rs2164581

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CSMD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0218 (6521/29902,GnomAD)
G=0212 (6196/29118,TOPMED)
G=0351 (1760/5008,1000G)
G=0171 (660/3854,ALSPAC)
G=0172 (637/3708,TWINSUK)

Position: chr1:34025957 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 232 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.34025957A>G
GRCh37.p13 chr 1	NC_000001.10:g.34491558A>G

Gene: CSMD2, CUB and Sushi multiple domains 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CSMD2 transcript variant 1	NM_001281956.1:c.	N/A	Intron Variant
CSMD2 transcript variant 2	NM_052896.4:c.	N/A	Intron Variant
CSMD2 transcript variant X1	XM_017000185.1:c.	N/A	Intron Variant
CSMD2 transcript variant X2	XM_017000186.1:c.	N/A	Intron Variant
CSMD2 transcript variant X3	XM_017000187.1:c.	N/A	Intron Variant
CSMD2 transcript variant X4	XM_017000188.1:c.	N/A	Intron Variant
CSMD2 transcript variant X5	XM_017000189.1:c.	N/A	Intron Variant
CSMD2 transcript variant X6	XM_017000190.1:c.	N/A	Intron Variant
CSMD2 transcript variant X7	XM_017000191.1:c.	N/A	Intron Variant
CSMD2 transcript variant X8	XM_017000192.1:c.	N/A	Intron Variant
CSMD2 transcript variant X9	XM_017000193.1:c.	N/A	Intron Variant
CSMD2 transcript variant X10	XM_017000194.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.750	G=0.250
1000Genomes	American	Sub	694	A=0.680	G=0.320
1000Genomes	East Asian	Sub	1008	A=0.411	G=0.589
1000Genomes	Europe	Sub	1006	A=0.844	G=0.156
1000Genomes	Global	Study-wide	5008	A=0.649	G=0.351
1000Genomes	South Asian	Sub	978	A=0.530	G=0.470
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.829	G=0.171
The Genome Aggregation Database	African	Sub	8704	A=0.762	G=0.238
The Genome Aggregation Database	American	Sub	836	A=0.690	G=0.310
The Genome Aggregation Database	East Asian	Sub	1602	A=0.429	G=0.571
The Genome Aggregation Database	Europe	Sub	18458	A=0.824	G=0.175
The Genome Aggregation Database	Global	Study-wide	29902	A=0.781	G=0.218
The Genome Aggregation Database	Other	Sub	302	A=0.850	G=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.787	G=0.212
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.828	G=0.172

PMID	Title	Author	Journal

P-Value

SNP ID	p-value	Traits	Study
rs2164581	6.82E-05	alcoholism	pha002893

eQTL of rs2164581 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs2164581 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	34450616	34451178	E067	-40380
chr1	34451317	34451394	E067	-40164
chr1	34451412	34451583	E067	-39975
chr1	34452084	34452343	E067	-39215
chr1	34461986	34462151	E067	-29407
chr1	34462824	34462905	E067	-28653
chr1	34463010	34463147	E067	-28411
chr1	34502818	34503047	E067	11260
chr1	34503230	34503423	E067	11672
chr1	34503600	34503695	E067	12042
chr1	34504173	34504232	E067	12615
chr1	34504641	34504793	E067	13083
chr1	34516352	34516594	E067	24794
chr1	34518289	34518383	E067	26731
chr1	34522996	34523366	E067	31438
chr1	34523450	34523609	E067	31892
chr1	34523741	34523836	E067	32183
chr1	34525497	34525608	E067	33939
chr1	34525779	34526397	E067	34221
chr1	34526464	34526736	E067	34906
chr1	34526861	34527020	E067	35303
chr1	34535813	34536444	E067	44255
chr1	34536567	34536669	E067	45009
chr1	34536719	34536787	E067	45161
chr1	34540994	34541216	E067	49436
chr1	34450616	34451178	E068	-40380
chr1	34451317	34451394	E068	-40164
chr1	34451412	34451583	E068	-39975
chr1	34452084	34452343	E068	-39215
chr1	34462824	34462905	E068	-28653
chr1	34463010	34463147	E068	-28411
chr1	34510064	34510297	E068	18506
chr1	34516352	34516594	E068	24794
chr1	34516629	34517048	E068	25071
chr1	34517130	34517324	E068	25572
chr1	34517679	34517756	E068	26121
chr1	34518289	34518383	E068	26731
chr1	34522781	34522842	E068	31223
chr1	34522996	34523366	E068	31438
chr1	34523450	34523609	E068	31892
chr1	34523741	34523836	E068	32183
chr1	34525497	34525608	E068	33939
chr1	34525779	34526397	E068	34221
chr1	34526464	34526736	E068	34906
chr1	34526861	34527020	E068	35303
chr1	34535813	34536444	E068	44255
chr1	34536567	34536669	E068	45009
chr1	34536719	34536787	E068	45161
chr1	34540994	34541216	E068	49436
chr1	34450616	34451178	E069	-40380
chr1	34451317	34451394	E069	-40164
chr1	34451412	34451583	E069	-39975
chr1	34452084	34452343	E069	-39215
chr1	34461986	34462151	E069	-29407
chr1	34462824	34462905	E069	-28653
chr1	34463010	34463147	E069	-28411
chr1	34469969	34470043	E069	-21515
chr1	34516352	34516594	E069	24794
chr1	34516629	34517048	E069	25071
chr1	34517130	34517324	E069	25572
chr1	34517679	34517756	E069	26121
chr1	34518289	34518383	E069	26731
chr1	34522781	34522842	E069	31223
chr1	34522996	34523366	E069	31438
chr1	34523450	34523609	E069	31892
chr1	34523741	34523836	E069	32183
chr1	34525497	34525608	E069	33939
chr1	34525779	34526397	E069	34221
chr1	34526464	34526736	E069	34906
chr1	34526861	34527020	E069	35303
chr1	34532620	34533084	E069	41062
chr1	34535813	34536444	E069	44255
chr1	34536567	34536669	E069	45009
chr1	34536719	34536787	E069	45161
chr1	34540994	34541216	E069	49436
chr1	34450616	34451178	E070	-40380
chr1	34451317	34451394	E070	-40164
chr1	34451412	34451583	E070	-39975
chr1	34461986	34462151	E070	-29407
chr1	34462824	34462905	E070	-28653
chr1	34463010	34463147	E070	-28411
chr1	34469969	34470043	E070	-21515
chr1	34478651	34479000	E070	-12558
chr1	34497956	34498141	E070	6398
chr1	34498227	34498276	E070	6669
chr1	34498530	34498637	E070	6972
chr1	34523741	34523836	E070	32183
chr1	34525497	34525608	E070	33939
chr1	34525779	34526397	E070	34221
chr1	34526464	34526736	E070	34906
chr1	34526861	34527020	E070	35303
chr1	34535813	34536444	E070	44255
chr1	34536567	34536669	E070	45009
chr1	34536719	34536787	E070	45161
chr1	34451317	34451394	E071	-40164
chr1	34451412	34451583	E071	-39975
chr1	34452084	34452343	E071	-39215
chr1	34461986	34462151	E071	-29407
chr1	34462824	34462905	E071	-28653
chr1	34463010	34463147	E071	-28411
chr1	34465940	34466025	E071	-25533
chr1	34469969	34470043	E071	-21515
chr1	34509605	34509655	E071	18047
chr1	34510064	34510297	E071	18506
chr1	34510476	34510645	E071	18918
chr1	34516352	34516594	E071	24794
chr1	34516629	34517048	E071	25071
chr1	34517130	34517324	E071	25572
chr1	34517679	34517756	E071	26121
chr1	34518289	34518383	E071	26731
chr1	34522781	34522842	E071	31223
chr1	34522996	34523366	E071	31438
chr1	34523450	34523609	E071	31892
chr1	34523741	34523836	E071	32183
chr1	34525497	34525608	E071	33939
chr1	34525779	34526397	E071	34221
chr1	34526464	34526736	E071	34906
chr1	34526861	34527020	E071	35303
chr1	34532620	34533084	E071	41062
chr1	34535813	34536444	E071	44255
chr1	34540994	34541216	E071	49436
chr1	34450616	34451178	E072	-40380
chr1	34451317	34451394	E072	-40164
chr1	34451412	34451583	E072	-39975
chr1	34452084	34452343	E072	-39215
chr1	34460873	34461011	E072	-30547
chr1	34461986	34462151	E072	-29407
chr1	34462824	34462905	E072	-28653
chr1	34463010	34463147	E072	-28411
chr1	34478651	34479000	E072	-12558
chr1	34504173	34504232	E072	12615
chr1	34516352	34516594	E072	24794
chr1	34516629	34517048	E072	25071
chr1	34517130	34517324	E072	25572
chr1	34517679	34517756	E072	26121
chr1	34518289	34518383	E072	26731
chr1	34522781	34522842	E072	31223
chr1	34522996	34523366	E072	31438
chr1	34523450	34523609	E072	31892
chr1	34523741	34523836	E072	32183
chr1	34525497	34525608	E072	33939
chr1	34525779	34526397	E072	34221
chr1	34532620	34533084	E072	41062
chr1	34535813	34536444	E072	44255
chr1	34536567	34536669	E072	45009
chr1	34536719	34536787	E072	45161
chr1	34540994	34541216	E072	49436
chr1	34450616	34451178	E073	-40380
chr1	34451317	34451394	E073	-40164
chr1	34451412	34451583	E073	-39975
chr1	34452084	34452343	E073	-39215
chr1	34462824	34462905	E073	-28653
chr1	34463010	34463147	E073	-28411
chr1	34479684	34479922	E073	-11636
chr1	34503600	34503695	E073	12042
chr1	34516352	34516594	E073	24794
chr1	34522781	34522842	E073	31223
chr1	34522996	34523366	E073	31438
chr1	34523450	34523609	E073	31892
chr1	34523741	34523836	E073	32183
chr1	34525497	34525608	E073	33939
chr1	34525779	34526397	E073	34221
chr1	34526464	34526736	E073	34906
chr1	34526861	34527020	E073	35303
chr1	34535813	34536444	E073	44255
chr1	34540994	34541216	E073	49436
chr1	34450616	34451178	E074	-40380
chr1	34451317	34451394	E074	-40164
chr1	34451412	34451583	E074	-39975
chr1	34452084	34452343	E074	-39215
chr1	34461986	34462151	E074	-29407
chr1	34462824	34462905	E074	-28653
chr1	34463010	34463147	E074	-28411
chr1	34516352	34516594	E074	24794
chr1	34516629	34517048	E074	25071
chr1	34517130	34517324	E074	25572
chr1	34517679	34517756	E074	26121
chr1	34518289	34518383	E074	26731
chr1	34523450	34523609	E074	31892
chr1	34523741	34523836	E074	32183
chr1	34525497	34525608	E074	33939
chr1	34525779	34526397	E074	34221
chr1	34526464	34526736	E074	34906
chr1	34526861	34527020	E074	35303
chr1	34532620	34533084	E074	41062
chr1	34535813	34536444	E074	44255
chr1	34536567	34536669	E074	45009
chr1	34536719	34536787	E074	45161
chr1	34540994	34541216	E074	49436
chr1	34449979	34450033	E081	-41525
chr1	34450616	34451178	E081	-40380
chr1	34451317	34451394	E081	-40164
chr1	34451412	34451583	E081	-39975
chr1	34452084	34452343	E081	-39215
chr1	34461986	34462151	E081	-29407
chr1	34462824	34462905	E081	-28653
chr1	34463010	34463147	E081	-28411
chr1	34473453	34473763	E081	-17795
chr1	34478275	34478515	E081	-13043
chr1	34478567	34478637	E081	-12921
chr1	34478651	34479000	E081	-12558
chr1	34517679	34517756	E081	26121
chr1	34518289	34518383	E081	26731
chr1	34522781	34522842	E081	31223
chr1	34522996	34523366	E081	31438
chr1	34523450	34523609	E081	31892
chr1	34523741	34523836	E081	32183
chr1	34525497	34525608	E081	33939
chr1	34525779	34526397	E081	34221
chr1	34526464	34526736	E081	34906
chr1	34526861	34527020	E081	35303
chr1	34451317	34451394	E082	-40164
chr1	34452084	34452343	E082	-39215
chr1	34461986	34462151	E082	-29407
chr1	34462824	34462905	E082	-28653
chr1	34463010	34463147	E082	-28411
chr1	34469969	34470043	E082	-21515
chr1	34473204	34473305	E082	-18253
chr1	34478275	34478515	E082	-13043
chr1	34478567	34478637	E082	-12921
chr1	34478651	34479000	E082	-12558
chr1	34479517	34479567	E082	-11991
chr1	34479684	34479922	E082	-11636
chr1	34479998	34480275	E082	-11283
chr1	34518289	34518383	E082	26731
chr1	34523450	34523609	E082	31892
chr1	34523741	34523836	E082	32183
chr1	34525497	34525608	E082	33939
chr1	34525779	34526397	E082	34221
chr1	34526464	34526736	E082	34906
chr1	34526861	34527020	E082	35303
chr1	34540994	34541216	E082	49436