rs2358756

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CSMD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0199 (5984/29938,GnomAD)
C=0183 (5349/29118,TOPMED)
C=0327 (1639/5008,1000G)
C=0173 (665/3854,ALSPAC)
C=0172 (639/3708,TWINSUK)

Position: chr1:34014321 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 280 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.34014321T>C
GRCh37.p13 chr 1	NC_000001.10:g.34479922T>C

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	T=0.837	C=0.163
1000Genomes	American	Sub	694	T=0.690	C=0.310
1000Genomes	East Asian	Sub	1008	T=0.409	C=0.591
1000Genomes	Europe	Sub	1006	T=0.844	C=0.156
1000Genomes	Global	Study-wide	5008	T=0.673	C=0.327
1000Genomes	South Asian	Sub	978	T=0.530	C=0.470
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.827	C=0.173
The Genome Aggregation Database	African	Sub	8714	T=0.828	C=0.172
The Genome Aggregation Database	American	Sub	838	T=0.700	C=0.300
The Genome Aggregation Database	East Asian	Sub	1608	T=0.416	C=0.584
The Genome Aggregation Database	Europe	Sub	18476	T=0.824	C=0.175
The Genome Aggregation Database	Global	Study-wide	29938	T=0.800	C=0.199
The Genome Aggregation Database	Other	Sub	302	T=0.850	C=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.816	C=0.183
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.828	C=0.172

PMID	Title	Author	Journal

P-Value

SNP ID	p-value	Traits	Study
rs2358756	2.73E-05	alcoholism	pha002893

eQTL of rs2358756 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 rs2358756 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	34436872	34436950	E067	-42972
chr1	34436985	34437035	E067	-42887
chr1	34437068	34437170	E067	-42752
chr1	34437670	34437753	E067	-42169
chr1	34438469	34438523	E067	-41399
chr1	34438564	34438927	E067	-40995
chr1	34439191	34439263	E067	-40659
chr1	34439787	34440041	E067	-39881
chr1	34440187	34440241	E067	-39681
chr1	34450616	34451178	E067	-28744
chr1	34451317	34451394	E067	-28528
chr1	34451412	34451583	E067	-28339
chr1	34452084	34452343	E067	-27579
chr1	34461986	34462151	E067	-17771
chr1	34462824	34462905	E067	-17017
chr1	34463010	34463147	E067	-16775
chr1	34502818	34503047	E067	22896
chr1	34503230	34503423	E067	23308
chr1	34503600	34503695	E067	23678
chr1	34504173	34504232	E067	24251
chr1	34504641	34504793	E067	24719
chr1	34516352	34516594	E067	36430
chr1	34518289	34518383	E067	38367
chr1	34522996	34523366	E067	43074
chr1	34523450	34523609	E067	43528
chr1	34523741	34523836	E067	43819
chr1	34525497	34525608	E067	45575
chr1	34525779	34526397	E067	45857
chr1	34526464	34526736	E067	46542
chr1	34526861	34527020	E067	46939
chr1	34436872	34436950	E068	-42972
chr1	34436985	34437035	E068	-42887
chr1	34437068	34437170	E068	-42752
chr1	34437670	34437753	E068	-42169
chr1	34438469	34438523	E068	-41399
chr1	34438564	34438927	E068	-40995
chr1	34439191	34439263	E068	-40659
chr1	34439787	34440041	E068	-39881
chr1	34440187	34440241	E068	-39681
chr1	34450616	34451178	E068	-28744
chr1	34451317	34451394	E068	-28528
chr1	34451412	34451583	E068	-28339
chr1	34452084	34452343	E068	-27579
chr1	34462824	34462905	E068	-17017
chr1	34463010	34463147	E068	-16775
chr1	34510064	34510297	E068	30142
chr1	34516352	34516594	E068	36430
chr1	34516629	34517048	E068	36707
chr1	34517130	34517324	E068	37208
chr1	34517679	34517756	E068	37757
chr1	34518289	34518383	E068	38367
chr1	34522781	34522842	E068	42859
chr1	34522996	34523366	E068	43074
chr1	34523450	34523609	E068	43528
chr1	34523741	34523836	E068	43819
chr1	34525497	34525608	E068	45575
chr1	34525779	34526397	E068	45857
chr1	34526464	34526736	E068	46542
chr1	34526861	34527020	E068	46939
chr1	34436872	34436950	E069	-42972
chr1	34436985	34437035	E069	-42887
chr1	34437068	34437170	E069	-42752
chr1	34437670	34437753	E069	-42169
chr1	34438469	34438523	E069	-41399
chr1	34438564	34438927	E069	-40995
chr1	34439191	34439263	E069	-40659
chr1	34439787	34440041	E069	-39881
chr1	34440187	34440241	E069	-39681
chr1	34450616	34451178	E069	-28744
chr1	34451317	34451394	E069	-28528
chr1	34451412	34451583	E069	-28339
chr1	34452084	34452343	E069	-27579
chr1	34461986	34462151	E069	-17771
chr1	34462824	34462905	E069	-17017
chr1	34463010	34463147	E069	-16775
chr1	34469969	34470043	E069	-9879
chr1	34516352	34516594	E069	36430
chr1	34516629	34517048	E069	36707
chr1	34517130	34517324	E069	37208
chr1	34517679	34517756	E069	37757
chr1	34518289	34518383	E069	38367
chr1	34522781	34522842	E069	42859
chr1	34522996	34523366	E069	43074
chr1	34523450	34523609	E069	43528
chr1	34523741	34523836	E069	43819
chr1	34525497	34525608	E069	45575
chr1	34525779	34526397	E069	45857
chr1	34526464	34526736	E069	46542
chr1	34526861	34527020	E069	46939
chr1	34436872	34436950	E070	-42972
chr1	34436985	34437035	E070	-42887
chr1	34437068	34437170	E070	-42752
chr1	34438469	34438523	E070	-41399
chr1	34438564	34438927	E070	-40995
chr1	34439191	34439263	E070	-40659
chr1	34439787	34440041	E070	-39881
chr1	34440187	34440241	E070	-39681
chr1	34450616	34451178	E070	-28744
chr1	34451317	34451394	E070	-28528
chr1	34451412	34451583	E070	-28339
chr1	34461986	34462151	E070	-17771
chr1	34462824	34462905	E070	-17017
chr1	34463010	34463147	E070	-16775
chr1	34469969	34470043	E070	-9879
chr1	34478651	34479000	E070	-922
chr1	34497956	34498141	E070	18034
chr1	34498227	34498276	E070	18305
chr1	34498530	34498637	E070	18608
chr1	34523741	34523836	E070	43819
chr1	34525497	34525608	E070	45575
chr1	34525779	34526397	E070	45857
chr1	34526464	34526736	E070	46542
chr1	34526861	34527020	E070	46939
chr1	34436872	34436950	E071	-42972
chr1	34436985	34437035	E071	-42887
chr1	34437068	34437170	E071	-42752
chr1	34437670	34437753	E071	-42169
chr1	34438469	34438523	E071	-41399
chr1	34438564	34438927	E071	-40995
chr1	34439191	34439263	E071	-40659
chr1	34439787	34440041	E071	-39881
chr1	34440187	34440241	E071	-39681
chr1	34451317	34451394	E071	-28528
chr1	34451412	34451583	E071	-28339
chr1	34452084	34452343	E071	-27579
chr1	34461986	34462151	E071	-17771
chr1	34462824	34462905	E071	-17017
chr1	34463010	34463147	E071	-16775
chr1	34465940	34466025	E071	-13897
chr1	34469969	34470043	E071	-9879
chr1	34509605	34509655	E071	29683
chr1	34510064	34510297	E071	30142
chr1	34510476	34510645	E071	30554
chr1	34516352	34516594	E071	36430
chr1	34516629	34517048	E071	36707
chr1	34517130	34517324	E071	37208
chr1	34517679	34517756	E071	37757
chr1	34518289	34518383	E071	38367
chr1	34522781	34522842	E071	42859
chr1	34522996	34523366	E071	43074
chr1	34523450	34523609	E071	43528
chr1	34523741	34523836	E071	43819
chr1	34525497	34525608	E071	45575
chr1	34525779	34526397	E071	45857
chr1	34526464	34526736	E071	46542
chr1	34526861	34527020	E071	46939
chr1	34436872	34436950	E072	-42972
chr1	34436985	34437035	E072	-42887
chr1	34437068	34437170	E072	-42752
chr1	34437670	34437753	E072	-42169
chr1	34438469	34438523	E072	-41399
chr1	34438564	34438927	E072	-40995
chr1	34439787	34440041	E072	-39881
chr1	34440187	34440241	E072	-39681
chr1	34450616	34451178	E072	-28744
chr1	34451317	34451394	E072	-28528
chr1	34451412	34451583	E072	-28339
chr1	34452084	34452343	E072	-27579
chr1	34460873	34461011	E072	-18911
chr1	34461986	34462151	E072	-17771
chr1	34462824	34462905	E072	-17017
chr1	34463010	34463147	E072	-16775
chr1	34478651	34479000	E072	-922
chr1	34504173	34504232	E072	24251
chr1	34516352	34516594	E072	36430
chr1	34516629	34517048	E072	36707
chr1	34517130	34517324	E072	37208
chr1	34517679	34517756	E072	37757
chr1	34518289	34518383	E072	38367
chr1	34522781	34522842	E072	42859
chr1	34522996	34523366	E072	43074
chr1	34523450	34523609	E072	43528
chr1	34523741	34523836	E072	43819
chr1	34525497	34525608	E072	45575
chr1	34525779	34526397	E072	45857
chr1	34436872	34436950	E073	-42972
chr1	34436985	34437035	E073	-42887
chr1	34437068	34437170	E073	-42752
chr1	34437670	34437753	E073	-42169
chr1	34438469	34438523	E073	-41399
chr1	34438564	34438927	E073	-40995
chr1	34439787	34440041	E073	-39881
chr1	34440187	34440241	E073	-39681
chr1	34450616	34451178	E073	-28744
chr1	34451317	34451394	E073	-28528
chr1	34451412	34451583	E073	-28339
chr1	34452084	34452343	E073	-27579
chr1	34462824	34462905	E073	-17017
chr1	34463010	34463147	E073	-16775
chr1	34479684	34479922	E073	0
chr1	34503600	34503695	E073	23678
chr1	34516352	34516594	E073	36430
chr1	34522781	34522842	E073	42859
chr1	34522996	34523366	E073	43074
chr1	34523450	34523609	E073	43528
chr1	34523741	34523836	E073	43819
chr1	34525497	34525608	E073	45575
chr1	34525779	34526397	E073	45857
chr1	34526464	34526736	E073	46542
chr1	34526861	34527020	E073	46939
chr1	34436872	34436950	E074	-42972
chr1	34436985	34437035	E074	-42887
chr1	34437068	34437170	E074	-42752
chr1	34437670	34437753	E074	-42169
chr1	34438469	34438523	E074	-41399
chr1	34438564	34438927	E074	-40995
chr1	34439191	34439263	E074	-40659
chr1	34439787	34440041	E074	-39881
chr1	34440187	34440241	E074	-39681
chr1	34450616	34451178	E074	-28744
chr1	34451317	34451394	E074	-28528
chr1	34451412	34451583	E074	-28339
chr1	34452084	34452343	E074	-27579
chr1	34461986	34462151	E074	-17771
chr1	34462824	34462905	E074	-17017
chr1	34463010	34463147	E074	-16775
chr1	34516352	34516594	E074	36430
chr1	34516629	34517048	E074	36707
chr1	34517130	34517324	E074	37208
chr1	34517679	34517756	E074	37757
chr1	34518289	34518383	E074	38367
chr1	34523450	34523609	E074	43528
chr1	34523741	34523836	E074	43819
chr1	34525497	34525608	E074	45575
chr1	34525779	34526397	E074	45857
chr1	34526464	34526736	E074	46542
chr1	34526861	34527020	E074	46939
chr1	34437670	34437753	E081	-42169
chr1	34438469	34438523	E081	-41399
chr1	34438564	34438927	E081	-40995
chr1	34439191	34439263	E081	-40659
chr1	34439787	34440041	E081	-39881
chr1	34440187	34440241	E081	-39681
chr1	34449979	34450033	E081	-29889
chr1	34450616	34451178	E081	-28744
chr1	34451317	34451394	E081	-28528
chr1	34451412	34451583	E081	-28339
chr1	34452084	34452343	E081	-27579
chr1	34461986	34462151	E081	-17771
chr1	34462824	34462905	E081	-17017
chr1	34463010	34463147	E081	-16775
chr1	34473453	34473763	E081	-6159
chr1	34478275	34478515	E081	-1407
chr1	34478567	34478637	E081	-1285
chr1	34478651	34479000	E081	-922
chr1	34517679	34517756	E081	37757
chr1	34518289	34518383	E081	38367
chr1	34522781	34522842	E081	42859
chr1	34522996	34523366	E081	43074
chr1	34523450	34523609	E081	43528
chr1	34523741	34523836	E081	43819
chr1	34525497	34525608	E081	45575
chr1	34525779	34526397	E081	45857
chr1	34526464	34526736	E081	46542
chr1	34526861	34527020	E081	46939
chr1	34438469	34438523	E082	-41399
chr1	34438564	34438927	E082	-40995
chr1	34439191	34439263	E082	-40659
chr1	34439787	34440041	E082	-39881
chr1	34440187	34440241	E082	-39681
chr1	34451317	34451394	E082	-28528
chr1	34452084	34452343	E082	-27579
chr1	34461986	34462151	E082	-17771
chr1	34462824	34462905	E082	-17017
chr1	34463010	34463147	E082	-16775
chr1	34469969	34470043	E082	-9879
chr1	34473204	34473305	E082	-6617
chr1	34478275	34478515	E082	-1407
chr1	34478567	34478637	E082	-1285
chr1	34478651	34479000	E082	-922
chr1	34479517	34479567	E082	-355
chr1	34479684	34479922	E082	0
chr1	34479998	34480275	E082	76
chr1	34518289	34518383	E082	38367
chr1	34523450	34523609	E082	43528
chr1	34523741	34523836	E082	43819
chr1	34525497	34525608	E082	45575
chr1	34525779	34526397	E082	45857
chr1	34526464	34526736	E082	46542
chr1	34526861	34527020	E082	46939