U.S. flag

An official website of the United States government

nstd66 (Sebat et al. 2004)

Organism:
Human
Study Type:
Control Set
Submitter:
Database of Genomic Variants
Description:
The extent to which large duplications and deletions contribute to human genetic variation and diversity is unknown. Here, we show that large-scale copy number polymorphisms (CNPs) - about 100 kilobases and greater - contribute substantially to genomic variation between normal humans. Representational oligonucleotide microarray analysis of 20 individuals revealed a total of 221 copy number differences representing 76 unique CNPs. On average, individuals differed by 11 CNPs, and the average length of a CNP interval was 465 kilobases. We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease. See Variant Summary counts for nstd66 in dbVar Variant Summary.
Publication(s):
Sebat et al. 2004

Detailed Information: Download 81 Variant Regions, Download 239 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI35 (hg17)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr1715RemappedNC_000001.11
NC_000002.12Chr2825RemappedNC_000002.12
NC_000003.12Chr311RemappedNC_000003.12
NC_000004.12Chr4625RemappedNC_000004.12
NC_000005.10Chr5518RemappedNC_000005.10
NC_000006.12Chr6726RemappedNC_000006.12
NC_000007.14Chr736RemappedNC_000007.14
NC_000008.11Chr8715RemappedNC_000008.11
NC_000009.12Chr9622RemappedNC_000009.12
NC_000010.11Chr1011RemappedNC_000010.11
NC_000011.10Chr1122RemappedNC_000011.10
NC_000012.12Chr1233RemappedNC_000012.12
NC_000013.11Chr1345RemappedNC_000013.11
NC_000014.9Chr14333RemappedNC_000014.9
NC_000015.10Chr15524RemappedNC_000015.10
NC_000016.10Chr1636RemappedNC_000016.10
NC_000017.11Chr1724RemappedNC_000017.11
NC_000019.10Chr1911RemappedNC_000019.10
NC_000021.9Chr2111RemappedNC_000021.9
NC_000022.11Chr2233RemappedNC_000022.11
NW_018654714.1Chr7|NW_018654714.113RemappedNW_018654714.1
NT_187576.1Chr8|NT_187576.111RemappedNT_187576.1
NT_187600.1Chr14|NT_187600.1114RemappedNT_187600.1
NT_187660.1Chr15|NT_187660.111RemappedNT_187660.1
NW_011332701.1Chr15|NW_011332701.122RemappedNW_011332701.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr1715RemappedNC_000001.10
NC_000002.11Chr2825RemappedNC_000002.11
NC_000003.11Chr311RemappedNC_000003.11
NC_000004.11Chr4625RemappedNC_000004.11
NC_000005.9Chr5518RemappedNC_000005.9
NC_000006.11Chr6827RemappedNC_000006.11
NC_000007.13Chr736RemappedNC_000007.13
NC_000008.10Chr8715RemappedNC_000008.10
NC_000009.11Chr9622RemappedNC_000009.11
NC_000010.10Chr1011RemappedNC_000010.10
NC_000011.9Chr1122RemappedNC_000011.9
NC_000012.11Chr1233RemappedNC_000012.11
NC_000013.10Chr1345RemappedNC_000013.10
NC_000014.8Chr14333RemappedNC_000014.8
NC_000015.9Chr15524RemappedNC_000015.9
NC_000016.9Chr1636RemappedNC_000016.9
NC_000017.10Chr1724RemappedNC_000017.10
NC_000019.9Chr1911RemappedNC_000019.9
NC_000021.8Chr2111RemappedNC_000021.8
NC_000022.10Chr2233RemappedNC_000022.10
NW_004775427.1Chr4|NW_004775427.112RemappedNW_004775427.1
NW_003315917.2Chr5|NW_003315917.2112RemappedNW_003315917.2
NW_003571042.1Chr8|NW_003571042.111RemappedNW_003571042.1
NW_003871068.1Chr10|NW_003871068.111RemappedNW_003871068.1
NT_167251.1Chr17|NT_167251.113RemappedNT_167251.1
NW_003315949.1Chr17|NW_003315949.111RemappedNW_003315949.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.8Chr1816SubmittedNC_000001.8
NC_000002.9Chr2825SubmittedNC_000002.9
NC_000003.9Chr311SubmittedNC_000003.9
NC_000004.9Chr4625SubmittedNC_000004.9
NC_000005.8Chr5518SubmittedNC_000005.8
NC_000006.9Chr6827SubmittedNC_000006.9
NC_000007.11Chr736SubmittedNC_000007.11
NC_000008.9Chr8715SubmittedNC_000008.9
NC_000009.9Chr9622SubmittedNC_000009.9
NC_000010.8Chr1011SubmittedNC_000010.8
NC_000011.8Chr1122SubmittedNC_000011.8
NC_000012.9Chr1233SubmittedNC_000012.9
NC_000013.9Chr1345SubmittedNC_000013.9
NC_000014.7Chr14333SubmittedNC_000014.7
NC_000015.8Chr15524SubmittedNC_000015.8
NC_000016.8Chr1636SubmittedNC_000016.8
NC_000017.9Chr1735SubmittedNC_000017.9
NC_000019.8Chr1911SubmittedNC_000019.8
NC_000021.7Chr2111SubmittedNC_000021.7
NC_000022.8Chr2233SubmittedNC_000022.8

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.8Chr18502101670810
NC_000002.9Chr2870100251001500
NC_000003.9Chr3110000110000
NC_000004.9Chr465000125230002
NC_000005.8Chr554000118600012
NC_000006.9Chr688000027270000
NC_000007.11Chr7330000660000
NC_000008.9Chr87420011559001
NC_000009.9Chr964020022501700
NC_000010.8Chr10100001100001
NC_000011.8Chr11220000220000
NC_000012.9Chr12330000330000
NC_000013.9Chr13440000550000
NC_000014.7Chr1433000033330000
NC_000015.8Chr1554010024601800
NC_000016.8Chr16330000660000
NC_000017.9Chr17310101510103
NC_000019.8Chr19110000110000
NC_000021.7Chr21110000110000
NC_000022.8Chr22330000330000
Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.8Chr18403101660910
NC_000002.9Chr2870100251001500
NC_000003.9Chr3110000110000
NC_000004.9Chr465100025232000
NC_000005.8Chr555000018180000
NC_000006.9Chr686011027250110
NC_000007.11Chr7320001630003
NC_000008.9Chr87420011559001
NC_000009.9Chr964010122505012
NC_000010.8Chr10100100100100
NC_000011.8Chr11220000220000
NC_000012.9Chr12330000330000
NC_000013.9Chr13440000550000
NC_000014.7Chr14311001331810014
NC_000015.8Chr1552010224401802
NC_000016.8Chr16320100630300
NC_000017.9Chr17311010513010
NC_000019.8Chr19110000110000
NC_000021.7Chr21110000110000
NC_000022.8Chr22321000321000

Samplesets

Number of Samplesets: 1

Description:
Our study population consisted of 20 individuals from a variety of geographic backgrounds.
Size:
30
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
  • Download Samples as CSV file
    • Samples for sampleset 1
    Sample IDCell TypeSubject ID SexEthnicitySubject Phenotype
    NA12550Lymphoblastoid Cell LineGM12550FemaleFrenchNot reported
    CG0003Lymphoblastoid Cell Line5738Not reported
    SP0002Sperm2Not reported
    B0002Whole Blood2Not reported
    CG0008Whole Blood5256Not reported
    CG0009Lymphoblastoid Cell Line5256Not reported
    CG0005Lymphoblastoid Cell Line5179Not reported
    NA12548Lymphoblastoid Cell LineGM12548FemaleFrenchNot reported
    NA11524Lymphoblastoid Cell LineGM11524DruzeNot reported
    SP0004Sperm4Not reported
    NA10975Lymphoblastoid Cell LineGM10975MayanNot reported
    NA12552Lymphoblastoid Cell LineGM12552MaleFrenchNot reported
    B0008BWhole Blood8Not reported
    B0009Whole Blood9Not reported
    NA10540Lymphoblastoid Cell LineGM10540MelanesianNot reported
    NA10470Lymphoblastoid Cell LineGM10470Biaka PygmyNot reported
    CG00014Whole Blood5737Not reported
    CG0004Whole Blood5179Not reported
    B0008ASperm8Not reported
    CG10Whole Blood5264Not reported
    SP0008ASperm8Not reported
    NA10495Lymphoblastoid Cell LineGM10495Mbuti PygmyNot reported
    SP0008BWhole Blood8Not reported
    CG0002Whole Blood5738Not reported
    B0004Whole Blood4Not reported
    NA11376Lymphoblastoid Cell LineGM11376CambodianNot reported
    NA12547Lymphoblastoid Cell LineGM12547MaleFrenchNot reported
    SP0009Sperm9Not reported
    NA13181Lymphoblastoid Cell LineGM13181VenezuelanNot reported
    CG00015Lymphoblastoid Cell Line5737Not reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsNumber of Variant Calls
    1DiscoveryROMAProbe signal intensityA custom Nimblegen photoprint 85,000 probe ROMA oligo array platform was used.239

    Validations

    No validation data were submitted for this study.

    You are here: NCBI
    Support Center