rs9876025

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CLASP2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0020 (622/29962,GnomAD)
A=0030 (894/29118,TOPMED)
A=0020 (101/5008,1000G)
A=0001 (2/3854,ALSPAC)
A=0000 (0/3708,TWINSUK)

Position: chr3:33656680 (GRCh38.p7) (3p22.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 82 Enhancers around

Promoter: 49 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.33656680G>A
GRCh37.p13 chr 3	NC_000003.11:g.33698172G>A

Gene: CLASP2, cytoplasmic linker associated protein 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLASP2 transcript variant 2	NM_001207044.1:c.	N/A	Intron Variant
CLASP2 transcript variant 1	NM_015097.2:c.	N/A	Intron Variant
CLASP2 transcript variant X1	XM_006713040.1:c.	N/A	Intron Variant
CLASP2 transcript variant X2	XM_006713041.1:c.	N/A	Intron Variant
CLASP2 transcript variant X3	XM_006713042.1:c.	N/A	Intron Variant
CLASP2 transcript variant X12	XM_006713048.1:c.	N/A	Intron Variant
CLASP2 transcript variant X15	XM_006713049.1:c.	N/A	Intron Variant
CLASP2 transcript variant X17	XM_006713050.1:c.	N/A	Intron Variant
CLASP2 transcript variant X19	XM_006713052.1:c.	N/A	Intron Variant
CLASP2 transcript variant X24	XM_006713053.1:c.	N/A	Intron Variant
CLASP2 transcript variant X6	XM_011533515.1:c.	N/A	Intron Variant
CLASP2 transcript variant X4	XM_017005947.1:c.	N/A	Intron Variant
CLASP2 transcript variant X5	XM_017005948.1:c.	N/A	Intron Variant
CLASP2 transcript variant X7	XM_017005949.1:c.	N/A	Intron Variant
CLASP2 transcript variant X8	XM_017005950.1:c.	N/A	Intron Variant
CLASP2 transcript variant X9	XM_017005951.1:c.	N/A	Intron Variant
CLASP2 transcript variant X10	XM_017005952.1:c.	N/A	Intron Variant
CLASP2 transcript variant X11	XM_017005953.1:c.	N/A	Intron Variant
CLASP2 transcript variant X13	XM_017005954.1:c.	N/A	Intron Variant
CLASP2 transcript variant X14	XM_017005955.1:c.	N/A	Intron Variant
CLASP2 transcript variant X16	XM_017005956.1:c.	N/A	Intron Variant
CLASP2 transcript variant X18	XM_017005957.1:c.	N/A	Intron Variant
CLASP2 transcript variant X20	XM_017005958.1:c.	N/A	Intron Variant
CLASP2 transcript variant X21	XM_017005959.1:c.	N/A	Intron Variant
CLASP2 transcript variant X22	XM_017005960.1:c.	N/A	Intron Variant
CLASP2 transcript variant X23	XM_017005961.1:c.	N/A	Intron Variant
CLASP2 transcript variant X25	XM_017005962.1:c.	N/A	Intron Variant
CLASP2 transcript variant X26	XM_017005963.1:c.	N/A	Intron Variant
CLASP2 transcript variant X27	XM_017005964.1:c.	N/A	Intron Variant
CLASP2 transcript variant X28	XM_017005965.1:c.	N/A	Intron Variant
CLASP2 transcript variant X29	XM_017005966.1:c.	N/A	Intron Variant
CLASP2 transcript variant X30	XM_017005967.1:c.	N/A	Intron Variant
CLASP2 transcript variant X33	XM_017005970.1:c.	N/A	Intron Variant
CLASP2 transcript variant X35	XM_017005972.1:c.	N/A	Intron Variant
CLASP2 transcript variant X36	XM_017005973.1:c.	N/A	Intron Variant
CLASP2 transcript variant X37	XM_017005974.1:c.	N/A	Intron Variant
CLASP2 transcript variant X40	XM_017005977.1:c.	N/A	Intron Variant
CLASP2 transcript variant X43	XM_017005980.1:c.	N/A	Intron Variant
CLASP2 transcript variant X46	XM_017005983.1:c.	N/A	Intron Variant
CLASP2 transcript variant X47	XM_017005984.1:c.	N/A	Intron Variant
CLASP2 transcript variant X48	XM_017005985.1:c.	N/A	Intron Variant
CLASP2 transcript variant X49	XM_017005986.1:c.	N/A	Intron Variant
CLASP2 transcript variant X31	XM_017005968.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X32	XM_017005969.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X34	XM_017005971.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X38	XM_017005975.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X39	XM_017005976.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X41	XM_017005978.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X42	XM_017005979.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X44	XM_017005981.1:c.	N/A	Genic Upstream Transcript Variant
CLASP2 transcript variant X45	XM_017005982.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.927	A=0.073
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.980	A=0.020
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.999	A=0.001
The Genome Aggregation Database	African	Sub	8732	G=0.930	A=0.070
The Genome Aggregation Database	American	Sub	836	G=0.990	A=0.010
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18472	G=0.999	A=0.000
The Genome Aggregation Database	Global	Study-wide	29962	G=0.979	A=0.020
The Genome Aggregation Database	Other	Sub	302	G=1.000	A=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.969	A=0.030
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=1.000	A=0.000

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs9876025	0.000469	alcohol dependence	21314694

eQTL of rs9876025 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 rs9876025 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 )
chr3	33654007	33655117	E067	-43055
chr3	33670858	33671027	E067	-27145
chr3	33671135	33671304	E067	-26868
chr3	33677528	33677614	E067	-20558
chr3	33677637	33677867	E067	-20305
chr3	33693615	33693960	E067	-4212
chr3	33694437	33694494	E067	-3678
chr3	33702377	33702427	E067	4205
chr3	33703103	33703295	E067	4931
chr3	33654007	33655117	E068	-43055
chr3	33670858	33671027	E068	-27145
chr3	33671135	33671304	E068	-26868
chr3	33688027	33688137	E068	-10035
chr3	33688261	33688350	E068	-9822
chr3	33693615	33693960	E068	-4212
chr3	33702377	33702427	E068	4205
chr3	33703103	33703295	E068	4931
chr3	33654007	33655117	E069	-43055
chr3	33670858	33671027	E069	-27145
chr3	33671135	33671304	E069	-26868
chr3	33677528	33677614	E069	-20558
chr3	33677637	33677867	E069	-20305
chr3	33678082	33678150	E069	-20022
chr3	33693615	33693960	E069	-4212
chr3	33697597	33697653	E069	-519
chr3	33702377	33702427	E069	4205
chr3	33688919	33688979	E070	-9193
chr3	33693615	33693960	E070	-4212
chr3	33654007	33655117	E071	-43055
chr3	33670858	33671027	E071	-27145
chr3	33671135	33671304	E071	-26868
chr3	33677528	33677614	E071	-20558
chr3	33677637	33677867	E071	-20305
chr3	33678082	33678150	E071	-20022
chr3	33688027	33688137	E071	-10035
chr3	33688261	33688350	E071	-9822
chr3	33688919	33688979	E071	-9193
chr3	33693615	33693960	E071	-4212
chr3	33702377	33702427	E071	4205
chr3	33703103	33703295	E071	4931
chr3	33654007	33655117	E072	-43055
chr3	33670858	33671027	E072	-27145
chr3	33671135	33671304	E072	-26868
chr3	33677528	33677614	E072	-20558
chr3	33677637	33677867	E072	-20305
chr3	33678082	33678150	E072	-20022
chr3	33688027	33688137	E072	-10035
chr3	33688261	33688350	E072	-9822
chr3	33693615	33693960	E072	-4212
chr3	33694238	33694298	E072	-3874
chr3	33694316	33694390	E072	-3782
chr3	33694437	33694494	E072	-3678
chr3	33702377	33702427	E072	4205
chr3	33703103	33703295	E072	4931
chr3	33654007	33655117	E073	-43055
chr3	33670858	33671027	E073	-27145
chr3	33671135	33671304	E073	-26868
chr3	33688919	33688979	E073	-9193
chr3	33693615	33693960	E073	-4212
chr3	33694238	33694298	E073	-3874
chr3	33694316	33694390	E073	-3782
chr3	33694437	33694494	E073	-3678
chr3	33702377	33702427	E073	4205
chr3	33703103	33703295	E073	4931
chr3	33654007	33655117	E074	-43055
chr3	33670858	33671027	E074	-27145
chr3	33671135	33671304	E074	-26868
chr3	33677528	33677614	E074	-20558
chr3	33678082	33678150	E074	-20022
chr3	33688027	33688137	E074	-10035
chr3	33688261	33688350	E074	-9822
chr3	33693615	33693960	E074	-4212
chr3	33702377	33702427	E074	4205
chr3	33677528	33677614	E081	-20558
chr3	33677637	33677867	E081	-20305
chr3	33678082	33678150	E081	-20022
chr3	33697597	33697653	E081	-519
chr3	33702377	33702427	E081	4205
chr3	33688027	33688137	E082	-10035
chr3	33688261	33688350	E082	-9822
chr3	33688919	33688979	E082	-9193
chr3	33702377	33702427	E082	4205

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	33685706	33685867	E067	-12305
chr3	33686090	33686401	E067	-11771
chr3	33686641	33687585	E067	-10587
chr3	33699159	33699433	E067	987
chr3	33700050	33701771	E067	1878
chr3	33685706	33685867	E068	-12305
chr3	33686090	33686401	E068	-11771
chr3	33686641	33687585	E068	-10587
chr3	33699159	33699433	E068	987
chr3	33700050	33701771	E068	1878
chr3	33685706	33685867	E069	-12305
chr3	33686090	33686401	E069	-11771
chr3	33686641	33687585	E069	-10587
chr3	33699159	33699433	E069	987
chr3	33700050	33701771	E069	1878
chr3	33685706	33685867	E070	-12305
chr3	33686090	33686401	E070	-11771
chr3	33686641	33687585	E070	-10587
chr3	33699159	33699433	E070	987
chr3	33700050	33701771	E070	1878
chr3	33685706	33685867	E071	-12305
chr3	33686090	33686401	E071	-11771
chr3	33686641	33687585	E071	-10587
chr3	33699159	33699433	E071	987
chr3	33700050	33701771	E071	1878
chr3	33685706	33685867	E072	-12305
chr3	33686090	33686401	E072	-11771
chr3	33686641	33687585	E072	-10587
chr3	33699159	33699433	E072	987
chr3	33700050	33701771	E072	1878
chr3	33685706	33685867	E073	-12305
chr3	33686090	33686401	E073	-11771
chr3	33686641	33687585	E073	-10587
chr3	33699159	33699433	E073	987
chr3	33700050	33701771	E073	1878
chr3	33686090	33686401	E074	-11771
chr3	33686641	33687585	E074	-10587
chr3	33699159	33699433	E074	987
chr3	33700050	33701771	E074	1878
chr3	33685706	33685867	E081	-12305
chr3	33686090	33686401	E081	-11771
chr3	33686641	33687585	E081	-10587
chr3	33699159	33699433	E081	987
chr3	33700050	33701771	E081	1878
chr3	33685706	33685867	E082	-12305
chr3	33686090	33686401	E082	-11771
chr3	33686641	33687585	E082	-10587
chr3	33699159	33699433	E082	987
chr3	33700050	33701771	E082	1878