Variant Details

Variant: nsv442286

Internal ID

15501005

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr7:157545673..157558146	hg38	UCSC Ensembl
Inner	chr7:157338367..157350840	hg19	UCSC Ensembl
Inner	chr7:157031128..157043601	hg18	UCSC Ensembl
Inner	chr7:156837843..156850316	hg17	UCSC Ensembl

Cytoband

7q36.3

Allele length

Assembly	Allele length
hg38	12474
hg19	12474
hg18	12474
hg17	12474

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1635737, nssv1635718, nssv1635645, nssv1635768, nssv1635752, nssv1635699, nssv1635640, nssv1635653, nssv1635690, nssv1635687, nssv1635655, nssv1635733, nssv1635662, nssv1635772, nssv1635712, nssv1635702, nssv1635753, nssv1635703, nssv1635689, nssv1635749, nssv1635720, nssv1635723, nssv1635715, nssv1635705, nssv1635729, nssv1635755, nssv1635650, nssv1635764, nssv1635721, nssv1635692, nssv1635746, nssv1635682, nssv1635756, nssv1635676, nssv1635738, nssv1635656, nssv1635659, nssv1635735, nssv1635700, nssv1635748, nssv1635706, nssv1635754, nssv1635693, nssv1635661, nssv1635671, nssv1635665, nssv1635698, nssv1635769, nssv1635711, nssv1635728, nssv1635717, nssv1635709, nssv1635704, nssv1635740, nssv1635678, nssv1635670, nssv1635642, nssv1635683, nssv1635713, nssv1635724, nssv1635686, nssv1635725, nssv1635757, nssv1635707, nssv1635657, nssv1635677, nssv1635651, nssv1635758, nssv1635669, nssv1635694, nssv1635719, nssv1635646, nssv1635697, nssv1635751, nssv1635685, nssv1635681, nssv1635744, nssv1635675, nssv1635664, nssv1635658, nssv1635742, nssv1635663, nssv1635739, nssv1635716, nssv1635745, nssv1635727, nssv1635701, nssv1635695, nssv1635773, nssv1635732, nssv1635714, nssv1635647, nssv1635741, nssv1635762, nssv1635652, nssv1635684, nssv1635761, nssv1635734, nssv1635747, nssv1635643, nssv1635710, nssv1635666, nssv1635771, nssv1635763, nssv1635641, nssv1635731, nssv1635654, nssv1635730, nssv1635668, nssv1635667, nssv1635696, nssv1635765, nssv1635759, nssv1635672, nssv1635760, nssv1635673, nssv1635743, nssv1635750, nssv1635644, nssv1635660, nssv1635770, nssv1635691, nssv1635688, nssv1635722, nssv1635680, nssv1635679, nssv1635674, nssv1635649, nssv1635708, nssv1635736, nssv1635766, nssv1635648, nssv1635767, nssv1635726

Samples

NA18998, NA18502, NA19222, NA11830, NA11995, NA19204, NA18862, NA18592, NA18508, NA10851, NA18524, NA18507, NA12751, NA18545, NA12004, NA18504, NA12248, NA12146, NA12865, NA10857, NA19098, NA18870, NA12155, NA07357, NA12813, NA19192, NA19171, NA18944, NA18940, NA12812, NA10835, NA10854, NA12802, NA19119, NA18635, NA18860, NA12891, NA19131, NA11992, NA07048, NA06993, NA19130, NA07019, NA19137, NA19238, NA11994, NA18966, NA12815, NA10855, NA19239, NA10839, NA18975, NA19200, NA11831, NA10847, NA18951, NA19210, NA12752, NA07022, NA19194, NA12753, NA12003, NA10863, NA10831, NA12878, NA19161, NA18859, NA19205, NA18516, NA19103, NA18503, NA11839, NA10838, NA12234, NA19202, NA18566, NA11840, NA10830, NA18856, NA12249, NA12056, NA18912, NA12892, NA18857, NA12239, NA12264, NA12145, NA18555, NA06985, NA18523, NA19160, NA19132, NA18570, NA18858, NA18945, NA18974, NA12043, NA18953, NA19094, NA19003, NA18914, NA11882, NA19206, NA06991, NA11881, NA18961, NA18517, NA12057, NA10859, NA10861, NA19193, NA12874, NA12763, NA19143, NA18501, NA12740, NA06994, NA19173, NA19093, NA18521, NA18500, NA18506, NA19102, NA12875, NA18854, NA18972, NA18872, NA18505, NA12006, NA12154, NA07034, NA18622, NA19153, NA11832

Known Genes

PTPRN2

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)

nsv442286

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	134
Observed Complex	0
Frequency	n/a