nstd159 - Kucukkilic et al 2018 - dbVar Study

nstd159 (Kucukkilic et al. 2018)

Organism:: Human
Study Type:: Control Set
Submitter:: Edward Hollox
Description:: Complement receptor 1 (CR1) gene long copy repeat (LCR) copy number analysis of selected 1000 Genomes samples using paralogue ratio tests and Illumina sequence read depth data. See Variant Summary counts for nstd159 in dbVar Variant Summary.
Publication(s):: Kucukkilic et al. 2018

Links

Source: NCBI

Detailed Information: Download 2 Variant Regions, Download 350 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

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

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	2	350	Remapped	NC_000001.11

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	2	350	Submitted	NC_000001.10

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000001.10	Chr1	2	2	0	0	0	0	350	350	0	0	0	0

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Size:: 174
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1 (displaying 100 of the 174 samples)
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA18570	B-Lymphocyte	NA18570	Female			Not reported
NA12812	B-Lymphocyte	NA12812	Male	Caucasian		Not reported
NA18870	B-Lymphocyte	NA18870	Female			Not reported
NA18502	B-Lymphocyte	NA18502	Female			Not reported
NA18577	B-Lymphocyte	NA18577	Female			Not reported
NA18611	B-Lymphocyte	NA18611	Male			Not reported
NA18558	B-Lymphocyte	NA18558	Male			Not reported
NA18582	B-Lymphocyte	NA18582	Female			Not reported
NA12813	B-Lymphocyte	NA12813	Female	Caucasian		Not reported
NA18912	B-Lymphocyte	NA18912	Female			Not reported
NA18603	B-Lymphocyte	NA18603	Male			Not reported
NA12761	B-Lymphocyte	NA12761	Female	Caucasian		Not reported
NA18608	B-Lymphocyte	NA18608	Male			Not reported
NA12154	B-Lymphocyte	NA12154	Male	Caucasian	92 Years	Not reported
NA12156	B-Lymphocyte	NA12156	Female	Caucasian	81 Years	Not reported
NA11881	B-Lymphocyte	NA11881	Male	Caucasian	62 Years	Not reported
NA18609	B-Lymphocyte	NA18609	Male			Not reported
NA11831	B-Lymphocyte	NA11831	Male	Caucasian	73 Years	Not reported
NA18532	B-Lymphocyte	NA18532	Female			Not reported
NA07048	B-Lymphocyte	NA07048	Male	Caucasian	43 Years	Not reported
NA18858	B-Lymphocyte	NA18858	Female			Not reported
NA18636	B-Lymphocyte	NA18636	Male			Not reported
NA18566	B-Lymphocyte	NA18566	Female			Not reported
NA18635	B-Lymphocyte	NA18635	Male			Not reported
NA12155	B-Lymphocyte	NA12155	Male	Caucasian	86 Years	Not reported
NA12751	B-Lymphocyte	NA12751	Female	Caucasian		Not reported
NA18605	B-Lymphocyte	NA18605	Male			Not reported
NA18563	B-Lymphocyte	NA18563	Male			Not reported
NA18537	B-Lymphocyte	NA18537	Female			Not reported
NA18637	B-Lymphocyte	NA18637	Male			Not reported
NA12872	B-Lymphocyte	NA12872	Male	Caucasian		Not reported
NA11830	B-Lymphocyte	NA11830	Female	Caucasian	63 Years	Not reported
NA12249	B-Lymphocyte	NA12249	Female	Caucasian	77 Years	Not reported
NA12716	B-Lymphocyte	NA12716	Male	Caucasian		Not reported
NA18555	B-Lymphocyte	NA18555	Female			Not reported
NA12760	B-Lymphocyte	NA12760	Male	Caucasian		Not reported
NA12763	B-Lymphocyte	NA12763	Female	Caucasian		Not reported
NA18856	B-Lymphocyte	NA18856	Male			Not reported
NA18861	B-Lymphocyte	NA18861	Female			Not reported
NA11995	B-Lymphocyte	NA11995	Female	Caucasian	84 Years	Not reported
NA18526	B-Lymphocyte	NA18526	Female			Not reported
NA18853	B-Lymphocyte	NA18853	Male			Not reported
NA18612	B-Lymphocyte	NA18612	Male			Not reported
NA18564	B-Lymphocyte	NA18564	Female			Not reported
NA11829	B-Lymphocyte	NA11829	Male	Caucasian	72 Years	Not reported
NA11992	B-Lymphocyte	NA11992	Male	Caucasian	86 Years	Not reported
NA18633	B-Lymphocyte	NA18633	Male			Not reported
NA12043	B-Lymphocyte	NA12043	Male	Caucasian	74 Years	Not reported
NA18542	B-Lymphocyte	NA18542	Female			Not reported
NA12003	B-Lymphocyte	NA12003	Male	Caucasian	97 Years	Not reported
NA18501	B-Lymphocyte	NA18501	Male			Not reported
NA06985	B-Lymphocyte	NA06985	Female	Caucasian	69 Years	Not reported
NA18593	B-Lymphocyte	NA18593	Female			Not reported
NA18508	B-Lymphocyte	NA18508	Female			Not reported
NA18505	B-Lymphocyte	NA18505	Female			Not reported
NA12234	B-Lymphocyte	NA12234	Female	Caucasian	74 Years	Not reported
NA10851	B-Lymphocyte	NA10851	Male	Caucasian	52 Years	Not reported
NA12874	B-Lymphocyte	NA12874	Male	Caucasian		Not reported
NA18561	B-Lymphocyte	NA18561	Male			Not reported
NA12004	B-Lymphocyte	NA12004	Female	Caucasian	92 Years	Not reported
NA07357	B-Lymphocyte	NA07357	Male	Caucasian	69 Years	Not reported
NA06994	B-Lymphocyte	NA06994	Male	Caucasian	68 Years	Not reported
NA18550	B-Lymphocyte	NA18550	Female			Not reported
NA18620	B-Lymphocyte	NA18620	Male			Not reported
NA18579	B-Lymphocyte	NA18579	Female			Not reported
NA18562	B-Lymphocyte	NA18562	Male			Not reported
NA11840	B-Lymphocyte	NA11840	Female	Caucasian	67 Years	Not reported
NA12878	B-Lymphocyte	NA12878	Female	Caucasian		Not reported
NA18573	B-Lymphocyte	NA18573	Female			Not reported
NA18623	B-Lymphocyte	NA18623	Male			Not reported
NA11994	B-Lymphocyte	NA11994	Male	Caucasian	80 Years	Not reported
NA18571	B-Lymphocyte	NA18571	Female			Not reported
NA12005	B-Lymphocyte	NA12005	Male	Caucasian	77 Years	Not reported
NA10847	B-Lymphocyte	NA10847	Female	Caucasian	38 Years	Not reported
NA18545	B-Lymphocyte	NA18545	Female			Not reported
NA12006	B-Lymphocyte	NA12006	Female	Caucasian	75 Years	Not reported
NA12762	B-Lymphocyte	NA12762	Male	Caucasian		Not reported
NA18632	B-Lymphocyte	NA18632	Male			Not reported
NA12144	B-Lymphocyte	NA12144	Male	Caucasian	71 Years	Not reported
NA18522	B-Lymphocyte	NA18522	Male			Not reported
NA12814	B-Lymphocyte	NA12814	Male	Caucasian		Not reported
NA18622	B-Lymphocyte	NA18622	Male			Not reported
NA18523	B-Lymphocyte	NA18523	Female			Not reported
NA18624	B-Lymphocyte	NA18624	Male			Not reported
NA18516	B-Lymphocyte	NA18516	Male			Not reported
NA18547	B-Lymphocyte	NA18547	Female			Not reported
NA18572	B-Lymphocyte	NA18572	Male			Not reported
NA12717	B-Lymphocyte	NA12717	Female	Caucasian		Not reported
NA12873	B-Lymphocyte	NA12873	Female	Caucasian		Not reported
NA18871	B-Lymphocyte	NA18871	Male			Not reported
NA18621	B-Lymphocyte	NA18621	Male			Not reported
NA07056	B-Lymphocyte	NA07056	Female	Caucasian	65 Years	Not reported
NA18507	B-Lymphocyte	NA18507	Male			Not reported
NA12750	B-Lymphocyte	NA12750	Male	Caucasian		Not reported
NA18552	B-Lymphocyte	NA18552	Female			Not reported
NA07000	B-Lymphocyte	NA07000	Female	Caucasian	66 Years	Not reported
NA18517	B-Lymphocyte	NA18517	Female			Not reported
NA11832	B-Lymphocyte	NA11832	Female	Caucasian	58 Years	Not reported
NA18592	B-Lymphocyte	NA18592	Female			Not reported
NA18504	B-Lymphocyte	NA18504	Male			Not reported

Sampleset ID:: 2
Size:: 7
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Sex	Subject Phenotype
NA18555	B-Lymphocyte	NA18555	Female	Not reported
C0182		C0182		Not reported
NA19239	B-Lymphocyte	NA19239	Male	Not reported
NA18572	B-Lymphocyte	NA18572	Male	Not reported
NA18507	B-Lymphocyte	NA18507	Male	Not reported
NA18517	B-Lymphocyte	NA18517	Female	Not reported
C0140		C0140		Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Read depth	174
2	Discovery	qPCR	Probe signal intensity	176

dbVar

Database of genomic structural variation

nstd159 (Kucukkilic et al. 2018)

Links

Detailed Information: Download 2 Variant Regions, Download 350 Variant Calls, Download Both, FTP

Variant Summary

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

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd159 (Kucukkilic et al. 2018)

Links

Detailed Information: Download 2 Variant Regions, Download 350 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: