nstd142 - Rahbari et al 2017 - dbVar Study

nstd142 (Rahbari et al. 2017)

Organism:: Human
Study Type:: Control Set
Submitter:: Edward Hollox
Description:: Fcγ receptors are a family of cell-surface receptors that are expressed by a host of different innate and adaptive immune cells and mediate inflammatory responses by binding the Fc portion of immunoglobulin G (IgG). In humans, five low affinity receptors are encoded by the genes FCGR2A, FCGR2B, FCGR2C, FCGR3A and FCGR3B, which are located in a 82.5kb segmental tandem duplication on chromosome 1q23.3, which shows extensive copy number variation (CNV). We identify several alleles with gene conversion events using fosmid sequencing data. See Variant Summary counts for nstd142 in dbVar Variant Summary.
Publication(s):: Rahbari et al. 2017

Links

Source: NCBI

Detailed Information: Download 3 Variant Regions, Download 7 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	3	7	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	3	7	Remapped	NC_000001.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	3	7	Submitted	NC_000001.9

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_000001.9	Chr1	3	3	0	0	0	0	7	7	0	0	0	0

	Variant Region remap status		Variant Call remap status
NC_000001.9	Chr1	3	3	0	0	0	0	7	7	0	0	0	0

Samplesets

Number of Samplesets: 1

Description:: Fosmid sequences from eight individuals, previously submitted under accession number ERA168468
Size:: 8
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA12156	B-Lymphocyte	NA12156	Female	CEU	81 Years	Not reported
NA18507	B-Lymphocyte	NA18507	Male	YRI		Not reported
NA12878	B-Lymphocyte	NA12878	Female	CEU		Not reported
NA19129	B-Lymphocyte	NA19129	Female	YRI		Not reported
NA18956	B-Lymphocyte	NA18956	Female	JPT		Not reported
NA18517	B-Lymphocyte	NA18517	Female	YRI		Not reported
NA19240	B-Lymphocyte	NA19240	Female	YRI		Not reported
NA18555	B-Lymphocyte	NA18555	Female	CHB		Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Data	Number of Variant Calls
1	Discovery	Sequencing	Sequence alignment	SRA	7

dbVar

Database of genomic structural variation

nstd142 (Rahbari et al. 2017)

Links

Detailed Information: Download 3 Variant Regions, Download 7 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd142 (Rahbari et al. 2017)

Links

Detailed Information: Download 3 Variant Regions, Download 7 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI36 (hg18)

Remapping summary: NCBI36->GRCh37.p13NCBI36->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: