563, NA07357, NA18623, NA12873, NA18990, NA18991, NA18636, NA12740, NA18856, NA18956, NA18959, NA18547, NA11831, NA18976, NA18637, NA18973, NA11995, NA18593, NA19100, NA12234, NA12144, NA18970, NA12751, NA12239, NA19153, NA18620, NA18515, NA19129, NA19103, NA19206, NA18968, NA18522, NA19238, NA19005, NA18502, NA19119, NA18558, NA19098, NA19154, NA19139, NA12872, NA18504, NA18978, NA18564, NA18942, NA18961, NA18540, NA18997, NA19221, NA18579, NA18974, NA18945, NA18940, NA19145, NA18987, NA10851, NA18582, NA18999, NA12146, NA19101, NA19201, NA18995, NA06991, NA19193, NA18872, NA19128, NA12812, NA12156, NA19116, NA18971, NA19132, NA18577, NA19099, NA07022, NA11830, NA11992, NA12003, NA18944, NA19205, NA19160, NA12248, NA18571, NA12236, NA19130, NA19171, NA12717, NA18853, NA19204, NA18981, NA18913, NA12760, NA19092, NA18555, NA19200, NA19007, NA19202, NA07000, NA18980, NA10861
Known GenesCROCC, CROCCP2, CROCCP3, ESPNP, LOC729574, MFAP2, MIR3675, MST1L, MST1P2, NBPF1
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)esv2756838
Frequency
Sample Size270
Observed Gain170
Observed Loss10
Observed Complex0
Frequencyn/a


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