Variant Details

Variant: nsv442967

Internal ID

15501686

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:109681762..109700331	hg38	UCSC Ensembl
Inner	chr1:110224384..110242953	hg19	UCSC Ensembl
Inner	chr1:110025907..110044476	hg18	UCSC Ensembl
Inner	chr1:109936426..109954995	hg17	UCSC Ensembl

Cytoband

1p13.3

Allele length

Assembly	Allele length
hg38	18570
hg19	18570
hg18	18570
hg17	18570

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1617152, nssv1617164, nssv1617018, nssv1617000, nssv1617093, nssv1617030, nssv1617073, nssv1617042, nssv1617028, nssv1616922, nssv1616960, nssv1617166, nssv1617089, nssv1616968, nssv1617159, nssv1617139, nssv1617148, nssv1616949, nssv1617175, nssv1617106, nssv1617162, nssv1617034, nssv1617003, nssv1617001, nssv1617090, nssv1617142, nssv1617019, nssv1617144, nssv1617081, nssv1617044, nssv1617084, nssv1617161, nssv1617160, nssv1617131, nssv1617050, nssv1616933, nssv1617097, nssv1616984, nssv1616944, nssv1616940, nssv1616990, nssv1617052, nssv1617078, nssv1617011, nssv1617010, nssv1617094, nssv1617009, nssv1617004, nssv1616957, nssv1616986, nssv1616970, nssv1617110, nssv1616983, nssv1617107, nssv1616931, nssv1616965, nssv1617111, nssv1617076, nssv1617083, nssv1617045, nssv1616961, nssv1616948, nssv1617026, nssv1617136, nssv1616978, nssv1617138, nssv1617123, nssv1617036, nssv1616993, nssv1616938, nssv1617056, nssv1616939, nssv1616992, nssv1617096, nssv1617049, nssv1617047, nssv1616995, nssv1616982, nssv1616932, nssv1617126, nssv1617174, nssv1617121, nssv1617071, nssv1616927, nssv1617015, nssv1616953, nssv1616950, nssv1616921, nssv1616956, nssv1617149, nssv1616962, nssv1616941, nssv1617066, nssv1616926, nssv1617141, nssv1616973, nssv1616996, nssv1617173, nssv1617070, nssv1616989, nssv1617055, nssv1616975, nssv1617155, nssv1617088, nssv1616966, nssv1616963, nssv1617156, nssv1617103, nssv1617154, nssv1617145, nssv1616936, nssv1617085, nssv1617170, nssv1616994, nssv1616987, nssv1617105, nssv1617116, nssv1617104, nssv1616988, nssv1616959, nssv1617074, nssv1616981, nssv1617043, nssv1617023, nssv1616925, nssv1617075, nssv1616942, nssv1616954, nssv1617100, nssv1617134, nssv1617014, nssv1616943, nssv1616967, nssv1616920, nssv1617167, nssv1617153, nssv1617021, nssv1617163, nssv1617119, nssv1617048, nssv1617129, nssv1617127, nssv1616998, nssv1617118, nssv1617039, nssv1616951, nssv1617171, nssv1617053, nssv1617005, nssv1617114, nssv1617172, nssv1617101, nssv1617079, nssv1617020, nssv1617112, nssv1617151, nssv1617099, nssv1617032, nssv1616928, nssv1616930, nssv1616952, nssv1617128, nssv1616985, nssv1617061, nssv1617143, nssv1616945, nssv1617150, nssv1617082, nssv1617147, nssv1617108, nssv1617038, nssv1617012, nssv1617022, nssv1617016, nssv1617017, nssv1617031, nssv1616972, nssv1617006, nssv1617095, nssv1617132, nssv1617051, nssv1617065, nssv1617122, nssv1617086, nssv1617027, nssv1617067, nssv1617098, nssv1617063, nssv1617029, nssv1616999, nssv1617072, nssv1617092, nssv1616997, nssv1617060, nssv1616971, nssv1617040, nssv1617054, nssv1617133, nssv1617125, nssv1617062, nssv1617025, nssv1617041, nssv1617130, nssv1617077, nssv1617087, nssv1617064, nssv1616976, nssv1617068, nssv1617165, nssv1616955, nssv1616937, nssv1617117, nssv1617059, nssv1617007, nssv1616934, nssv1616923, nssv1616964, nssv1617115, nssv1617158, nssv1617137, nssv1617109, nssv1617008, nssv1617120, nssv1617037, nssv1617033, nssv1616974, nssv1616977, nssv1617140, nssv1616979, nssv1616929

Samples

NA18998, NA18502, NA12717, NA19222, NA11830, NA18947, NA11995, NA19204, NA18862, NA18592, NA18508, NA12814, NA10851, NA18524, NA18980, NA18855, NA12236, NA18561, NA18507, NA19145, NA18999, NA18603, NA19092, NA12751, NA18545, NA07029, NA12004, NA12801, NA18504, NA12248, NA12146, NA12865, NA10857, NA18870, NA18526, NA18633, NA12750, NA12155, NA07357, NA18969, NA12813, NA18967, NA18563, NA19127, NA19192, NA19171, NA18944, NA18940, NA18550, NA12812, NA10835, NA10846, NA18995, NA10854, NA12802, NA19119, NA12891, NA18558, NA18547, NA19131, NA18960, NA18942, NA11992, NA07048, NA18582, NA18571, NA12762, NA19138, NA18964, NA18949, NA18611, NA12761, NA12005, NA18970, NA07019, NA12156, NA19137, NA19238, NA12044, NA11994, NA19207, NA19128, NA18966, NA19159, NA18990, NA10855, NA19209, NA10839, NA18975, NA11993, NA19007, NA11831, NA10847, NA18951, NA18605, NA19210, NA12760, NA12752, NA19120, NA07022, NA19194, NA12753, NA12003, NA10863, NA10831, NA19152, NA12878, NA12872, NA19161, NA18956, NA18859, NA19205, NA18991, NA18529, NA18516, NA18637, NA18579, NA18572, NA18976, NA18948, NA18503, NA11839, NA10838, NA18981, NA12234, NA19208, NA19221, NA18537, NA18566, NA18573, NA19000, NA11840, NA10830, NA12249, NA12056, NA18912, NA12892, NA19154, NA18857, NA18532, NA12239, NA18853, NA12264, NA12145, NA12707, NA18555, NA07345, NA12144, NA06985, NA18523, NA19160, NA19132, NA10856, NA18570, NA18593, NA18945, NA19012, NA18974, NA18576, NA12043, NA18608, NA18953, NA19094, NA19003, NA18978, NA18914, NA18632, NA11882, NA19206, NA18542, NA12716, NA11881, NA18961, NA18952, NA12864, NA18564, NA12057, NA10859, NA19140, NA18913, NA12873, NA19144, NA18992, NA10861, NA18943, NA19193, NA12874, NA07348, NA12763, NA07055, NA18594, NA19143, NA12740, NA06994, NA18971, NA19223, NA19173, NA18987, NA19211, NA19093, NA10860, NA18636, NA18521, NA18609, NA18506, NA19102, NA12875, NA18854, NA19116, NA18552, NA18852, NA07056, NA18505, NA19129, NA18968, NA18624, NA19139, NA12006, NA18522, NA12154, NA07034, NA18612, NA18622, NA19153, NA18562, NA18965, NA18577, NA11832, NA18620, NA18997

Known Genes

GSTM1, GSTM2

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)

nsv442967

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	230
Observed Complex	0
Frequency	n/a