A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv469918



Internal ID15209791
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:136359865..137173890hg38UCSC Ensembl
Innerchr9:139254317..140068342hg19UCSC Ensembl
Innerchr9:138374138..139188163hg18UCSC Ensembl
Cytoband9q34.3
Allele length
AssemblyAllele length
hg38814026
hg19814026
hg18814026
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545968, nssv545967, nssv545969, nssv545991, nssv545978, nssv545989, nssv545973, nssv545975, nssv545988, nssv545963, nssv545994, nssv545974, nssv545977, nssv545993, nssv545980, nssv545962, nssv545970, nssv545979, nssv545984, nssv545990, nssv545982, nssv545981, nssv545995, nssv545985, nssv545983, nssv545960, nssv545961, nssv545986, nssv545964, nssv545992, nssv545972, nssv545966, nssv545971
SamplesHGDP00313, HGDP00962, HGDP00288, HGDP00546, HGDP00951, HGDP00298, HGDP00789, HGDP01398, HGDP00302, HGDP00883, HGDP00591, HGDP00866, HGDP00290, HGDP00315, HGDP00825, HGDP00881, HGDP00556, HGDP00877, HGDP00697, HGDP00328, HGDP00882, HGDP00894, HGDP01397, HGDP00960, HGDP00657
Known GenesABCA2, AGPAT2, C8G, C9orf139, C9orf142, C9orf163, C9orf172, CARD9, CCDC183, CCDC183-AS1, CLIC3, DNLZ, DPP7, EDF1, EGFL7, ENTPD2, FAM69B, FBXW5, FUT7, GRIN1, INPP5E, LCN10, LCN12, LCN15, LCN6, LCN8, LCNL1, LOC100128593, LRRC26, MAMDC4, MAN1B1, MAN1B1-AS1, MIR126, MIR3621, MIR4292, MIR4479, MIR4673, MIR4674, MIR6722, NOTCH1, NPDC1, PHPT1, PMPCA, PTGDS, RABL6, SAPCD2, SDCCAG3, SEC16A, SNAPC4, SNHG7, SNORA17, SNORA43, TMEM141, TMEM210, TRAF2, UAP1L1
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)nsv469918
Frequency
Sample Size443
Observed Gain0
Observed Loss25
Observed Complex0
Frequencyn/a


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