Variant Details

Variant: nsv469918

Internal ID

15209791

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr9:136359865..137173890	hg38	UCSC Ensembl
Inner	chr9:139254317..140068342	hg19	UCSC Ensembl
Inner	chr9:138374138..139188163	hg18	UCSC Ensembl

Cytoband

9q34.3

Allele length

Assembly	Allele length
hg38	814026
hg19	814026
hg18	814026

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv545993, nssv545985, nssv545992, nssv545974, nssv545967, nssv545990, nssv545983, nssv545962, nssv545972, nssv545970, nssv545978, nssv545968, nssv545964, nssv545973, nssv545986, nssv545994, nssv545981, nssv545961, nssv545971, nssv545989, nssv545977, nssv545969, nssv545984, nssv545960, nssv545982, nssv545980, nssv545963, nssv545966, nssv545995, nssv545991, nssv545975, nssv545988, nssv545979

Samples

HGDP00960, HGDP00315, HGDP00290, HGDP00894, HGDP00288, HGDP00881, HGDP00883, HGDP00298, HGDP00556, HGDP00591, HGDP00882, HGDP01398, HGDP00546, HGDP00951, HGDP01397, HGDP00697, HGDP00789, HGDP00657, HGDP00866, HGDP00962, HGDP00877, HGDP00825, HGDP00328, HGDP00313, HGDP00302

Known Genes

ABCA2, 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

Method

SNP array

Analysis

We 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.

Platform

Illumina HumanHap550 Genotyping BeadChip v3

Comments

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nsv469918

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	25
Observed Complex	0
Frequency	n/a