rs2625684

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CSMD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0309 (9277/29936,GnomAD)
T==0300 (8754/29118,TOPMED)
T==0245 (1229/5008,1000G)
T==0343 (1323/3854,ALSPAC)
T==0338 (1252/3708,TWINSUK)

Position: chr1:34039514 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 217 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.34039514T>C
GRCh37.p13 chr 1	NC_000001.10:g.34505115T>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=0.248	C=0.752
1000Genomes	American	Sub	694	T=0.210	C=0.790
1000Genomes	East Asian	Sub	1008	T=0.196	C=0.804
1000Genomes	Europe	Sub	1006	T=0.340	C=0.660
1000Genomes	Global	Study-wide	5008	T=0.245	C=0.755
1000Genomes	South Asian	Sub	978	T=0.220	C=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.343	C=0.657
The Genome Aggregation Database	African	Sub	8718	T=0.272	C=0.728
The Genome Aggregation Database	American	Sub	834	T=0.200	C=0.800
The Genome Aggregation Database	East Asian	Sub	1616	T=0.181	C=0.819
The Genome Aggregation Database	Europe	Sub	18466	T=0.342	C=0.657
The Genome Aggregation Database	Global	Study-wide	29936	T=0.309	C=0.690
The Genome Aggregation Database	Other	Sub	302	T=0.380	C=0.620
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.300	C=0.699
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.338	C=0.662

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs2625684	0.000765	alcohol consumption (maxi-drinks)	24277619

eQTL of rs2625684 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 rs2625684 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	34461986	34462151	E067	-42964
chr1	34462824	34462905	E067	-42210
chr1	34463010	34463147	E067	-41968
chr1	34502818	34503047	E067	-2068
chr1	34503230	34503423	E067	-1692
chr1	34503600	34503695	E067	-1420
chr1	34504173	34504232	E067	-883
chr1	34504641	34504793	E067	-322
chr1	34516352	34516594	E067	11237
chr1	34518289	34518383	E067	13174
chr1	34522996	34523366	E067	17881
chr1	34523450	34523609	E067	18335
chr1	34523741	34523836	E067	18626
chr1	34525497	34525608	E067	20382
chr1	34525779	34526397	E067	20664
chr1	34526464	34526736	E067	21349
chr1	34526861	34527020	E067	21746
chr1	34535813	34536444	E067	30698
chr1	34536567	34536669	E067	31452
chr1	34536719	34536787	E067	31604
chr1	34540994	34541216	E067	35879
chr1	34541231	34541578	E067	36116
chr1	34541597	34541662	E067	36482
chr1	34462824	34462905	E068	-42210
chr1	34463010	34463147	E068	-41968
chr1	34510064	34510297	E068	4949
chr1	34516352	34516594	E068	11237
chr1	34516629	34517048	E068	11514
chr1	34517130	34517324	E068	12015
chr1	34517679	34517756	E068	12564
chr1	34518289	34518383	E068	13174
chr1	34522781	34522842	E068	17666
chr1	34522996	34523366	E068	17881
chr1	34523450	34523609	E068	18335
chr1	34523741	34523836	E068	18626
chr1	34525497	34525608	E068	20382
chr1	34525779	34526397	E068	20664
chr1	34526464	34526736	E068	21349
chr1	34526861	34527020	E068	21746
chr1	34535813	34536444	E068	30698
chr1	34536567	34536669	E068	31452
chr1	34536719	34536787	E068	31604
chr1	34540994	34541216	E068	35879
chr1	34541231	34541578	E068	36116
chr1	34541597	34541662	E068	36482
chr1	34461986	34462151	E069	-42964
chr1	34462824	34462905	E069	-42210
chr1	34463010	34463147	E069	-41968
chr1	34469969	34470043	E069	-35072
chr1	34516352	34516594	E069	11237
chr1	34516629	34517048	E069	11514
chr1	34517130	34517324	E069	12015
chr1	34517679	34517756	E069	12564
chr1	34518289	34518383	E069	13174
chr1	34522781	34522842	E069	17666
chr1	34522996	34523366	E069	17881
chr1	34523450	34523609	E069	18335
chr1	34523741	34523836	E069	18626
chr1	34525497	34525608	E069	20382
chr1	34525779	34526397	E069	20664
chr1	34526464	34526736	E069	21349
chr1	34526861	34527020	E069	21746
chr1	34532620	34533084	E069	27505
chr1	34535813	34536444	E069	30698
chr1	34536567	34536669	E069	31452
chr1	34536719	34536787	E069	31604
chr1	34540994	34541216	E069	35879
chr1	34541231	34541578	E069	36116
chr1	34541597	34541662	E069	36482
chr1	34461986	34462151	E070	-42964
chr1	34462824	34462905	E070	-42210
chr1	34463010	34463147	E070	-41968
chr1	34469969	34470043	E070	-35072
chr1	34478651	34479000	E070	-26115
chr1	34497956	34498141	E070	-6974
chr1	34498227	34498276	E070	-6839
chr1	34498530	34498637	E070	-6478
chr1	34523741	34523836	E070	18626
chr1	34525497	34525608	E070	20382
chr1	34525779	34526397	E070	20664
chr1	34526464	34526736	E070	21349
chr1	34526861	34527020	E070	21746
chr1	34535813	34536444	E070	30698
chr1	34536567	34536669	E070	31452
chr1	34536719	34536787	E070	31604
chr1	34541231	34541578	E070	36116
chr1	34541597	34541662	E070	36482
chr1	34553670	34553841	E070	48555
chr1	34553913	34553963	E070	48798
chr1	34461986	34462151	E071	-42964
chr1	34462824	34462905	E071	-42210
chr1	34463010	34463147	E071	-41968
chr1	34465940	34466025	E071	-39090
chr1	34469969	34470043	E071	-35072
chr1	34509605	34509655	E071	4490
chr1	34510064	34510297	E071	4949
chr1	34510476	34510645	E071	5361
chr1	34516352	34516594	E071	11237
chr1	34516629	34517048	E071	11514
chr1	34517130	34517324	E071	12015
chr1	34517679	34517756	E071	12564
chr1	34518289	34518383	E071	13174
chr1	34522781	34522842	E071	17666
chr1	34522996	34523366	E071	17881
chr1	34523450	34523609	E071	18335
chr1	34523741	34523836	E071	18626
chr1	34525497	34525608	E071	20382
chr1	34525779	34526397	E071	20664
chr1	34526464	34526736	E071	21349
chr1	34526861	34527020	E071	21746
chr1	34532620	34533084	E071	27505
chr1	34535813	34536444	E071	30698
chr1	34540994	34541216	E071	35879
chr1	34541231	34541578	E071	36116
chr1	34541597	34541662	E071	36482
chr1	34460873	34461011	E072	-44104
chr1	34461986	34462151	E072	-42964
chr1	34462824	34462905	E072	-42210
chr1	34463010	34463147	E072	-41968
chr1	34478651	34479000	E072	-26115
chr1	34504173	34504232	E072	-883
chr1	34516352	34516594	E072	11237
chr1	34516629	34517048	E072	11514
chr1	34517130	34517324	E072	12015
chr1	34517679	34517756	E072	12564
chr1	34518289	34518383	E072	13174
chr1	34522781	34522842	E072	17666
chr1	34522996	34523366	E072	17881
chr1	34523450	34523609	E072	18335
chr1	34523741	34523836	E072	18626
chr1	34525497	34525608	E072	20382
chr1	34525779	34526397	E072	20664
chr1	34532620	34533084	E072	27505
chr1	34535813	34536444	E072	30698
chr1	34536567	34536669	E072	31452
chr1	34536719	34536787	E072	31604
chr1	34540994	34541216	E072	35879
chr1	34541231	34541578	E072	36116
chr1	34541597	34541662	E072	36482
chr1	34542062	34542178	E072	36947
chr1	34549656	34549699	E072	44541
chr1	34462824	34462905	E073	-42210
chr1	34463010	34463147	E073	-41968
chr1	34479684	34479922	E073	-25193
chr1	34503600	34503695	E073	-1420
chr1	34516352	34516594	E073	11237
chr1	34522781	34522842	E073	17666
chr1	34522996	34523366	E073	17881
chr1	34523450	34523609	E073	18335
chr1	34523741	34523836	E073	18626
chr1	34525497	34525608	E073	20382
chr1	34525779	34526397	E073	20664
chr1	34526464	34526736	E073	21349
chr1	34526861	34527020	E073	21746
chr1	34535813	34536444	E073	30698
chr1	34540994	34541216	E073	35879
chr1	34461986	34462151	E074	-42964
chr1	34462824	34462905	E074	-42210
chr1	34463010	34463147	E074	-41968
chr1	34516352	34516594	E074	11237
chr1	34516629	34517048	E074	11514
chr1	34517130	34517324	E074	12015
chr1	34517679	34517756	E074	12564
chr1	34518289	34518383	E074	13174
chr1	34523450	34523609	E074	18335
chr1	34523741	34523836	E074	18626
chr1	34525497	34525608	E074	20382
chr1	34525779	34526397	E074	20664
chr1	34526464	34526736	E074	21349
chr1	34526861	34527020	E074	21746
chr1	34532620	34533084	E074	27505
chr1	34535813	34536444	E074	30698
chr1	34536567	34536669	E074	31452
chr1	34536719	34536787	E074	31604
chr1	34540994	34541216	E074	35879
chr1	34541231	34541578	E074	36116
chr1	34541597	34541662	E074	36482
chr1	34461986	34462151	E081	-42964
chr1	34462824	34462905	E081	-42210
chr1	34463010	34463147	E081	-41968
chr1	34473453	34473763	E081	-31352
chr1	34478275	34478515	E081	-26600
chr1	34478567	34478637	E081	-26478
chr1	34478651	34479000	E081	-26115
chr1	34517679	34517756	E081	12564
chr1	34518289	34518383	E081	13174
chr1	34522781	34522842	E081	17666
chr1	34522996	34523366	E081	17881
chr1	34523450	34523609	E081	18335
chr1	34523741	34523836	E081	18626
chr1	34525497	34525608	E081	20382
chr1	34525779	34526397	E081	20664
chr1	34526464	34526736	E081	21349
chr1	34526861	34527020	E081	21746
chr1	34553670	34553841	E081	48555
chr1	34553913	34553963	E081	48798
chr1	34461986	34462151	E082	-42964
chr1	34462824	34462905	E082	-42210
chr1	34463010	34463147	E082	-41968
chr1	34469969	34470043	E082	-35072
chr1	34473204	34473305	E082	-31810
chr1	34478275	34478515	E082	-26600
chr1	34478567	34478637	E082	-26478
chr1	34478651	34479000	E082	-26115
chr1	34479517	34479567	E082	-25548
chr1	34479684	34479922	E082	-25193
chr1	34479998	34480275	E082	-24840
chr1	34518289	34518383	E082	13174
chr1	34523450	34523609	E082	18335
chr1	34523741	34523836	E082	18626
chr1	34525497	34525608	E082	20382
chr1	34525779	34526397	E082	20664
chr1	34526464	34526736	E082	21349
chr1	34526861	34527020	E082	21746
chr1	34540994	34541216	E082	35879
chr1	34541231	34541578	E082	36116
chr1	34541597	34541662	E082	36482