rs591833

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PTP4A2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0283 (8490/29934,GnomAD)
A=0351 (10231/29118,TOPMED)
A=0387 (1936/5008,1000G)
A=0144 (554/3854,ALSPAC)
A=0138 (510/3708,TWINSUK)

Position: chr1:31932289 (GRCh38.p7) (1p35.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 306 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.31932289G>A
GRCh37.p13 chr 1	NC_000001.10:g.32397890G>A

Gene: PTP4A2, protein tyrosine phosphatase type IVA, member 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTP4A2 transcript variant 1	NM_080391.3:c.	N/A	Intron Variant
PTP4A2 transcript variant 3	NM_001195100.1:c.	N/A	Genic Upstream Transcript Variant
PTP4A2 transcript variant 4	NM_001195101.1:c.	N/A	Genic Upstream Transcript Variant
PTP4A2 transcript variant X2	XM_005271231.3:c.	N/A	Intron Variant
PTP4A2 transcript variant X3	XM_005271232.3:c.	N/A	Intron Variant
PTP4A2 transcript variant X4	XM_017002401.1:c.	N/A	Intron Variant
PTP4A2 transcript variant X2	XR_001737441.1:n.	N/A	Intron Variant
PTP4A2 transcript variant X3	XR_001737442.1:n.	N/A	Intron Variant
PTP4A2 transcript variant X5	XR_001737444.1:n.	N/A	Intron Variant
PTP4A2 transcript variant X6	XR_001737445.1:n.	N/A	Intron Variant
PTP4A2 transcript variant X7	XR_001737446.1:n.	N/A	Intron Variant
PTP4A2 transcript variant X1	XR_946766.2:n.	N/A	Intron Variant
PTP4A2 transcript variant X4	XR_001737443.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.357	A=0.643
1000Genomes	American	Sub	694	G=0.690	A=0.310
1000Genomes	East Asian	Sub	1008	G=0.604	A=0.396
1000Genomes	Europe	Sub	1006	G=0.864	A=0.136
1000Genomes	Global	Study-wide	5008	G=0.613	A=0.387
1000Genomes	South Asian	Sub	978	G=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.856	A=0.144
The Genome Aggregation Database	African	Sub	8712	G=0.418	A=0.582
The Genome Aggregation Database	American	Sub	836	G=0.800	A=0.200
The Genome Aggregation Database	East Asian	Sub	1616	G=0.626	A=0.374
The Genome Aggregation Database	Europe	Sub	18468	G=0.859	A=0.140
The Genome Aggregation Database	Global	Study-wide	29934	G=0.716	A=0.283
The Genome Aggregation Database	Other	Sub	302	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.648	A=0.351
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.862	A=0.138

PMID	Title	Author	Journal
23953852	Genome-wide association studies of maximum number of drinks.	Pan Y	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs591833	1.98E-06	alcohol consumption	23953852

eQTL of rs591833 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 rs591833 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 )
chr1	32370412	32370729	E067	-27161
chr1	32371284	32371398	E067	-26492
chr1	32378578	32378622	E067	-19268
chr1	32378643	32378693	E067	-19197
chr1	32379604	32379667	E067	-18223
chr1	32380100	32380170	E067	-17720
chr1	32389492	32389989	E067	-7901
chr1	32389994	32390099	E067	-7791
chr1	32390599	32391077	E067	-6813
chr1	32391998	32392108	E067	-5782
chr1	32392120	32392281	E067	-5609
chr1	32392433	32392473	E067	-5417
chr1	32392517	32392752	E067	-5138
chr1	32392886	32393536	E067	-4354
chr1	32394326	32394681	E067	-3209
chr1	32395089	32395201	E067	-2689
chr1	32395427	32395613	E067	-2277
chr1	32395854	32395894	E067	-1996
chr1	32395972	32396093	E067	-1797
chr1	32396155	32396359	E067	-1531
chr1	32396361	32396900	E067	-990
chr1	32396911	32397116	E067	-774
chr1	32397184	32397575	E067	-315
chr1	32397704	32397807	E067	-83
chr1	32398074	32398522	E067	184
chr1	32398649	32398882	E067	759
chr1	32399423	32399582	E067	1533
chr1	32399678	32399766	E067	1788
chr1	32399937	32400151	E067	2047
chr1	32400344	32400648	E067	2454
chr1	32401468	32401590	E067	3578
chr1	32401685	32401769	E067	3795
chr1	32420141	32421206	E067	22251
chr1	32376634	32376863	E068	-21027
chr1	32377790	32377851	E068	-20039
chr1	32377947	32378272	E068	-19618
chr1	32379604	32379667	E068	-18223
chr1	32380100	32380170	E068	-17720
chr1	32386600	32386853	E068	-11037
chr1	32386890	32387077	E068	-10813
chr1	32387152	32387271	E068	-10619
chr1	32387286	32387420	E068	-10470
chr1	32387608	32387706	E068	-10184
chr1	32387791	32387839	E068	-10051
chr1	32388070	32388176	E068	-9714
chr1	32388230	32388527	E068	-9363
chr1	32388658	32388740	E068	-9150
chr1	32388809	32388905	E068	-8985
chr1	32389492	32389989	E068	-7901
chr1	32389994	32390099	E068	-7791
chr1	32390599	32391077	E068	-6813
chr1	32391998	32392108	E068	-5782
chr1	32392120	32392281	E068	-5609
chr1	32392433	32392473	E068	-5417
chr1	32392517	32392752	E068	-5138
chr1	32392886	32393536	E068	-4354
chr1	32393617	32393701	E068	-4189
chr1	32394138	32394227	E068	-3663
chr1	32394326	32394681	E068	-3209
chr1	32395089	32395201	E068	-2689
chr1	32395427	32395613	E068	-2277
chr1	32395854	32395894	E068	-1996
chr1	32395972	32396093	E068	-1797
chr1	32396155	32396359	E068	-1531
chr1	32396361	32396900	E068	-990
chr1	32396911	32397116	E068	-774
chr1	32397184	32397575	E068	-315
chr1	32397704	32397807	E068	-83
chr1	32398074	32398522	E068	184
chr1	32398649	32398882	E068	759
chr1	32398932	32399040	E068	1042
chr1	32399107	32399159	E068	1217
chr1	32399318	32399418	E068	1428
chr1	32399423	32399582	E068	1533
chr1	32400344	32400648	E068	2454
chr1	32401468	32401590	E068	3578
chr1	32401685	32401769	E068	3795
chr1	32404662	32404728	E068	6772
chr1	32404811	32404882	E068	6921
chr1	32420141	32421206	E068	22251
chr1	32421557	32422224	E068	23667
chr1	32429629	32430220	E068	31739
chr1	32376634	32376863	E069	-21027
chr1	32377790	32377851	E069	-20039
chr1	32377947	32378272	E069	-19618
chr1	32378484	32378545	E069	-19345
chr1	32378578	32378622	E069	-19268
chr1	32379604	32379667	E069	-18223
chr1	32386600	32386853	E069	-11037
chr1	32386890	32387077	E069	-10813
chr1	32387152	32387271	E069	-10619
chr1	32387286	32387420	E069	-10470
chr1	32387608	32387706	E069	-10184
chr1	32387791	32387839	E069	-10051
chr1	32388070	32388176	E069	-9714
chr1	32389492	32389989	E069	-7901
chr1	32389994	32390099	E069	-7791
chr1	32390599	32391077	E069	-6813
chr1	32392120	32392281	E069	-5609
chr1	32392433	32392473	E069	-5417
chr1	32392517	32392752	E069	-5138
chr1	32392886	32393536	E069	-4354
chr1	32393617	32393701	E069	-4189
chr1	32393972	32394019	E069	-3871
chr1	32394138	32394227	E069	-3663
chr1	32394326	32394681	E069	-3209
chr1	32396155	32396359	E069	-1531
chr1	32396361	32396900	E069	-990
chr1	32396911	32397116	E069	-774
chr1	32397184	32397575	E069	-315
chr1	32397704	32397807	E069	-83
chr1	32398074	32398522	E069	184
chr1	32398649	32398882	E069	759
chr1	32398932	32399040	E069	1042
chr1	32399107	32399159	E069	1217
chr1	32399678	32399766	E069	1788
chr1	32399937	32400151	E069	2047
chr1	32400344	32400648	E069	2454
chr1	32401468	32401590	E069	3578
chr1	32401685	32401769	E069	3795
chr1	32404662	32404728	E069	6772
chr1	32420141	32421206	E069	22251
chr1	32421453	32421518	E069	23563
chr1	32421557	32422224	E069	23667
chr1	32429629	32430220	E069	31739
chr1	32430278	32430328	E069	32388
chr1	32430332	32430376	E069	32442
chr1	32392120	32392281	E070	-5609
chr1	32392433	32392473	E070	-5417
chr1	32392517	32392752	E070	-5138
chr1	32392886	32393536	E070	-4354
chr1	32446430	32446504	E070	48540
chr1	32446576	32446706	E070	48686
chr1	32447056	32447515	E070	49166
chr1	32369499	32369666	E071	-28224
chr1	32369794	32369887	E071	-28003
chr1	32376634	32376863	E071	-21027
chr1	32377790	32377851	E071	-20039
chr1	32377947	32378272	E071	-19618
chr1	32378484	32378545	E071	-19345
chr1	32378578	32378622	E071	-19268
chr1	32378643	32378693	E071	-19197
chr1	32378746	32378820	E071	-19070
chr1	32379604	32379667	E071	-18223
chr1	32386600	32386853	E071	-11037
chr1	32386890	32387077	E071	-10813
chr1	32387152	32387271	E071	-10619
chr1	32388230	32388527	E071	-9363
chr1	32388658	32388740	E071	-9150
chr1	32388809	32388905	E071	-8985
chr1	32389492	32389989	E071	-7901
chr1	32389994	32390099	E071	-7791
chr1	32390599	32391077	E071	-6813
chr1	32391666	32391716	E071	-6174
chr1	32391775	32391972	E071	-5918
chr1	32391998	32392108	E071	-5782
chr1	32393617	32393701	E071	-4189
chr1	32394326	32394681	E071	-3209
chr1	32395089	32395201	E071	-2689
chr1	32395427	32395613	E071	-2277
chr1	32395854	32395894	E071	-1996
chr1	32395972	32396093	E071	-1797
chr1	32396155	32396359	E071	-1531
chr1	32396361	32396900	E071	-990
chr1	32397704	32397807	E071	-83
chr1	32398074	32398522	E071	184
chr1	32398649	32398882	E071	759
chr1	32398932	32399040	E071	1042
chr1	32399107	32399159	E071	1217
chr1	32399318	32399418	E071	1428
chr1	32399423	32399582	E071	1533
chr1	32399678	32399766	E071	1788
chr1	32399937	32400151	E071	2047
chr1	32400344	32400648	E071	2454
chr1	32401468	32401590	E071	3578
chr1	32401685	32401769	E071	3795
chr1	32404811	32404882	E071	6921
chr1	32405016	32406047	E071	7126
chr1	32410828	32410878	E071	12938
chr1	32411119	32411163	E071	13229
chr1	32411272	32411334	E071	13382
chr1	32411385	32411487	E071	13495
chr1	32420141	32421206	E071	22251
chr1	32421453	32421518	E071	23563
chr1	32421557	32422224	E071	23667
chr1	32429629	32430220	E071	31739
chr1	32430278	32430328	E071	32388
chr1	32430332	32430376	E071	32442
chr1	32446237	32446309	E071	48347
chr1	32446369	32446409	E071	48479
chr1	32446430	32446504	E071	48540
chr1	32446576	32446706	E071	48686
chr1	32379604	32379667	E072	-18223
chr1	32386890	32387077	E072	-10813
chr1	32387152	32387271	E072	-10619
chr1	32387286	32387420	E072	-10470
chr1	32389492	32389989	E072	-7901
chr1	32389994	32390099	E072	-7791
chr1	32390599	32391077	E072	-6813
chr1	32392433	32392473	E072	-5417
chr1	32392517	32392752	E072	-5138
chr1	32392886	32393536	E072	-4354
chr1	32393617	32393701	E072	-4189
chr1	32394326	32394681	E072	-3209
chr1	32395089	32395201	E072	-2689
chr1	32395427	32395613	E072	-2277
chr1	32395854	32395894	E072	-1996
chr1	32395972	32396093	E072	-1797
chr1	32396155	32396359	E072	-1531
chr1	32396361	32396900	E072	-990
chr1	32397184	32397575	E072	-315
chr1	32398074	32398522	E072	184
chr1	32398649	32398882	E072	759
chr1	32398932	32399040	E072	1042
chr1	32399107	32399159	E072	1217
chr1	32399318	32399418	E072	1428
chr1	32399423	32399582	E072	1533
chr1	32399678	32399766	E072	1788
chr1	32399937	32400151	E072	2047
chr1	32400344	32400648	E072	2454
chr1	32401468	32401590	E072	3578
chr1	32401685	32401769	E072	3795
chr1	32420141	32421206	E072	22251
chr1	32421453	32421518	E072	23563
chr1	32421557	32422224	E072	23667
chr1	32429629	32430220	E072	31739
chr1	32389492	32389989	E073	-7901
chr1	32389994	32390099	E073	-7791
chr1	32390599	32391077	E073	-6813
chr1	32392433	32392473	E073	-5417
chr1	32392517	32392752	E073	-5138
chr1	32392886	32393536	E073	-4354
chr1	32395427	32395613	E073	-2277
chr1	32395854	32395894	E073	-1996
chr1	32395972	32396093	E073	-1797
chr1	32396155	32396359	E073	-1531
chr1	32396361	32396900	E073	-990
chr1	32398074	32398522	E073	184
chr1	32404662	32404728	E073	6772
chr1	32420141	32421206	E073	22251
chr1	32429629	32430220	E073	31739
chr1	32377790	32377851	E074	-20039
chr1	32379604	32379667	E074	-18223
chr1	32380100	32380170	E074	-17720
chr1	32386600	32386853	E074	-11037
chr1	32386890	32387077	E074	-10813
chr1	32387152	32387271	E074	-10619
chr1	32387286	32387420	E074	-10470
chr1	32389492	32389989	E074	-7901
chr1	32389994	32390099	E074	-7791
chr1	32390599	32391077	E074	-6813
chr1	32391998	32392108	E074	-5782
chr1	32392120	32392281	E074	-5609
chr1	32392433	32392473	E074	-5417
chr1	32392517	32392752	E074	-5138
chr1	32393617	32393701	E074	-4189
chr1	32394326	32394681	E074	-3209
chr1	32395089	32395201	E074	-2689
chr1	32395427	32395613	E074	-2277
chr1	32395854	32395894	E074	-1996
chr1	32395972	32396093	E074	-1797
chr1	32396155	32396359	E074	-1531
chr1	32396361	32396900	E074	-990
chr1	32396911	32397116	E074	-774
chr1	32397184	32397575	E074	-315
chr1	32397704	32397807	E074	-83
chr1	32398074	32398522	E074	184
chr1	32398649	32398882	E074	759
chr1	32398932	32399040	E074	1042
chr1	32399107	32399159	E074	1217
chr1	32399318	32399418	E074	1428
chr1	32399423	32399582	E074	1533
chr1	32399678	32399766	E074	1788
chr1	32399937	32400151	E074	2047
chr1	32400344	32400648	E074	2454
chr1	32401468	32401590	E074	3578
chr1	32401685	32401769	E074	3795
chr1	32404662	32404728	E074	6772
chr1	32404811	32404882	E074	6921
chr1	32405016	32406047	E074	7126
chr1	32420141	32421206	E074	22251
chr1	32421453	32421518	E074	23563
chr1	32421557	32422224	E074	23667
chr1	32429629	32430220	E074	31739
chr1	32399678	32399766	E081	1788
chr1	32399937	32400151	E081	2047
chr1	32400344	32400648	E081	2454
chr1	32401468	32401590	E081	3578
chr1	32401685	32401769	E081	3795
chr1	32425225	32425609	E081	27335
chr1	32425633	32425827	E081	27743
chr1	32446760	32446888	E081	48870
chr1	32447056	32447515	E081	49166
chr1	32401468	32401590	E082	3578
chr1	32401685	32401769	E082	3795
chr1	32425225	32425609	E082	27335
chr1	32425633	32425827	E082	27743
chr1	32426930	32426996	E082	29040
chr1	32430278	32430328	E082	32388
chr1	32430332	32430376	E082	32442
chr1	32446237	32446309	E082	48347
chr1	32446369	32446409	E082	48479
chr1	32446430	32446504	E082	48540
chr1	32446576	32446706	E082	48686
chr1	32446760	32446888	E082	48870
chr1	32447056	32447515	E082	49166

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	32402218	32404616	E067	4328
chr1	32402218	32404616	E068	4328
chr1	32402218	32404616	E069	4328
chr1	32402218	32404616	E070	4328
chr1	32402218	32404616	E071	4328
chr1	32402218	32404616	E072	4328
chr1	32402218	32404616	E073	4328
chr1	32402218	32404616	E074	4328
chr1	32402218	32404616	E082	4328