rs4234445

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

TRAK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0279 (33795/120890,ExAC)
T==0284 (8510/29944,GnomAD)
T==0333 (9702/29118,TOPMED)
C=0325 (4238/13006,GO-ESP)
T==0257 (1288/5008,1000G)
T==0321 (1238/3854,ALSPAC)
T==0330 (1223/3708,TWINSUK)

Position: chr3:42184659 (GRCh38.p7) (3p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 399 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.42184659T>C
GRCh37.p13 chr 3	NC_000003.11:g.42226151T>C

Gene: TRAK1, trafficking protein, kinesin binding 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRAK1 transcript variant 1	NM_001042646.2:c.	N/A	Intron Variant
TRAK1 transcript variant 3	NM_001265608.1:c.	N/A	Intron Variant
TRAK1 transcript variant 4	NM_001265609.1:c.	N/A	Intron Variant
TRAK1 transcript variant 5	NM_001265610.1:c.	N/A	Intron Variant
TRAK1 transcript variant 2	NM_014965.4:c.	N/A	Intron Variant
TRAK1 transcript variant X2	XM_005264956.2:c.	N/A	Intron Variant
TRAK1 transcript variant X6	XM_005264958.2:c.	N/A	Intron Variant
TRAK1 transcript variant X10	XM_005264960.3:c.	N/A	Intron Variant
TRAK1 transcript variant X14	XM_005264962.3:c.	N/A	Intron Variant
TRAK1 transcript variant X17	XM_005264963.3:c.	N/A	Intron Variant
TRAK1 transcript variant X15	XM_006713029.2:c.	N/A	Intron Variant
TRAK1 transcript variant X18	XM_006713030.2:c.	N/A	Intron Variant
TRAK1 transcript variant X19	XM_006713031.3:c.	N/A	Intron Variant
TRAK1 transcript variant X16	XM_011533489.2:c.	N/A	Intron Variant
TRAK1 transcript variant X2	XM_017005906.1:c.	N/A	Intron Variant
TRAK1 transcript variant X3	XM_017005907.1:c.	N/A	Intron Variant
TRAK1 transcript variant X7	XM_017005908.1:c.	N/A	Intron Variant
TRAK1 transcript variant X8	XM_017005909.1:c.	N/A	Intron Variant
TRAK1 transcript variant X7	XM_017005910.1:c.	N/A	Intron Variant
TRAK1 transcript variant X9	XM_017005911.1:c.	N/A	Intron Variant
TRAK1 transcript variant X9	XM_017005912.1:c.	N/A	Intron Variant
TRAK1 transcript variant X12	XM_017005913.1:c.	N/A	Intron Variant
TRAK1 transcript variant X11	XR_001740058.1:n.	N/A	Intron Variant
TRAK1 transcript variant X13	XR_001740059.1:n.	N/A	Intron Variant
TRAK1 transcript variant X20	XR_001740060.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.354	C=0.646
1000Genomes	American	Sub	694	T=0.180	C=0.820
1000Genomes	East Asian	Sub	1008	T=0.021	C=0.979
1000Genomes	Europe	Sub	1006	T=0.304	C=0.696
1000Genomes	Global	Study-wide	5008	T=0.257	C=0.743
1000Genomes	South Asian	Sub	978	T=0.380	C=0.620
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.321	C=0.679
The Exome Aggregation Consortium	American	Sub	21976	T=0.235	C=0.764
The Exome Aggregation Consortium	Asian	Sub	24874	T=0.238	C=0.761
The Exome Aggregation Consortium	Europe	Sub	73136	T=0.306	C=0.693
The Exome Aggregation Consortium	Global	Study-wide	120890	T=0.279	C=0.720
The Exome Aggregation Consortium	Other	Sub	904	T=0.270	C=0.730
The Genome Aggregation Database	African	Sub	8706	T=0.344	C=0.656
The Genome Aggregation Database	American	Sub	836	T=0.150	C=0.850
The Genome Aggregation Database	East Asian	Sub	1622	T=0.018	C=0.982
The Genome Aggregation Database	Europe	Sub	18478	T=0.284	C=0.715
The Genome Aggregation Database	Global	Study-wide	29944	T=0.284	C=0.715
The Genome Aggregation Database	Other	Sub	302	T=0.310	C=0.690
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.333	C=0.666
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.330	C=0.670

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
rs4234445	0.000939	alcohol dependence	24277619

eQTL of rs4234445 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 rs4234445 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg04558973	chr3:42244357	TRAK1	-0.0350271063248282	6.1670e-14

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	42181089	42181855	E067	-44296
chr3	42182318	42182611	E067	-43540
chr3	42194052	42194144	E067	-32007
chr3	42194386	42194449	E067	-31702
chr3	42200855	42200970	E067	-25181
chr3	42201061	42201171	E067	-24980
chr3	42201208	42201991	E067	-24160
chr3	42202109	42202170	E067	-23981
chr3	42202239	42202312	E067	-23839
chr3	42202341	42202393	E067	-23758
chr3	42205107	42205219	E067	-20932
chr3	42205269	42205319	E067	-20832
chr3	42205490	42205616	E067	-20535
chr3	42205734	42206039	E067	-20112
chr3	42206076	42206166	E067	-19985
chr3	42206190	42206404	E067	-19747
chr3	42206712	42206752	E067	-19399
chr3	42206914	42206968	E067	-19183
chr3	42207591	42208091	E067	-18060
chr3	42208252	42208380	E067	-17771
chr3	42208538	42208654	E067	-17497
chr3	42211498	42211548	E067	-14603
chr3	42212952	42213002	E067	-13149
chr3	42216729	42216790	E067	-9361
chr3	42218165	42218399	E067	-7752
chr3	42218963	42219013	E067	-7138
chr3	42219060	42219221	E067	-6930
chr3	42219327	42219397	E067	-6754
chr3	42219705	42219755	E067	-6396
chr3	42219758	42219969	E067	-6182
chr3	42220527	42221292	E067	-4859
chr3	42221494	42221549	E067	-4602
chr3	42225279	42225380	E067	-771
chr3	42225644	42225764	E067	-387
chr3	42225779	42226155	E067	0
chr3	42226235	42226415	E067	84
chr3	42226552	42226944	E067	401
chr3	42232463	42233216	E067	6312
chr3	42233999	42234336	E067	7848
chr3	42237001	42237079	E067	10850
chr3	42237615	42237684	E067	11464
chr3	42237715	42237821	E067	11564
chr3	42255328	42255821	E067	29177
chr3	42256969	42257059	E067	30818
chr3	42257063	42257113	E067	30912
chr3	42271257	42271379	E067	45106
chr3	42271451	42271715	E067	45300
chr3	42201208	42201991	E068	-24160
chr3	42203291	42203411	E068	-22740
chr3	42203496	42203561	E068	-22590
chr3	42203964	42204317	E068	-21834
chr3	42205490	42205616	E068	-20535
chr3	42205734	42206039	E068	-20112
chr3	42206076	42206166	E068	-19985
chr3	42206190	42206404	E068	-19747
chr3	42206712	42206752	E068	-19399
chr3	42206914	42206968	E068	-19183
chr3	42207591	42208091	E068	-18060
chr3	42208252	42208380	E068	-17771
chr3	42208538	42208654	E068	-17497
chr3	42211213	42211279	E068	-14872
chr3	42211498	42211548	E068	-14603
chr3	42211735	42211785	E068	-14366
chr3	42211883	42211934	E068	-14217
chr3	42212952	42213002	E068	-13149
chr3	42215298	42215373	E068	-10778
chr3	42216729	42216790	E068	-9361
chr3	42217192	42217933	E068	-8218
chr3	42218165	42218399	E068	-7752
chr3	42218963	42219013	E068	-7138
chr3	42219060	42219221	E068	-6930
chr3	42219327	42219397	E068	-6754
chr3	42219705	42219755	E068	-6396
chr3	42219758	42219969	E068	-6182
chr3	42220527	42221292	E068	-4859
chr3	42221494	42221549	E068	-4602
chr3	42225078	42225194	E068	-957
chr3	42225279	42225380	E068	-771
chr3	42225644	42225764	E068	-387
chr3	42225779	42226155	E068	0
chr3	42226235	42226415	E068	84
chr3	42226552	42226944	E068	401
chr3	42229847	42229959	E068	3696
chr3	42229961	42230154	E068	3810
chr3	42232463	42233216	E068	6312
chr3	42237001	42237079	E068	10850
chr3	42237615	42237684	E068	11464
chr3	42237715	42237821	E068	11564
chr3	42255917	42256036	E068	29766
chr3	42256191	42256340	E068	30040
chr3	42256478	42256646	E068	30327
chr3	42256969	42257059	E068	30818
chr3	42257063	42257113	E068	30912
chr3	42265760	42265951	E068	39609
chr3	42266285	42266376	E068	40134
chr3	42271257	42271379	E068	45106
chr3	42271451	42271715	E068	45300
chr3	42272438	42272582	E068	46287
chr3	42189132	42189226	E069	-36925
chr3	42193246	42193357	E069	-32794
chr3	42194052	42194144	E069	-32007
chr3	42194386	42194449	E069	-31702
chr3	42201061	42201171	E069	-24980
chr3	42202109	42202170	E069	-23981
chr3	42202239	42202312	E069	-23839
chr3	42202341	42202393	E069	-23758
chr3	42203496	42203561	E069	-22590
chr3	42205269	42205319	E069	-20832
chr3	42205734	42206039	E069	-20112
chr3	42206076	42206166	E069	-19985
chr3	42206190	42206404	E069	-19747
chr3	42206712	42206752	E069	-19399
chr3	42206914	42206968	E069	-19183
chr3	42207591	42208091	E069	-18060
chr3	42209698	42209793	E069	-16358
chr3	42212952	42213002	E069	-13149
chr3	42216729	42216790	E069	-9361
chr3	42217192	42217933	E069	-8218
chr3	42218165	42218399	E069	-7752
chr3	42218963	42219013	E069	-7138
chr3	42219060	42219221	E069	-6930
chr3	42219327	42219397	E069	-6754
chr3	42219705	42219755	E069	-6396
chr3	42219758	42219969	E069	-6182
chr3	42220527	42221292	E069	-4859
chr3	42225078	42225194	E069	-957
chr3	42225279	42225380	E069	-771
chr3	42225644	42225764	E069	-387
chr3	42225779	42226155	E069	0
chr3	42226235	42226415	E069	84
chr3	42226552	42226944	E069	401
chr3	42229585	42229688	E069	3434
chr3	42231734	42231784	E069	5583
chr3	42231985	42232084	E069	5834
chr3	42232192	42232242	E069	6041
chr3	42232463	42233216	E069	6312
chr3	42233999	42234336	E069	7848
chr3	42234419	42234639	E069	8268
chr3	42265623	42265673	E069	39472
chr3	42265760	42265951	E069	39609
chr3	42266285	42266376	E069	40134
chr3	42266556	42266865	E069	40405
chr3	42271257	42271379	E069	45106
chr3	42271451	42271715	E069	45300
chr3	42185520	42185653	E070	-40498
chr3	42193246	42193357	E070	-32794
chr3	42194052	42194144	E070	-32007
chr3	42194386	42194449	E070	-31702
chr3	42200651	42200701	E070	-25450
chr3	42200855	42200970	E070	-25181
chr3	42201061	42201171	E070	-24980
chr3	42202109	42202170	E070	-23981
chr3	42202659	42202791	E070	-23360
chr3	42212952	42213002	E070	-13149
chr3	42217037	42217121	E070	-9030
chr3	42217192	42217933	E070	-8218
chr3	42225078	42225194	E070	-957
chr3	42225279	42225380	E070	-771
chr3	42225644	42225764	E070	-387
chr3	42225779	42226155	E070	0
chr3	42226235	42226415	E070	84
chr3	42226552	42226944	E070	401
chr3	42271451	42271715	E070	45300
chr3	42193246	42193357	E071	-32794
chr3	42194052	42194144	E071	-32007
chr3	42194386	42194449	E071	-31702
chr3	42200651	42200701	E071	-25450
chr3	42200855	42200970	E071	-25181
chr3	42201061	42201171	E071	-24980
chr3	42201208	42201991	E071	-24160
chr3	42205107	42205219	E071	-20932
chr3	42205269	42205319	E071	-20832
chr3	42205490	42205616	E071	-20535
chr3	42205734	42206039	E071	-20112
chr3	42206076	42206166	E071	-19985
chr3	42206190	42206404	E071	-19747
chr3	42206712	42206752	E071	-19399
chr3	42206914	42206968	E071	-19183
chr3	42207591	42208091	E071	-18060
chr3	42208252	42208380	E071	-17771
chr3	42208538	42208654	E071	-17497
chr3	42211213	42211279	E071	-14872
chr3	42211498	42211548	E071	-14603
chr3	42211735	42211785	E071	-14366
chr3	42211883	42211934	E071	-14217
chr3	42212952	42213002	E071	-13149
chr3	42216729	42216790	E071	-9361
chr3	42218165	42218399	E071	-7752
chr3	42218963	42219013	E071	-7138
chr3	42219060	42219221	E071	-6930
chr3	42219327	42219397	E071	-6754
chr3	42219705	42219755	E071	-6396
chr3	42219758	42219969	E071	-6182
chr3	42220527	42221292	E071	-4859
chr3	42221494	42221549	E071	-4602
chr3	42225078	42225194	E071	-957
chr3	42225279	42225380	E071	-771
chr3	42225644	42225764	E071	-387
chr3	42225779	42226155	E071	0
chr3	42226235	42226415	E071	84
chr3	42226552	42226944	E071	401
chr3	42231341	42231560	E071	5190
chr3	42231734	42231784	E071	5583
chr3	42231985	42232084	E071	5834
chr3	42232192	42232242	E071	6041
chr3	42232463	42233216	E071	6312
chr3	42234419	42234639	E071	8268
chr3	42271257	42271379	E071	45106
chr3	42271451	42271715	E071	45300
chr3	42194052	42194144	E072	-32007
chr3	42194386	42194449	E072	-31702
chr3	42200651	42200701	E072	-25450
chr3	42201208	42201991	E072	-24160
chr3	42202109	42202170	E072	-23981
chr3	42202239	42202312	E072	-23839
chr3	42202341	42202393	E072	-23758
chr3	42202659	42202791	E072	-23360
chr3	42205107	42205219	E072	-20932
chr3	42205269	42205319	E072	-20832
chr3	42205490	42205616	E072	-20535
chr3	42205734	42206039	E072	-20112
chr3	42206076	42206166	E072	-19985
chr3	42206190	42206404	E072	-19747
chr3	42206712	42206752	E072	-19399
chr3	42206914	42206968	E072	-19183
chr3	42207591	42208091	E072	-18060
chr3	42208252	42208380	E072	-17771
chr3	42208538	42208654	E072	-17497
chr3	42211498	42211548	E072	-14603
chr3	42211735	42211785	E072	-14366
chr3	42212952	42213002	E072	-13149
chr3	42216729	42216790	E072	-9361
chr3	42218165	42218399	E072	-7752
chr3	42218963	42219013	E072	-7138
chr3	42219060	42219221	E072	-6930
chr3	42219327	42219397	E072	-6754
chr3	42220527	42221292	E072	-4859
chr3	42224181	42224304	E072	-1847
chr3	42225078	42225194	E072	-957
chr3	42225279	42225380	E072	-771
chr3	42225644	42225764	E072	-387
chr3	42225779	42226155	E072	0
chr3	42226235	42226415	E072	84
chr3	42226552	42226944	E072	401
chr3	42230285	42231006	E072	4134
chr3	42231985	42232084	E072	5834
chr3	42232192	42232242	E072	6041
chr3	42232463	42233216	E072	6312
chr3	42234419	42234639	E072	8268
chr3	42254954	42255266	E072	28803
chr3	42255328	42255821	E072	29177
chr3	42255917	42256036	E072	29766
chr3	42256191	42256340	E072	30040
chr3	42256478	42256646	E072	30327
chr3	42265623	42265673	E072	39472
chr3	42265760	42265951	E072	39609
chr3	42266285	42266376	E072	40134
chr3	42266556	42266865	E072	40405
chr3	42271451	42271715	E072	45300
chr3	42194052	42194144	E073	-32007
chr3	42194386	42194449	E073	-31702
chr3	42201061	42201171	E073	-24980
chr3	42201208	42201991	E073	-24160
chr3	42203496	42203561	E073	-22590
chr3	42203964	42204317	E073	-21834
chr3	42205490	42205616	E073	-20535
chr3	42205734	42206039	E073	-20112
chr3	42206076	42206166	E073	-19985
chr3	42206190	42206404	E073	-19747
chr3	42206712	42206752	E073	-19399
chr3	42206914	42206968	E073	-19183
chr3	42207591	42208091	E073	-18060
chr3	42208252	42208380	E073	-17771
chr3	42208538	42208654	E073	-17497
chr3	42211498	42211548	E073	-14603
chr3	42212952	42213002	E073	-13149
chr3	42215298	42215373	E073	-10778
chr3	42215498	42215548	E073	-10603
chr3	42217037	42217121	E073	-9030
chr3	42217192	42217933	E073	-8218
chr3	42218165	42218399	E073	-7752
chr3	42218963	42219013	E073	-7138
chr3	42219060	42219221	E073	-6930
chr3	42219327	42219397	E073	-6754
chr3	42219705	42219755	E073	-6396
chr3	42219758	42219969	E073	-6182
chr3	42220527	42221292	E073	-4859
chr3	42225279	42225380	E073	-771
chr3	42225644	42225764	E073	-387
chr3	42225779	42226155	E073	0
chr3	42226235	42226415	E073	84
chr3	42226552	42226944	E073	401
chr3	42229585	42229688	E073	3434
chr3	42229847	42229959	E073	3696
chr3	42229961	42230154	E073	3810
chr3	42230285	42231006	E073	4134
chr3	42231341	42231560	E073	5190
chr3	42231734	42231784	E073	5583
chr3	42231985	42232084	E073	5834
chr3	42232192	42232242	E073	6041
chr3	42232463	42233216	E073	6312
chr3	42234419	42234639	E073	8268
chr3	42237001	42237079	E073	10850
chr3	42262145	42262263	E073	35994
chr3	42266285	42266376	E073	40134
chr3	42271257	42271379	E073	45106
chr3	42271451	42271715	E073	45300
chr3	42272438	42272582	E073	46287
chr3	42185520	42185653	E074	-40498
chr3	42185965	42186019	E074	-40132
chr3	42190049	42190156	E074	-35995
chr3	42191880	42192141	E074	-34010
chr3	42193246	42193357	E074	-32794
chr3	42200651	42200701	E074	-25450
chr3	42200855	42200970	E074	-25181
chr3	42201061	42201171	E074	-24980
chr3	42201208	42201991	E074	-24160
chr3	42202109	42202170	E074	-23981
chr3	42203496	42203561	E074	-22590
chr3	42203964	42204317	E074	-21834
chr3	42205107	42205219	E074	-20932
chr3	42205269	42205319	E074	-20832
chr3	42205490	42205616	E074	-20535
chr3	42205734	42206039	E074	-20112
chr3	42206076	42206166	E074	-19985
chr3	42206190	42206404	E074	-19747
chr3	42206712	42206752	E074	-19399
chr3	42206914	42206968	E074	-19183
chr3	42207591	42208091	E074	-18060
chr3	42209698	42209793	E074	-16358
chr3	42211498	42211548	E074	-14603
chr3	42211735	42211785	E074	-14366
chr3	42211883	42211934	E074	-14217
chr3	42212952	42213002	E074	-13149
chr3	42216729	42216790	E074	-9361
chr3	42217192	42217933	E074	-8218
chr3	42218165	42218399	E074	-7752
chr3	42218963	42219013	E074	-7138
chr3	42219060	42219221	E074	-6930
chr3	42219327	42219397	E074	-6754
chr3	42219705	42219755	E074	-6396
chr3	42219758	42219969	E074	-6182
chr3	42220527	42221292	E074	-4859
chr3	42222428	42222675	E074	-3476
chr3	42223010	42223218	E074	-2933
chr3	42224181	42224304	E074	-1847
chr3	42225078	42225194	E074	-957
chr3	42225279	42225380	E074	-771
chr3	42225644	42225764	E074	-387
chr3	42225779	42226155	E074	0
chr3	42226235	42226415	E074	84
chr3	42226552	42226944	E074	401
chr3	42230285	42231006	E074	4134
chr3	42231734	42231784	E074	5583
chr3	42231985	42232084	E074	5834
chr3	42232192	42232242	E074	6041
chr3	42232463	42233216	E074	6312
chr3	42233999	42234336	E074	7848
chr3	42234419	42234639	E074	8268
chr3	42254819	42254869	E074	28668
chr3	42254954	42255266	E074	28803
chr3	42262145	42262263	E074	35994
chr3	42271257	42271379	E074	45106
chr3	42181089	42181855	E081	-44296
chr3	42182194	42182254	E081	-43897
chr3	42182318	42182611	E081	-43540
chr3	42189132	42189226	E081	-36925
chr3	42190049	42190156	E081	-35995
chr3	42193246	42193357	E081	-32794
chr3	42194052	42194144	E081	-32007
chr3	42194386	42194449	E081	-31702
chr3	42200651	42200701	E081	-25450
chr3	42200855	42200970	E081	-25181
chr3	42201061	42201171	E081	-24980
chr3	42201208	42201991	E081	-24160
chr3	42202109	42202170	E081	-23981
chr3	42212952	42213002	E081	-13149
chr3	42271257	42271379	E081	45106
chr3	42181089	42181855	E082	-44296
chr3	42182194	42182254	E082	-43897
chr3	42182318	42182611	E082	-43540
chr3	42205490	42205616	E082	-20535
chr3	42205734	42206039	E082	-20112
chr3	42206076	42206166	E082	-19985
chr3	42206190	42206404	E082	-19747
chr3	42206712	42206752	E082	-19399
chr3	42206914	42206968	E082	-19183
chr3	42211735	42211785	E082	-14366
chr3	42211883	42211934	E082	-14217
chr3	42212952	42213002	E082	-13149
chr3	42220527	42221292	E082	-4859
chr3	42225279	42225380	E082	-771
chr3	42225644	42225764	E082	-387
chr3	42225779	42226155	E082	0
chr3	42226235	42226415	E082	84
chr3	42226552	42226944	E082	401
chr3	42231985	42232084	E082	5834
chr3	42232192	42232242	E082	6041
chr3	42271451	42271715	E082	45300