nstd179 - Bertuzzi et al 2020 - dbVar Study

nstd179 (Bertuzzi et al. 2020)

Organism:: Human
Study Type:: Control Set
Submitter:: Stefano Gustincich
Description:: Minisatellites, also called Variable Number of Tandem Repeats (VNTRs), are a class of repetitive elements that may affect gene expression at multiple levels and have been correlated to disease. Using Cap Analysis of Gene Expression (CAGE), we describe a new example of a minisatellite hosting a TSS which expression is dependent on the repeat number. It is located in the third intron of the gene Nitrogen Permease Regulator Like Protein 3 (NPRL3). NPRL3 is a component of the GAP Activity Towards Rags 1 (GATOR1) protein complex that inhibits mammalian Target of Rapamycin Complex 1 (mTORC1) activity and it is found mutated in familial focal cortical dysplasia and familial focal epilepsy. This work provides an example of a minisatellite that is both a TSS and an eQTL as well as identifies a new VNTR that may modify mTORC1 activity. See Variant Summary counts for nstd179 in dbVar Variant Summary.
Publication(s):: Bertuzzi et al. 2020

Links

Source: NCBI

Detailed Information: Download 1 Variant Region, Download 1 Variant Call, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

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

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000016.10	Chr16	1	1	Submitted	NC_000016.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000016.9	Chr16	1	1	Remapped	NC_000016.9

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_000016.10	Chr16	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 1

Name:: Bertuzzi
Description:: Genomic DNA from blood
Size:: 1,124
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Unknown

Samples for sampleset 1 (displaying 100 of the 1124 samples)
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
1	1	Unknown	caucasian	Not reported
10	10	Unknown	caucasian	Not reported
100	100	Unknown	caucasian	Not reported
101	101	Unknown	caucasian	Not reported
102	102	Unknown	caucasian	Not reported
103	103	Unknown	caucasian	Not reported
104	104	Unknown	caucasian	Not reported
105	105	Unknown	caucasian	Not reported
106	106	Unknown	caucasian	Not reported
107	107	Unknown	caucasian	Not reported
108	108	Unknown	caucasian	Not reported
1000	1000	Unknown	caucasian	Not reported
1001	1001	Unknown	caucasian	Not reported
1002	1002	Unknown	caucasian	Not reported
1003	1003	Unknown	caucasian	Not reported
1004	1004	Unknown	caucasian	Not reported
1005	1005	Unknown	caucasian	Not reported
1006	1006	Unknown	caucasian	Not reported
1007	1007	Unknown	caucasian	Not reported
1008	1008	Unknown	caucasian	Not reported
1009	1009	Unknown	caucasian	Not reported
1010	1010	Unknown	caucasian	Not reported
1011	1011	Unknown	caucasian	Not reported
1012	1012	Unknown	caucasian	Not reported
1013	1013	Unknown	caucasian	Not reported
1014	1014	Unknown	caucasian	Not reported
1015	1015	Unknown	caucasian	Not reported
1016	1016	Unknown	caucasian	Not reported
1017	1017	Unknown	caucasian	Not reported
1018	1018	Unknown	caucasian	Not reported
1019	1019	Unknown	caucasian	Not reported
1020	1020	Unknown	caucasian	Not reported
1021	1021	Unknown	caucasian	Not reported
1022	1022	Unknown	caucasian	Not reported
1023	1023	Unknown	caucasian	Not reported
1024	1024	Unknown	caucasian	Not reported
1025	1025	Unknown	caucasian	Not reported
1026	1026	Unknown	caucasian	Not reported
1027	1027	Unknown	caucasian	Not reported
1028	1028	Unknown	caucasian	Not reported
1029	1029	Unknown	caucasian	Not reported
1030	1030	Unknown	caucasian	Not reported
1031	1031	Unknown	caucasian	Not reported
1032	1032	Unknown	caucasian	Not reported
1033	1033	Unknown	caucasian	Not reported
1034	1034	Unknown	caucasian	Not reported
1035	1035	Unknown	caucasian	Not reported
1036	1036	Unknown	caucasian	Not reported
1037	1037	Unknown	caucasian	Not reported
1038	1038	Unknown	caucasian	Not reported
1039	1039	Unknown	caucasian	Not reported
1040	1040	Unknown	caucasian	Not reported
1041	1041	Unknown	caucasian	Not reported
1042	1042	Unknown	caucasian	Not reported
1043	1043	Unknown	caucasian	Not reported
1044	1044	Unknown	caucasian	Not reported
1045	1045	Unknown	caucasian	Not reported
1046	1046	Unknown	caucasian	Not reported
1047	1047	Unknown	caucasian	Not reported
1048	1048	Unknown	caucasian	Not reported
1049	1049	Unknown	caucasian	Not reported
1050	1050	Unknown	caucasian	Not reported
1051	1051	Unknown	caucasian	Not reported
1052	1052	Unknown	caucasian	Not reported
1053	1053	Unknown	caucasian	Not reported
1054	1054	Unknown	caucasian	Not reported
1055	1055	Unknown	caucasian	Not reported
1056	1056	Unknown	caucasian	Not reported
1057	1057	Unknown	caucasian	Not reported
1058	1058	Unknown	caucasian	Not reported
1059	1059	Unknown	caucasian	Not reported
1060	1060	Unknown	caucasian	Not reported
1061	1061	Unknown	caucasian	Not reported
1062	1062	Unknown	caucasian	Not reported
1063	1063	Unknown	caucasian	Not reported
1064	1064	Unknown	caucasian	Not reported
1065	1065	Unknown	caucasian	Not reported
1066	1066	Unknown	caucasian	Not reported
1067	1067	Unknown	caucasian	Not reported
1068	1068	Unknown	caucasian	Not reported
1069	1069	Unknown	caucasian	Not reported
1070	1070	Unknown	caucasian	Not reported
1071	1071	Unknown	caucasian	Not reported
1072	1072	Unknown	caucasian	Not reported
1073	1073	Unknown	caucasian	Not reported
1074	1074	Unknown	caucasian	Not reported
1075	1075	Unknown	caucasian	Not reported
1076	1076	Unknown	caucasian	Not reported
1077	1077	Unknown	caucasian	Not reported
1078	1078	Unknown	caucasian	Not reported
1079	1079	Unknown	caucasian	Not reported
1080	1080	Unknown	caucasian	Not reported
1081	1081	Unknown	caucasian	Not reported
1082	1082	Unknown	caucasian	Not reported
1083	1083	Unknown	caucasian	Not reported
1084	1084	Unknown	caucasian	Not reported
1085	1085	Unknown	caucasian	Not reported
1086	1086	Unknown	caucasian	Not reported
1087	1087	Unknown	caucasian	Not reported
1088	1088	Unknown	caucasian	Not reported

Experimental Details

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

dbVar

Database of genomic structural variation

nstd179 (Bertuzzi et al. 2020)

Links

Detailed Information: Download 1 Variant Region, Download 1 Variant Call, Download Both, FTP

Variant Summary

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

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

nstd179 (Bertuzzi et al. 2020)

Links

Detailed Information: Download 1 Variant Region, Download 1 Variant Call, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh38->GRCh37.p13

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: