A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv469958



Internal ID15209831
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:55603544..55828837hg38UCSC Ensembl
Innerchr11:55371020..55596313hg19UCSC Ensembl
Innerchr11:55127596..55352889hg18UCSC Ensembl
Cytoband11q11
Allele length
AssemblyAllele length
hg38225294
hg19225294
hg18225294
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546136, nssv546134, nssv546123, nssv546135, nssv546116, nssv546159, nssv546156, nssv546158, nssv546125, nssv546149, nssv546150, nssv546171, nssv546166, nssv546160, nssv546168, nssv546172, nssv546130, nssv546127, nssv546163, nssv546119, nssv546173, nssv546167, nssv546148, nssv546126, nssv546117, nssv546137, nssv546122, nssv546118, nssv546157, nssv546169, nssv546145, nssv546129, nssv546155, nssv546124, nssv546161, nssv546141, nssv546132, nssv546147, nssv546139, nssv546151, nssv546115, nssv546121, nssv546146, nssv546138, nssv546162, nssv546164, nssv546170, nssv546152, nssv546133, nssv546140, nssv546128, nssv546153, nssv546144, nssv546174
SamplesHGDP00880, HGDP01231, HGDP00576, HGDP00655, HGDP00654, HGDP01388, HGDP00614, HGDP00695, HGDP01263, HGDP00903, HGDP00632, HGDP01039, HGDP00686, HGDP01046, HGDP00930, HGDP00643, HGDP00867, HGDP01262, HGDP00789, HGDP00876, HGDP01358, HGDP00615, HGDP01418, HGDP00591, HGDP01387, HGDP00568, HGDP00696, HGDP00054, HGDP00620, HGDP00566, HGDP00978, HGDP00676, HGDP00564, HGDP00647, HGDP00874, HGDP00491, HGDP01223, HGDP00864, HGDP00570, HGDP01317, HGDP00697, HGDP00926, HGDP00602, HGDP00453, HGDP00543, HGDP00388, HGDP00913, HGDP00657, HGDP00694, HGDP01260, HGDP00572, HGDP01217, HGDP00940, HGDP00058
Known GenesOR4C11, OR4C6, OR4P4, OR4S2, OR5D13, OR5D14, OR5D18, OR5L1, OR5L2
MethodSNP array
AnalysisWe used the previously validated default quality control criteria, excluding samples with a log R ratio standard deviation of >0.28, a median B allele frequency of >0.55 or <0.45, or a B allele frequency drift of >0.002 (for more details see Wang et al. 2007). As the PennCNV algorithm is more sensitive and specific to CNVs covering greater numbers of SNPs in the HumanHap550 array, use of a minimum number of SNPs in CNV detection increases the reliability of CNV calls (with a consequent reduction in calls per individual). We set 10 SNPs as the minimum detection threshold in the algorithm.
PlatformIllumina HumanHap550 Genotyping BeadChip v3
Comments
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nsv469958
Frequency
Sample Size443
Observed Gain0
Observed Loss54
Observed Complex0
Frequencyn/a


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