Variant Details

Variant: nsv442826

Internal ID

15154859

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrY:24894982..26029114	hg38	UCSC Ensembl
Inner	chrY:27041129..28175261	hg19	UCSC Ensembl
Inner	chrY:25450517..26584649	hg18	UCSC Ensembl
Inner	chrY:25379254..26513386	hg17	UCSC Ensembl

Cytoband

Yq11.23

Allele length

Assembly	Allele length
hg38	1134133
hg19	1134133
hg18	1134133
hg17	1134133

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1656374, nssv1656405, nssv1656331, nssv1656300, nssv1656383, nssv1656392, nssv1656304, nssv1656345, nssv1656313, nssv1656427, nssv1656375, nssv1656349, nssv1656341, nssv1656317, nssv1656425, nssv1656371, nssv1656342, nssv1656305, nssv1656318, nssv1656379, nssv1656399, nssv1656413, nssv1656322, nssv1656409, nssv1656386, nssv1656431, nssv1656426, nssv1656400, nssv1656366, nssv1656310, nssv1656348, nssv1656339, nssv1656330, nssv1656367, nssv1656416, nssv1656428, nssv1656420, nssv1656346, nssv1656351, nssv1656417, nssv1656302, nssv1656365, nssv1656324, nssv1656406, nssv1656414, nssv1656311, nssv1656296, nssv1656344, nssv1656398, nssv1656395, nssv1656307, nssv1656404, nssv1656411, nssv1656364, nssv1656361, nssv1656316, nssv1656312, nssv1656394, nssv1656359, nssv1656362, nssv1656340, nssv1656424, nssv1656401, nssv1656298, nssv1656354, nssv1656415, nssv1656412, nssv1656321, nssv1656306, nssv1656421, nssv1656326, nssv1656372, nssv1656334, nssv1656308, nssv1656315, nssv1656360, nssv1656314, nssv1656407, nssv1656378, nssv1656350, nssv1656336, nssv1656408, nssv1656402, nssv1656376, nssv1656353, nssv1656347, nssv1656422, nssv1656368, nssv1656423, nssv1656299, nssv1656352, nssv1656295, nssv1656369, nssv1656388, nssv1656320, nssv1656358, nssv1656319, nssv1656397, nssv1656328, nssv1656301, nssv1656390, nssv1656381, nssv1656410, nssv1656389, nssv1656357, nssv1656380, nssv1656337, nssv1656387, nssv1656332, nssv1656335, nssv1656355, nssv1656327, nssv1656403, nssv1656370, nssv1656418, nssv1656333, nssv1656382, nssv1656309, nssv1656323, nssv1656294, nssv1656419, nssv1656325, nssv1656391, nssv1656393, nssv1656363, nssv1656329, nssv1656297, nssv1656356, nssv1656385, nssv1656377, nssv1656343, nssv1656396, nssv1656430, nssv1656429, nssv1656384, nssv1656373, nssv1656303, nssv1656338

Samples

NA18998, NA18502, NA19141, NA12717, NA19222, NA11830, NA18947, NA11995, NA19204, NA18861, NA18592, NA18508, NA18524, NA18980, NA18855, NA12236, NA18999, NA12751, NA18545, NA12004, NA12865, NA18870, NA18526, NA18969, NA12813, NA19127, NA19192, NA18550, NA19201, NA10854, NA12802, NA18547, NA19131, NA18942, NA18582, NA18571, NA18964, NA18949, NA12761, NA07019, NA12156, NA19137, NA19238, NA12044, NA19207, NA19172, NA12815, NA19159, NA10855, NA19209, NA10839, NA18975, NA18973, NA11993, NA10847, NA18951, NA19194, NA12753, NA10863, NA10831, NA19152, NA12878, NA18956, NA18991, NA18529, NA18579, NA18871, NA18976, NA18981, NA12234, NA19208, NA19221, NA19202, NA18537, NA18566, NA18573, NA19142, NA11840, NA12249, NA18912, NA12892, NA18532, NA12239, NA12145, NA19099, NA18555, NA07345, NA06985, NA18523, NA19132, NA18570, NA18858, NA18593, NA18974, NA18576, NA19094, NA19003, NA18978, NA11882, NA19206, NA18542, NA06991, NA18517, NA18540, NA18564, NA12057, NA10859, NA19140, NA19240, NA19100, NA12873, NA18992, NA10861, NA19193, NA07348, NA12763, NA07055, NA18594, NA19143, NA12740, NA18987, NA19093, NA19102, NA12875, NA19116, NA18972, NA18872, NA18552, NA18852, NA07056, NA18505, NA19129, NA18968, NA12006, NA07000, NA18577, NA11832, NA18997

Known Genes

BPY2, BPY2B, BPY2C, CDY1, CDY1B, CSPG4P1Y, DAZ2, DAZ3, DAZ4, GOLGA2P2Y, GOLGA2P3Y, TTTY17A, TTTY17B, TTTY17C, TTTY3, TTTY3B, TTTY4, TTTY4B, TTTY4C

Method

SNP array

Analysis

We used two computational approaches to identify CNVs: the hidden Markov model Birdseye, and an approach based on correlation between nearby probes across a population sample. To maximize the quality of reported findings, we ran duplicate experiments in independent labs, and report the CNVs that were observed in both experiments, in the same samples and at essentially identical genomic locations.

Platform

[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array

Comments

Reference

McCarroll_et_al_2008

Pubmed ID

18776908

Accession Number(s)

nsv442826

Frequency

Sample Size	270
Observed Gain	10
Observed Loss	128
Observed Complex	0
Frequency	n/a