rs203339

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CIT : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0275 (8243/29940,GnomAD)
C=0289 (8415/29118,TOPMED)
C=0340 (1705/5008,1000G)
C=0186 (715/3854,ALSPAC)
C=0202 (750/3708,TWINSUK)

Position: chr12:119798950 (GRCh38.p7) (12q24.23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 75 Enhancers around

Promoter: 76 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.119798950T>C
GRCh37.p13 chr 12	NC_000012.11:g.120236754T>C
CIT RefSeqGene	NG_029792.1:g.83342A>G

Gene: CIT, citron rho-interacting serine/threonine kinase(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CIT transcript variant 1	NM_001206999.1:c.	N/A	Intron Variant
CIT transcript variant 2	NM_007174.2:c.	N/A	Intron Variant
CIT transcript variant X6	XM_006719206.2:c.	N/A	Intron Variant
CIT transcript variant X1	XM_011537783.1:c.	N/A	Intron Variant
CIT transcript variant X2	XM_011537784.1:c.	N/A	Intron Variant
CIT transcript variant X3	XM_011537785.1:c.	N/A	Intron Variant
CIT transcript variant X8	XM_011537787.1:c.	N/A	Intron Variant
CIT transcript variant X9	XM_011537788.1:c.	N/A	Intron Variant
CIT transcript variant X10	XM_011537789.1:c.	N/A	Intron Variant
CIT transcript variant X11	XM_011537790.2:c.	N/A	Intron Variant
CIT transcript variant X12	XM_011537791.2:c.	N/A	Intron Variant
CIT transcript variant X15	XM_011537792.2:c.	N/A	Intron Variant
CIT transcript variant X4	XM_017018735.1:c.	N/A	Intron Variant
CIT transcript variant X5	XM_017018736.1:c.	N/A	Intron Variant
CIT transcript variant X7	XM_017018737.1:c.	N/A	Intron Variant
CIT transcript variant X14	XM_017018739.1:c.	N/A	Intron Variant
CIT transcript variant X13	XM_017018738.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.630	C=0.370
1000Genomes	American	Sub	694	T=0.800	C=0.200
1000Genomes	East Asian	Sub	1008	T=0.452	C=0.548
1000Genomes	Europe	Sub	1006	T=0.800	C=0.200
1000Genomes	Global	Study-wide	5008	T=0.660	C=0.340
1000Genomes	South Asian	Sub	978	T=0.670	C=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.814	C=0.186
The Genome Aggregation Database	African	Sub	8700	T=0.629	C=0.371
The Genome Aggregation Database	American	Sub	838	T=0.750	C=0.250
The Genome Aggregation Database	East Asian	Sub	1618	T=0.392	C=0.608
The Genome Aggregation Database	Europe	Sub	18482	T=0.795	C=0.204
The Genome Aggregation Database	Global	Study-wide	29940	T=0.724	C=0.275
The Genome Aggregation Database	Other	Sub	302	T=0.860	C=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.711	C=0.289
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.798	C=0.202

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs203339	8.2E-05	alcoholism (heaviness of drinking)	21529783

eQTL of rs203339 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 rs203339 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 )
chr12	120187126	120187176	E067	-49578
chr12	120187309	120187353	E067	-49401
chr12	120187555	120187877	E067	-48877
chr12	120235402	120235452	E067	-1302
chr12	120235493	120235585	E067	-1169
chr12	120213978	120214028	E068	-22726
chr12	120214452	120214527	E068	-22227
chr12	120217355	120217411	E068	-19343
chr12	120217738	120217809	E068	-18945
chr12	120218977	120219035	E068	-17719
chr12	120219274	120219354	E068	-17400
chr12	120224452	120224534	E068	-12220
chr12	120224547	120224652	E068	-12102
chr12	120226720	120226884	E068	-9870
chr12	120226948	120226998	E068	-9756
chr12	120228707	120228806	E068	-7948
chr12	120234915	120235004	E068	-1750
chr12	120235402	120235452	E068	-1302
chr12	120235493	120235585	E068	-1169
chr12	120235995	120236045	E068	-709
chr12	120236306	120236408	E068	-346
chr12	120236540	120236580	E068	-174
chr12	120187309	120187353	E069	-49401
chr12	120187555	120187877	E069	-48877
chr12	120228707	120228806	E069	-7948
chr12	120228994	120229264	E069	-7490
chr12	120234915	120235004	E069	-1750
chr12	120235402	120235452	E069	-1302
chr12	120235493	120235585	E069	-1169
chr12	120235995	120236045	E069	-709
chr12	120242745	120242870	E069	5991
chr12	120187126	120187176	E070	-49578
chr12	120187309	120187353	E070	-49401
chr12	120276348	120276442	E070	39594
chr12	120277447	120277500	E070	40693
chr12	120277526	120277576	E070	40772
chr12	120277814	120277864	E070	41060
chr12	120278077	120278332	E070	41323
chr12	120278385	120278435	E070	41631
chr12	120187126	120187176	E071	-49578
chr12	120187309	120187353	E071	-49401
chr12	120187126	120187176	E072	-49578
chr12	120187309	120187353	E072	-49401
chr12	120187555	120187877	E072	-48877
chr12	120187927	120187977	E072	-48777
chr12	120188229	120188319	E072	-48435
chr12	120192128	120192189	E072	-44565
chr12	120234915	120235004	E072	-1750
chr12	120242745	120242870	E072	5991
chr12	120187126	120187176	E073	-49578
chr12	120187309	120187353	E073	-49401
chr12	120187555	120187877	E073	-48877
chr12	120217355	120217411	E073	-19343
chr12	120228572	120228669	E073	-8085
chr12	120228707	120228806	E073	-7948
chr12	120228994	120229264	E073	-7490
chr12	120236306	120236408	E073	-346
chr12	120236540	120236580	E073	-174
chr12	120242745	120242870	E073	5991
chr12	120218977	120219035	E074	-17719
chr12	120281020	120281194	E074	44266
chr12	120242745	120242870	E081	5991
chr12	120276644	120276703	E081	39890
chr12	120276751	120277056	E081	39997
chr12	120277447	120277500	E081	40693
chr12	120277526	120277576	E081	40772
chr12	120277814	120277864	E081	41060
chr12	120278077	120278332	E081	41323
chr12	120281020	120281194	E081	44266
chr12	120242745	120242870	E082	5991
chr12	120257334	120257374	E082	20580
chr12	120277814	120277864	E082	41060
chr12	120278077	120278332	E082	41323
chr12	120278385	120278435	E082	41631
chr12	120278449	120278764	E082	41695

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	120238799	120238894	E067	2045
chr12	120239477	120239591	E067	2723
chr12	120239624	120239678	E067	2870
chr12	120239797	120239911	E067	3043
chr12	120239997	120240061	E067	3243
chr12	120240151	120240244	E067	3397
chr12	120240308	120240912	E067	3554
chr12	120240920	120240975	E067	4166
chr12	120240984	120242635	E067	4230
chr12	120238799	120238894	E068	2045
chr12	120239477	120239591	E068	2723
chr12	120239624	120239678	E068	2870
chr12	120239797	120239911	E068	3043
chr12	120239997	120240061	E068	3243
chr12	120240151	120240244	E068	3397
chr12	120240308	120240912	E068	3554
chr12	120240920	120240975	E068	4166
chr12	120240984	120242635	E068	4230
chr12	120238799	120238894	E069	2045
chr12	120239477	120239591	E069	2723
chr12	120239624	120239678	E069	2870
chr12	120239797	120239911	E069	3043
chr12	120239997	120240061	E069	3243
chr12	120240151	120240244	E069	3397
chr12	120240308	120240912	E069	3554
chr12	120240920	120240975	E069	4166
chr12	120240984	120242635	E069	4230
chr12	120239797	120239911	E070	3043
chr12	120239997	120240061	E070	3243
chr12	120240151	120240244	E070	3397
chr12	120240308	120240912	E070	3554
chr12	120240920	120240975	E070	4166
chr12	120240984	120242635	E070	4230
chr12	120239477	120239591	E071	2723
chr12	120239624	120239678	E071	2870
chr12	120239797	120239911	E071	3043
chr12	120239997	120240061	E071	3243
chr12	120240151	120240244	E071	3397
chr12	120240308	120240912	E071	3554
chr12	120240920	120240975	E071	4166
chr12	120240984	120242635	E071	4230
chr12	120238799	120238894	E072	2045
chr12	120239477	120239591	E072	2723
chr12	120239624	120239678	E072	2870
chr12	120239797	120239911	E072	3043
chr12	120239997	120240061	E072	3243
chr12	120240151	120240244	E072	3397
chr12	120240308	120240912	E072	3554
chr12	120240920	120240975	E072	4166
chr12	120240984	120242635	E072	4230
chr12	120238799	120238894	E073	2045
chr12	120239477	120239591	E073	2723
chr12	120239624	120239678	E073	2870
chr12	120239797	120239911	E073	3043
chr12	120239997	120240061	E073	3243
chr12	120240151	120240244	E073	3397
chr12	120240308	120240912	E073	3554
chr12	120240920	120240975	E073	4166
chr12	120240984	120242635	E073	4230
chr12	120239477	120239591	E074	2723
chr12	120239624	120239678	E074	2870
chr12	120239797	120239911	E074	3043
chr12	120239997	120240061	E074	3243
chr12	120240151	120240244	E074	3397
chr12	120240308	120240912	E074	3554
chr12	120240920	120240975	E074	4166
chr12	120240984	120242635	E074	4230
chr12	120240984	120242635	E081	4230
chr12	120239477	120239591	E082	2723
chr12	120239624	120239678	E082	2870
chr12	120239797	120239911	E082	3043
chr12	120239997	120240061	E082	3243
chr12	120240151	120240244	E082	3397
chr12	120240308	120240912	E082	3554
chr12	120240920	120240975	E082	4166
chr12	120240984	120242635	E082	4230