U.S. flag

An official website of the United States government

nstd189 (Perez-Palma et al. 2020)

Organism:
Human
Study Type:
Case-Control
Submitter:
Eduardo Perez-Palma
Submitter URL:
https://www.ebi.ac.uk/ena/browser/view/PRJEB33136
Description:
We examined a sample of 4,778 individuals (1,929 GSD cases and 2,849 controls) including two European cohorts from Germany (n = 3,702) and one admixed Latin American cohort from Chile (n = 1,076). We detected 4,336 large and rare CNVs events (size > 100 kb, frequency < 1%). CNV burden analysis revealed a significant association of CNVs with GSD, with the strongest effect observed in men with CNVs overlapping lipid metabolism genes. See Variant Summary counts for nstd189 in dbVar Variant Summary.
Project:
PRJEB33136
Publication(s):
Pérez-Palma et al. 2020

Detailed Information: Download 2181 Variant Regions, Download 2498 Variant Calls, Download Both, FTP

Variant Summary

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

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr18486RemappedNC_000001.11
NC_000002.12Chr2101101RemappedNC_000002.12
NC_000003.12Chr39494RemappedNC_000003.12
NC_000004.12Chr48788RemappedNC_000004.12
NC_000005.10Chr54343RemappedNC_000005.10
NC_000006.12Chr6149154RemappedNC_000006.12
NC_000007.14Chr7153166RemappedNC_000007.14
NC_000008.11Chr87880RemappedNC_000008.11
NC_000009.12Chr98888RemappedNC_000009.12
NC_000010.11Chr10188204RemappedNC_000010.11
NC_000011.10Chr118585RemappedNC_000011.10
NC_000012.12Chr127177RemappedNC_000012.12
NC_000013.11Chr134950RemappedNC_000013.11
NC_000014.9Chr1486106RemappedNC_000014.9
NC_000015.10Chr15281469RemappedNC_000015.10
NC_000016.10Chr16116130RemappedNC_000016.10
NC_000017.11Chr175252RemappedNC_000017.11
NC_000018.10Chr182525RemappedNC_000018.10
NC_000019.10Chr194547RemappedNC_000019.10
NC_000020.11Chr203636RemappedNC_000020.11
NC_000021.9Chr213032RemappedNC_000021.9
NC_000022.11Chr22151194RemappedNC_000022.11
NC_000023.11ChrX8183RemappedNC_000023.11
NT_187515.1Chr1|NT_187515.111RemappedNT_187515.1
NT_187529.1Chr2|NT_187529.111RemappedNT_187529.1
NW_003315913.1Chr3|NW_003315913.111RemappedNW_003315913.1
NT_187540.1Chr4|NT_187540.111RemappedNT_187540.1
NT_187558.1Chr7|NT_187558.111RemappedNT_187558.1
NT_187561.1Chr7|NT_187561.111RemappedNT_187561.1
NT_187653.1Chr7|NT_187653.111RemappedNT_187653.1
NW_018654714.1Chr7|NW_018654714.122RemappedNW_018654714.1
NW_019805493.1Chr7|NW_019805493.166RemappedNW_019805493.1
NT_187576.1Chr8|NT_187576.11616RemappedNT_187576.1
NW_018654717.1Chr8|NW_018654717.144RemappedNW_018654717.1
NT_187581.1Chr11|NT_187581.111RemappedNT_187581.1
NW_019805497.1Chr11|NW_019805497.111RemappedNW_019805497.1
NT_187587.1Chr12|NT_187587.122RemappedNT_187587.1
NW_018654718.1Chr12|NW_018654718.111RemappedNW_018654718.1
NW_019805499.1Chr12|NW_019805499.111RemappedNW_019805499.1
NT_187600.1Chr14|NT_187600.177RemappedNT_187600.1
NT_187660.1Chr15|NT_187660.12325RemappedNT_187660.1
NT_187603.1Chr15|NT_187603.1810RemappedNT_187603.1
NW_011332701.1Chr15|NW_011332701.12325RemappedNW_011332701.1
NT_187607.1Chr16|NT_187607.11010RemappedNT_187607.1
NT_187663.1Chr17|NT_187663.111RemappedNT_187663.1
NT_187614.1Chr17|NT_187614.144RemappedNT_187614.1
NW_017363817.1Chr17|NW_017363817.111RemappedNW_017363817.1
NT_187693.1Chr19|NT_187693.144RemappedNT_187693.1
NW_003571061.2Chr19|NW_003571061.211RemappedNW_003571061.2
NW_003571055.2Chr19|NW_003571055.211RemappedNW_003571055.2
NW_003571054.1Chr19|NW_003571054.111RemappedNW_003571054.1
NT_187626.1Chr21|NT_187626.111RemappedNT_187626.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr19092SubmittedNC_000001.10
NC_000002.11Chr2101101SubmittedNC_000002.11
NC_000003.11Chr39494SubmittedNC_000003.11
NC_000004.11Chr48788SubmittedNC_000004.11
NC_000005.9Chr54343SubmittedNC_000005.9
NC_000006.11Chr6149154SubmittedNC_000006.11
NC_000007.13Chr7150163SubmittedNC_000007.13
NC_000008.10Chr87880SubmittedNC_000008.10
NC_000009.11Chr99191SubmittedNC_000009.11
NC_000010.10Chr10189205SubmittedNC_000010.10
NC_000011.9Chr118787SubmittedNC_000011.9
NC_000012.11Chr127177SubmittedNC_000012.11
NC_000013.10Chr134950SubmittedNC_000013.10
NC_000014.8Chr1486106SubmittedNC_000014.8
NC_000015.9Chr15281469SubmittedNC_000015.9
NC_000016.9Chr16111125SubmittedNC_000016.9
NC_000017.10Chr175252SubmittedNC_000017.10
NC_000018.9Chr182525SubmittedNC_000018.9
NC_000019.9Chr194850SubmittedNC_000019.9
NC_000020.10Chr203434SubmittedNC_000020.10
NC_000021.8Chr213032SubmittedNC_000021.8
NC_000022.10Chr22154197SubmittedNC_000022.10
NC_000023.10ChrX8183SubmittedNC_000023.10

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.10Chr19076451492764714
NC_000002.11Chr210177617011017761701
NC_000003.11Chr39486610194866101
NC_000004.11Chr48780240188812401
NC_000005.9Chr54342100043421000
NC_000006.11Chr614914540001541504000
NC_000007.13Chr7150123152010163133182010
NC_000008.10Chr8785521020805721020
NC_000009.11Chr9916915412916915412
NC_000010.10Chr101897321131020573212910
NC_000011.9Chr118777152287771522
NC_000012.11Chr127165020477710204
NC_000013.10Chr134947110050481100
NC_000014.8Chr148649426071065244307
NC_000015.9Chr15281421337403246942247144036
NC_000016.9Chr161113716301012537177010
NC_000017.10Chr175236550652365506
NC_000018.9Chr182524100025241000
NC_000019.9Chr194844210150462101
NC_000020.10Chr203431210034312100
NC_000021.8Chr213026300132283001
NC_000022.10Chr221549545950197132501050
NC_000023.10ChrX813934800833936800

Samplesets

Number of Samplesets: 2

Sampleset ID:
1
Name:
GSD Case
Sampleset Type:
Case
Description:
Includes samples from two European cohorts from Germany and one admixed Latin American cohort from Chile
Size:
1,929 (sample data not available)
Organisms:
Homo sapiens
Sampleset Phenotype(s):
Gallstone disease
Sampleset ID:
2
Name:
GSD Control
Sampleset Type:
Control
Description:
Includes samples from two European cohorts from Germany and one admixed Latin American cohort from Chile
Size:
2,849 (sample data not available)
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported

Experimental Details

Experiment IDTypeMethodAnalysisPlatformsNumber of Variant Calls
1DiscoverySNP arraySNP genotyping analysisAffymetrix2,498

Validations

No validation data were submitted for this study.

Support Center