rs11928109

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

TRAK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0186 (5572/29918,GnomAD)
A=0243 (7086/29118,TOPMED)
A=0207 (1039/5008,1000G)
A=0079 (305/3854,ALSPAC)
A=0070 (258/3708,TWINSUK)

Position: chr3:42217807 (GRCh38.p7) (3p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 248 Enhancers around

Promoter: 12 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.42217807G>A
GRCh37.p13 chr 3	NC_000003.11:g.42259299G>A

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	Genic Downstream Transcript Variant
TRAK1 transcript variant 4	NM_001265609.1:c.	N/A	Genic Downstream Transcript Variant
TRAK1 transcript variant 5	NM_001265610.1:c.	N/A	Genic Downstream Transcript Variant
TRAK1 transcript variant 2	NM_014965.4:c.	N/A	Genic Downstream Transcript 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 X15	XM_006713029.2:c.	N/A	Intron Variant
TRAK1 transcript variant X18	XM_006713030.2: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 X14	XM_005264962.3:c.	N/A	3 Prime UTR Variant
TRAK1 transcript variant X17	XM_005264963.3:c.	N/A	3 Prime UTR Variant
TRAK1 transcript variant X19	XM_006713031.3:c.	N/A	Genic Downstream Transcript Variant
TRAK1 transcript variant X16	XM_011533489.2:c.	N/A	Genic Downstream Transcript 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	G=0.480	A=0.520
1000Genomes	American	Sub	694	G=0.880	A=0.120
1000Genomes	East Asian	Sub	1008	G=0.907	A=0.093
1000Genomes	Europe	Sub	1006	G=0.914	A=0.086
1000Genomes	Global	Study-wide	5008	G=0.793	A=0.207
1000Genomes	South Asian	Sub	978	G=0.910	A=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.921	A=0.079
The Genome Aggregation Database	African	Sub	8702	G=0.561	A=0.439
The Genome Aggregation Database	American	Sub	838	G=0.890	A=0.110
The Genome Aggregation Database	East Asian	Sub	1620	G=0.910	A=0.090
The Genome Aggregation Database	Europe	Sub	18456	G=0.918	A=0.081
The Genome Aggregation Database	Global	Study-wide	29918	G=0.813	A=0.186
The Genome Aggregation Database	Other	Sub	302	G=0.960	A=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.756	A=0.243
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.930	A=0.070

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
rs11928109	0.000586	alcohol consumption (maxi-drinks)	24277619

eQTL of rs11928109 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 rs11928109 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	42211498	42211548	E067	-47751
chr3	42212952	42213002	E067	-46297
chr3	42216729	42216790	E067	-42509
chr3	42218165	42218399	E067	-40900
chr3	42218963	42219013	E067	-40286
chr3	42219060	42219221	E067	-40078
chr3	42219327	42219397	E067	-39902
chr3	42219705	42219755	E067	-39544
chr3	42219758	42219969	E067	-39330
chr3	42220527	42221292	E067	-38007
chr3	42221494	42221549	E067	-37750
chr3	42225279	42225380	E067	-33919
chr3	42225644	42225764	E067	-33535
chr3	42225779	42226155	E067	-33144
chr3	42226235	42226415	E067	-32884
chr3	42226552	42226944	E067	-32355
chr3	42232463	42233216	E067	-26083
chr3	42233999	42234336	E067	-24963
chr3	42237001	42237079	E067	-22220
chr3	42237615	42237684	E067	-21615
chr3	42237715	42237821	E067	-21478
chr3	42255328	42255821	E067	-3478
chr3	42256969	42257059	E067	-2240
chr3	42257063	42257113	E067	-2186
chr3	42271257	42271379	E067	11958
chr3	42271451	42271715	E067	12152
chr3	42211213	42211279	E068	-48020
chr3	42211498	42211548	E068	-47751
chr3	42211735	42211785	E068	-47514
chr3	42211883	42211934	E068	-47365
chr3	42212952	42213002	E068	-46297
chr3	42215298	42215373	E068	-43926
chr3	42216729	42216790	E068	-42509
chr3	42217192	42217933	E068	-41366
chr3	42218165	42218399	E068	-40900
chr3	42218963	42219013	E068	-40286
chr3	42219060	42219221	E068	-40078
chr3	42219327	42219397	E068	-39902
chr3	42219705	42219755	E068	-39544
chr3	42219758	42219969	E068	-39330
chr3	42220527	42221292	E068	-38007
chr3	42221494	42221549	E068	-37750
chr3	42225078	42225194	E068	-34105
chr3	42225279	42225380	E068	-33919
chr3	42225644	42225764	E068	-33535
chr3	42225779	42226155	E068	-33144
chr3	42226235	42226415	E068	-32884
chr3	42226552	42226944	E068	-32355
chr3	42229847	42229959	E068	-29340
chr3	42229961	42230154	E068	-29145
chr3	42232463	42233216	E068	-26083
chr3	42237001	42237079	E068	-22220
chr3	42237615	42237684	E068	-21615
chr3	42237715	42237821	E068	-21478
chr3	42255917	42256036	E068	-3263
chr3	42256191	42256340	E068	-2959
chr3	42256478	42256646	E068	-2653
chr3	42256969	42257059	E068	-2240
chr3	42257063	42257113	E068	-2186
chr3	42265760	42265951	E068	6461
chr3	42266285	42266376	E068	6986
chr3	42271257	42271379	E068	11958
chr3	42271451	42271715	E068	12152
chr3	42272438	42272582	E068	13139
chr3	42288916	42289557	E068	29617
chr3	42289576	42289708	E068	30277
chr3	42209698	42209793	E069	-49506
chr3	42212952	42213002	E069	-46297
chr3	42216729	42216790	E069	-42509
chr3	42217192	42217933	E069	-41366
chr3	42218165	42218399	E069	-40900
chr3	42218963	42219013	E069	-40286
chr3	42219060	42219221	E069	-40078
chr3	42219327	42219397	E069	-39902
chr3	42219705	42219755	E069	-39544
chr3	42219758	42219969	E069	-39330
chr3	42220527	42221292	E069	-38007
chr3	42225078	42225194	E069	-34105
chr3	42225279	42225380	E069	-33919
chr3	42225644	42225764	E069	-33535
chr3	42225779	42226155	E069	-33144
chr3	42226235	42226415	E069	-32884
chr3	42226552	42226944	E069	-32355
chr3	42229585	42229688	E069	-29611
chr3	42231734	42231784	E069	-27515
chr3	42231985	42232084	E069	-27215
chr3	42232192	42232242	E069	-27057
chr3	42232463	42233216	E069	-26083
chr3	42233999	42234336	E069	-24963
chr3	42234419	42234639	E069	-24660
chr3	42265623	42265673	E069	6324
chr3	42265760	42265951	E069	6461
chr3	42266285	42266376	E069	6986
chr3	42266556	42266865	E069	7257
chr3	42271257	42271379	E069	11958
chr3	42271451	42271715	E069	12152
chr3	42289576	42289708	E069	30277
chr3	42212952	42213002	E070	-46297
chr3	42217037	42217121	E070	-42178
chr3	42217192	42217933	E070	-41366
chr3	42225078	42225194	E070	-34105
chr3	42225279	42225380	E070	-33919
chr3	42225644	42225764	E070	-33535
chr3	42225779	42226155	E070	-33144
chr3	42226235	42226415	E070	-32884
chr3	42226552	42226944	E070	-32355
chr3	42271451	42271715	E070	12152
chr3	42211213	42211279	E071	-48020
chr3	42211498	42211548	E071	-47751
chr3	42211735	42211785	E071	-47514
chr3	42211883	42211934	E071	-47365
chr3	42212952	42213002	E071	-46297
chr3	42216729	42216790	E071	-42509
chr3	42218165	42218399	E071	-40900
chr3	42218963	42219013	E071	-40286
chr3	42219060	42219221	E071	-40078
chr3	42219327	42219397	E071	-39902
chr3	42219705	42219755	E071	-39544
chr3	42219758	42219969	E071	-39330
chr3	42220527	42221292	E071	-38007
chr3	42221494	42221549	E071	-37750
chr3	42225078	42225194	E071	-34105
chr3	42225279	42225380	E071	-33919
chr3	42225644	42225764	E071	-33535
chr3	42225779	42226155	E071	-33144
chr3	42226235	42226415	E071	-32884
chr3	42226552	42226944	E071	-32355
chr3	42231341	42231560	E071	-27739
chr3	42231734	42231784	E071	-27515
chr3	42231985	42232084	E071	-27215
chr3	42232192	42232242	E071	-27057
chr3	42232463	42233216	E071	-26083
chr3	42234419	42234639	E071	-24660
chr3	42271257	42271379	E071	11958
chr3	42271451	42271715	E071	12152
chr3	42211498	42211548	E072	-47751
chr3	42211735	42211785	E072	-47514
chr3	42212952	42213002	E072	-46297
chr3	42216729	42216790	E072	-42509
chr3	42218165	42218399	E072	-40900
chr3	42218963	42219013	E072	-40286
chr3	42219060	42219221	E072	-40078
chr3	42219327	42219397	E072	-39902
chr3	42220527	42221292	E072	-38007
chr3	42224181	42224304	E072	-34995
chr3	42225078	42225194	E072	-34105
chr3	42225279	42225380	E072	-33919
chr3	42225644	42225764	E072	-33535
chr3	42225779	42226155	E072	-33144
chr3	42226235	42226415	E072	-32884
chr3	42226552	42226944	E072	-32355
chr3	42230285	42231006	E072	-28293
chr3	42231985	42232084	E072	-27215
chr3	42232192	42232242	E072	-27057
chr3	42232463	42233216	E072	-26083
chr3	42234419	42234639	E072	-24660
chr3	42254954	42255266	E072	-4033
chr3	42255328	42255821	E072	-3478
chr3	42255917	42256036	E072	-3263
chr3	42256191	42256340	E072	-2959
chr3	42256478	42256646	E072	-2653
chr3	42265623	42265673	E072	6324
chr3	42265760	42265951	E072	6461
chr3	42266285	42266376	E072	6986
chr3	42266556	42266865	E072	7257
chr3	42271451	42271715	E072	12152
chr3	42211498	42211548	E073	-47751
chr3	42212952	42213002	E073	-46297
chr3	42215298	42215373	E073	-43926
chr3	42215498	42215548	E073	-43751
chr3	42217037	42217121	E073	-42178
chr3	42217192	42217933	E073	-41366
chr3	42218165	42218399	E073	-40900
chr3	42218963	42219013	E073	-40286
chr3	42219060	42219221	E073	-40078
chr3	42219327	42219397	E073	-39902
chr3	42219705	42219755	E073	-39544
chr3	42219758	42219969	E073	-39330
chr3	42220527	42221292	E073	-38007
chr3	42225279	42225380	E073	-33919
chr3	42225644	42225764	E073	-33535
chr3	42225779	42226155	E073	-33144
chr3	42226235	42226415	E073	-32884
chr3	42226552	42226944	E073	-32355
chr3	42229585	42229688	E073	-29611
chr3	42229847	42229959	E073	-29340
chr3	42229961	42230154	E073	-29145
chr3	42230285	42231006	E073	-28293
chr3	42231341	42231560	E073	-27739
chr3	42231734	42231784	E073	-27515
chr3	42231985	42232084	E073	-27215
chr3	42232192	42232242	E073	-27057
chr3	42232463	42233216	E073	-26083
chr3	42234419	42234639	E073	-24660
chr3	42237001	42237079	E073	-22220
chr3	42262145	42262263	E073	2846
chr3	42266285	42266376	E073	6986
chr3	42271257	42271379	E073	11958
chr3	42271451	42271715	E073	12152
chr3	42272438	42272582	E073	13139
chr3	42209698	42209793	E074	-49506
chr3	42211498	42211548	E074	-47751
chr3	42211735	42211785	E074	-47514
chr3	42211883	42211934	E074	-47365
chr3	42212952	42213002	E074	-46297
chr3	42216729	42216790	E074	-42509
chr3	42217192	42217933	E074	-41366
chr3	42218165	42218399	E074	-40900
chr3	42218963	42219013	E074	-40286
chr3	42219060	42219221	E074	-40078
chr3	42219327	42219397	E074	-39902
chr3	42219705	42219755	E074	-39544
chr3	42219758	42219969	E074	-39330
chr3	42220527	42221292	E074	-38007
chr3	42222428	42222675	E074	-36624
chr3	42223010	42223218	E074	-36081
chr3	42224181	42224304	E074	-34995
chr3	42225078	42225194	E074	-34105
chr3	42225279	42225380	E074	-33919
chr3	42225644	42225764	E074	-33535
chr3	42225779	42226155	E074	-33144
chr3	42226235	42226415	E074	-32884
chr3	42226552	42226944	E074	-32355
chr3	42230285	42231006	E074	-28293
chr3	42231734	42231784	E074	-27515
chr3	42231985	42232084	E074	-27215
chr3	42232192	42232242	E074	-27057
chr3	42232463	42233216	E074	-26083
chr3	42233999	42234336	E074	-24963
chr3	42234419	42234639	E074	-24660
chr3	42254819	42254869	E074	-4430
chr3	42254954	42255266	E074	-4033
chr3	42262145	42262263	E074	2846
chr3	42271257	42271379	E074	11958
chr3	42212952	42213002	E081	-46297
chr3	42271257	42271379	E081	11958
chr3	42211735	42211785	E082	-47514
chr3	42211883	42211934	E082	-47365
chr3	42212952	42213002	E082	-46297
chr3	42220527	42221292	E082	-38007
chr3	42225279	42225380	E082	-33919
chr3	42225644	42225764	E082	-33535
chr3	42225779	42226155	E082	-33144
chr3	42226235	42226415	E082	-32884
chr3	42226552	42226944	E082	-32355
chr3	42231985	42232084	E082	-27215
chr3	42232192	42232242	E082	-27057
chr3	42271451	42271715	E082	12152

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	42304738	42305209	E067	45439
chr3	42305218	42305292	E067	45919
chr3	42305355	42305490	E067	46056
chr3	42304738	42305209	E068	45439
chr3	42305218	42305292	E068	45919
chr3	42305355	42305490	E068	46056
chr3	42304738	42305209	E072	45439
chr3	42305218	42305292	E072	45919
chr3	42305355	42305490	E072	46056
chr3	42304738	42305209	E073	45439
chr3	42305218	42305292	E073	45919
chr3	42305355	42305490	E073	46056