Variant Details

Variant: nsv442910

Internal ID

15501629

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:68494770..68620261	hg38	UCSC Ensembl
Inner	chr4:69360488..69485979	hg19	UCSC Ensembl
Inner	chr4:69043083..69168574	hg18	UCSC Ensembl
Inner	chr4:69189254..69314745	hg17	UCSC Ensembl

Cytoband

4q13.2

Allele length

Assembly	Allele length
hg38	125492
hg19	125492
hg18	125492
hg17	125492

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1626077, nssv1625745, nssv1626387, nssv1625259, nssv1625210, nssv1625703, nssv1625685, nssv1625808, nssv1625626, nssv1625830, nssv1625720, nssv1626318, nssv1625228, nssv1624977, nssv1625118, nssv1625498, nssv1626021, nssv1625681, nssv1626345, nssv1625915, nssv1626501, nssv1625669, nssv1625093, nssv1625823, nssv1625351, nssv1625217, nssv1626110, nssv1626388, nssv1625580, nssv1625620, nssv1625272, nssv1625023, nssv1625869, nssv1626270, nssv1625559, nssv1625866, nssv1625909, nssv1626480, nssv1625704, nssv1625499, nssv1626429, nssv1625964, nssv1626231, nssv1625734, nssv1625271, nssv1624999, nssv1625739, nssv1626579, nssv1626375, nssv1626569, nssv1625123, nssv1626191, nssv1625186, nssv1626290, nssv1625450, nssv1625184, nssv1626031, nssv1626543, nssv1625897, nssv1625491, nssv1625846, nssv1626085, nssv1626525, nssv1625508, nssv1625174, nssv1625831, nssv1625815, nssv1625918, nssv1625054, nssv1626281, nssv1626353, nssv1626538, nssv1626526, nssv1625473, nssv1625145, nssv1624951, nssv1625935, nssv1626583, nssv1624978, nssv1625423, nssv1625214, nssv1625572, nssv1626196, nssv1626402, nssv1626041, nssv1626420, nssv1626334, nssv1625146, nssv1625303, nssv1626481, nssv1626257, nssv1625801, nssv1625765, nssv1625264, nssv1625779, nssv1626374, nssv1626335, nssv1626544, nssv1625908, nssv1625408, nssv1626361, nssv1626004, nssv1625650, nssv1625865, nssv1625555, nssv1625633, nssv1625162, nssv1625511, nssv1626258, nssv1625137, nssv1625185, nssv1626407, nssv1626482, nssv1625494, nssv1626162, nssv1625368, nssv1625175, nssv1626567, nssv1625594, nssv1626063, nssv1625773, nssv1625771, nssv1626090, nssv1625424, nssv1626248, nssv1626547, nssv1625860, nssv1625606, nssv1625510, nssv1626233, nssv1625649, nssv1626183, nssv1626444, nssv1625207, nssv1626125, nssv1625443, nssv1625927, nssv1625199, nssv1625307, nssv1625178, nssv1626358, nssv1625953, nssv1626574, nssv1625504, nssv1626382, nssv1625338, nssv1625321, nssv1625914, nssv1625388, nssv1626590, nssv1626465, nssv1625083, nssv1625177, nssv1624982, nssv1625879, nssv1624953, nssv1625601, nssv1626175, nssv1625373, nssv1625803, nssv1625381, nssv1625403, nssv1625382, nssv1624993, nssv1625072, nssv1625630, nssv1626177, nssv1625478, nssv1626076, nssv1625680, nssv1625490

Samples

NA18998, NA18502, NA12717, NA11830, NA18947, NA11995, NA11829, NA18862, NA18592, NA10851, NA18524, NA18980, NA18855, NA18561, NA19145, NA18999, NA18603, NA12751, NA18545, NA07029, NA12004, NA12801, NA18504, NA12248, NA18959, NA10857, NA19098, NA18870, NA18526, NA18633, NA12750, NA12155, NA18969, NA12813, NA18967, NA18563, NA19005, NA18944, NA18940, NA10846, NA18995, NA19119, NA18635, NA18860, NA12891, NA18558, NA18547, NA18960, NA18942, NA11992, NA07048, NA18582, NA18571, NA18964, NA19130, NA18949, NA18611, NA12761, NA18970, NA07019, NA12156, NA19137, NA19172, NA18966, NA12815, NA19159, NA18990, NA19239, NA19209, NA18975, NA18973, NA19200, NA19007, NA18951, NA18605, NA12752, NA10863, NA10831, NA12878, NA19161, NA18991, NA18529, NA18637, NA18579, NA18871, NA18572, NA18976, NA18948, NA18503, NA11839, NA10838, NA18981, NA19202, NA18537, NA18566, NA18573, NA19142, NA19000, NA18856, NA12056, NA12892, NA18857, NA18532, NA12264, NA12145, NA12707, NA18555, NA07345, NA19160, NA10856, NA18570, NA18858, NA18593, NA18945, NA19012, NA18974, NA18576, NA12043, NA18608, NA18953, NA19003, NA18978, NA18632, NA11882, NA18542, NA12716, NA18961, NA18952, NA18517, NA12864, NA18863, NA18564, NA12057, NA19140, NA19240, NA19100, NA12873, NA18992, NA10861, NA18943, NA07348, NA07055, NA18594, NA19143, NA12740, NA06994, NA18971, NA19173, NA18987, NA18994, NA18636, NA18500, NA18609, NA19102, NA18972, NA18872, NA18552, NA07056, NA18968, NA18624, NA18623, NA12154, NA07034, NA18612, NA18622, NA18562, NA18965, NA18577, NA11832, NA18620, NA18997

Known Genes

TMPRSS11E, UGT2B17

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)

nsv442910

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	171
Observed Complex	0
Frequency	n/a