rs2244438

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

TRAK2 : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0283 (34414/121330,ExAC)
A=0280 (8384/29932,GnomAD)
A=0288 (8394/29118,TOPMED)
G==0280 (3644/13006,GO-ESP)
A=0239 (1197/5008,1000G)
A=0289 (1114/3854,ALSPAC)
A=0291 (1078/3708,TWINSUK)

Position: chr2:201387816 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 45 Enhancers around

Promoter: 50 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.201387816G>A
GRCh38.p7 chr 2	NC_000002.12:g.201387816G>T
GRCh37.p13 chr 2	NC_000002.11:g.202252539G>A
GRCh37.p13 chr 2	NC_000002.11:g.202252539G>T

Gene: TRAK2, trafficking protein, kinesin binding 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRAK2 transcript	NM_015049.2:c.158...NM_015049.2:c.1583C>T	T [ACA]> I [ATA]	Coding Sequence Variant
trafficking kinesin-binding protein 2	NP_055864.2:p.Thr...NP_055864.2:p.Thr528Ile	T [Thr]> I [Ile]	Missense Variant
TRAK2 transcript	NM_015049.2:c.158...NM_015049.2:c.1583C>A	T [ACA]> K [AAA]	Coding Sequence Variant
trafficking kinesin-binding protein 2	NP_055864.2:p.Thr...NP_055864.2:p.Thr528Lys	T [Thr]> K [Lys]	Missense Variant
TRAK2 transcript variant X1	XM_011511690.1:c....XM_011511690.1:c.1583C>T	T [ACA]> I [ATA]	Coding Sequence Variant
trafficking kinesin-binding protein 2 isoform X1	XP_011509992.1:p....XP_011509992.1:p.Thr528Ile	T [Thr]> I [Ile]	Missense Variant
TRAK2 transcript variant X1	XM_011511690.1:c....XM_011511690.1:c.1583C>A	T [ACA]> K [AAA]	Coding Sequence Variant
trafficking kinesin-binding protein 2 isoform X1	XP_011509992.1:p....XP_011509992.1:p.Thr528Lys	T [Thr]> K [Lys]	Missense Variant
TRAK2 transcript variant X2	XM_017004772.1:c....XM_017004772.1:c.950C>T	T [ACA]> I [ATA]	Coding Sequence Variant
trafficking kinesin-binding protein 2 isoform X2	XP_016860261.1:p....XP_016860261.1:p.Thr317Ile	T [Thr]> I [Ile]	Missense Variant
TRAK2 transcript variant X2	XM_017004772.1:c....XM_017004772.1:c.950C>A	T [ACA]> K [AAA]	Coding Sequence Variant
trafficking kinesin-binding protein 2 isoform X2	XP_016860261.1:p....XP_016860261.1:p.Thr317Lys	T [Thr]> K [Lys]	Missense Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.790	A=0.210
1000Genomes	American	Sub	694	G=0.610	A=0.390
1000Genomes	East Asian	Sub	1008	G=0.757	A=0.243
1000Genomes	Europe	Sub	1006	G=0.686	A=0.314
1000Genomes	Global	Study-wide	5008	G=0.761	A=0.239
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=0.711	A=0.289
The Exome Aggregation Consortium	American	Sub	21972	G=0.673	A=0.326
The Exome Aggregation Consortium	Asian	Sub	25146	G=0.835	A=0.164
The Exome Aggregation Consortium	Europe	Sub	73304	G=0.688	A=0.311
The Exome Aggregation Consortium	Global	Study-wide	121330	G=0.716	A=0.283
The Exome Aggregation Consortium	Other	Sub	908	G=0.690	A=0.310
The Genome Aggregation Database	African	Sub	8716	G=0.772	A=0.228
The Genome Aggregation Database	American	Sub	834	G=0.610	A=0.390
The Genome Aggregation Database	East Asian	Sub	1618	G=0.784	A=0.216
The Genome Aggregation Database	Europe	Sub	18462	G=0.695	A=0.304
The Genome Aggregation Database	Global	Study-wide	29932	G=0.719	A=0.280
The Genome Aggregation Database	Other	Sub	302	G=0.670	A=0.330
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.711	A=0.288
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.709	A=0.291

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2244438	0.00098	alcohol dependence	20201924

eQTL of rs2244438 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 rs2244438 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 )
chr2	73471052	73471623	E067	-34488
chr2	73471707	73471767	E067	-34344
chr2	73507757	73507983	E067	1646
chr2	73466321	73466507	E068	-39604
chr2	73513157	73513254	E068	7046
chr2	73513357	73513407	E068	7246
chr2	73513457	73513711	E068	7346
chr2	73535004	73535054	E068	28893
chr2	73463219	73463325	E069	-42786
chr2	73471052	73471623	E069	-34488
chr2	73497223	73497325	E069	-8786
chr2	73463219	73463325	E070	-42786
chr2	73463866	73463976	E070	-42135
chr2	73464327	73464435	E070	-41676
chr2	73464705	73464801	E070	-41310
chr2	73497223	73497325	E070	-8786
chr2	73509731	73509818	E070	3620
chr2	73517413	73517634	E070	11302
chr2	73471052	73471623	E071	-34488
chr2	73463219	73463325	E072	-42786
chr2	73463866	73463976	E072	-42135
chr2	73466975	73467178	E072	-38933
chr2	73478407	73478515	E072	-27596
chr2	73463219	73463325	E073	-42786
chr2	73463866	73463976	E073	-42135
chr2	73465321	73465532	E073	-40579
chr2	73465536	73465596	E073	-40515
chr2	73463219	73463325	E074	-42786
chr2	73478047	73478197	E074	-27914
chr2	73471707	73471767	E081	-34344
chr2	73509731	73509818	E081	3620
chr2	73510190	73510334	E081	4079
chr2	73510338	73510400	E081	4227
chr2	73513157	73513254	E081	7046
chr2	73513357	73513407	E081	7246
chr2	73513457	73513711	E081	7346
chr2	73524559	73524658	E081	18448
chr2	73463866	73463976	E082	-42135
chr2	73464327	73464435	E082	-41676
chr2	73464705	73464801	E082	-41310
chr2	73464885	73464935	E082	-41176
chr2	73471052	73471623	E082	-34488
chr2	73497223	73497325	E082	-8786
chr2	73513157	73513254	E082	7046
chr2	73524865	73524969	E082	18754

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	73459573	73462426	E067	-43685
chr2	73495717	73495830	E067	-10281
chr2	73495835	73496761	E067	-9350
chr2	73496922	73496988	E067	-9123
chr2	73511041	73512637	E067	4930
chr2	73518204	73518798	E067	12093
chr2	73519827	73520442	E067	13716
chr2	73520570	73521189	E067	14459
chr2	73459573	73462426	E068	-43685
chr2	73495717	73495830	E068	-10281
chr2	73495835	73496761	E068	-9350
chr2	73496922	73496988	E068	-9123
chr2	73511041	73512637	E068	4930
chr2	73518204	73518798	E068	12093
chr2	73519827	73520442	E068	13716
chr2	73520570	73521189	E068	14459
chr2	73459573	73462426	E069	-43685
chr2	73495717	73495830	E069	-10281
chr2	73495835	73496761	E069	-9350
chr2	73511041	73512637	E069	4930
chr2	73518814	73518960	E069	12703
chr2	73519827	73520442	E069	13716
chr2	73520570	73521189	E069	14459
chr2	73459573	73462426	E070	-43685
chr2	73496922	73496988	E070	-9123
chr2	73511041	73512637	E070	4930
chr2	73459573	73462426	E071	-43685
chr2	73495835	73496761	E071	-9350
chr2	73496922	73496988	E071	-9123
chr2	73511041	73512637	E071	4930
chr2	73518204	73518798	E071	12093
chr2	73459573	73462426	E072	-43685
chr2	73511041	73512637	E072	4930
chr2	73519827	73520442	E072	13716
chr2	73520570	73521189	E072	14459
chr2	73459573	73462426	E073	-43685
chr2	73495717	73495830	E073	-10281
chr2	73495835	73496761	E073	-9350
chr2	73496922	73496988	E073	-9123
chr2	73511041	73512637	E073	4930
chr2	73519827	73520442	E073	13716
chr2	73520570	73521189	E073	14459
chr2	73459573	73462426	E074	-43685
chr2	73511041	73512637	E074	4930
chr2	73459573	73462426	E081	-43685
chr2	73459573	73462426	E082	-43685
chr2	73495835	73496761	E082	-9350
chr2	73496922	73496988	E082	-9123
chr2	73511041	73512637	E082	4930
chr2	73520570	73521189	E082	14459