rs646370

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PTP4A2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0290 (8698/29946,GnomAD)
G=0357 (10408/29118,TOPMED)
G=0398 (1991/5008,1000G)
G=0158 (610/3854,ALSPAC)
G=0151 (561/3708,TWINSUK)

Position: chr1:31935565 (GRCh38.p7) (1p35.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 308 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.31935565A>G
GRCh37.p13 chr 1	NC_000001.10:g.32401166A>G

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	A=0.365	G=0.635
1000Genomes	American	Sub	694	A=0.680	G=0.320
1000Genomes	East Asian	Sub	1008	A=0.603	G=0.397
1000Genomes	Europe	Sub	1006	A=0.853	G=0.147
1000Genomes	Global	Study-wide	5008	A=0.602	G=0.398
1000Genomes	South Asian	Sub	978	A=0.610	G=0.390
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.842	G=0.158
The Genome Aggregation Database	African	Sub	8708	A=0.422	G=0.578
The Genome Aggregation Database	American	Sub	836	A=0.800	G=0.200
The Genome Aggregation Database	East Asian	Sub	1612	A=0.624	G=0.376
The Genome Aggregation Database	Europe	Sub	18488	A=0.847	G=0.152
The Genome Aggregation Database	Global	Study-wide	29946	A=0.709	G=0.290
The Genome Aggregation Database	Other	Sub	302	A=0.780	G=0.220
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.642	G=0.357
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.849	G=0.151

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
rs646370	4.06E-05	alcohol consumption	23953852

eQTL of rs646370 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 rs646370 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	-30437
chr1	32371284	32371398	E067	-29768
chr1	32378578	32378622	E067	-22544
chr1	32378643	32378693	E067	-22473
chr1	32379604	32379667	E067	-21499
chr1	32380100	32380170	E067	-20996
chr1	32389492	32389989	E067	-11177
chr1	32389994	32390099	E067	-11067
chr1	32390599	32391077	E067	-10089
chr1	32391998	32392108	E067	-9058
chr1	32392120	32392281	E067	-8885
chr1	32392433	32392473	E067	-8693
chr1	32392517	32392752	E067	-8414
chr1	32392886	32393536	E067	-7630
chr1	32394326	32394681	E067	-6485
chr1	32395089	32395201	E067	-5965
chr1	32395427	32395613	E067	-5553
chr1	32395854	32395894	E067	-5272
chr1	32395972	32396093	E067	-5073
chr1	32396155	32396359	E067	-4807
chr1	32396361	32396900	E067	-4266
chr1	32396911	32397116	E067	-4050
chr1	32397184	32397575	E067	-3591
chr1	32397704	32397807	E067	-3359
chr1	32398074	32398522	E067	-2644
chr1	32398649	32398882	E067	-2284
chr1	32399423	32399582	E067	-1584
chr1	32399678	32399766	E067	-1400
chr1	32399937	32400151	E067	-1015
chr1	32400344	32400648	E067	-518
chr1	32401468	32401590	E067	302
chr1	32401685	32401769	E067	519
chr1	32420141	32421206	E067	18975
chr1	32376634	32376863	E068	-24303
chr1	32377790	32377851	E068	-23315
chr1	32377947	32378272	E068	-22894
chr1	32379604	32379667	E068	-21499
chr1	32380100	32380170	E068	-20996
chr1	32386600	32386853	E068	-14313
chr1	32386890	32387077	E068	-14089
chr1	32387152	32387271	E068	-13895
chr1	32387286	32387420	E068	-13746
chr1	32387608	32387706	E068	-13460
chr1	32387791	32387839	E068	-13327
chr1	32388070	32388176	E068	-12990
chr1	32388230	32388527	E068	-12639
chr1	32388658	32388740	E068	-12426
chr1	32388809	32388905	E068	-12261
chr1	32389492	32389989	E068	-11177
chr1	32389994	32390099	E068	-11067
chr1	32390599	32391077	E068	-10089
chr1	32391998	32392108	E068	-9058
chr1	32392120	32392281	E068	-8885
chr1	32392433	32392473	E068	-8693
chr1	32392517	32392752	E068	-8414
chr1	32392886	32393536	E068	-7630
chr1	32393617	32393701	E068	-7465
chr1	32394138	32394227	E068	-6939
chr1	32394326	32394681	E068	-6485
chr1	32395089	32395201	E068	-5965
chr1	32395427	32395613	E068	-5553
chr1	32395854	32395894	E068	-5272
chr1	32395972	32396093	E068	-5073
chr1	32396155	32396359	E068	-4807
chr1	32396361	32396900	E068	-4266
chr1	32396911	32397116	E068	-4050
chr1	32397184	32397575	E068	-3591
chr1	32397704	32397807	E068	-3359
chr1	32398074	32398522	E068	-2644
chr1	32398649	32398882	E068	-2284
chr1	32398932	32399040	E068	-2126
chr1	32399107	32399159	E068	-2007
chr1	32399318	32399418	E068	-1748
chr1	32399423	32399582	E068	-1584
chr1	32400344	32400648	E068	-518
chr1	32401468	32401590	E068	302
chr1	32401685	32401769	E068	519
chr1	32404662	32404728	E068	3496
chr1	32404811	32404882	E068	3645
chr1	32420141	32421206	E068	18975
chr1	32421557	32422224	E068	20391
chr1	32429629	32430220	E068	28463
chr1	32376634	32376863	E069	-24303
chr1	32377790	32377851	E069	-23315
chr1	32377947	32378272	E069	-22894
chr1	32378484	32378545	E069	-22621
chr1	32378578	32378622	E069	-22544
chr1	32379604	32379667	E069	-21499
chr1	32386600	32386853	E069	-14313
chr1	32386890	32387077	E069	-14089
chr1	32387152	32387271	E069	-13895
chr1	32387286	32387420	E069	-13746
chr1	32387608	32387706	E069	-13460
chr1	32387791	32387839	E069	-13327
chr1	32388070	32388176	E069	-12990
chr1	32389492	32389989	E069	-11177
chr1	32389994	32390099	E069	-11067
chr1	32390599	32391077	E069	-10089
chr1	32392120	32392281	E069	-8885
chr1	32392433	32392473	E069	-8693
chr1	32392517	32392752	E069	-8414
chr1	32392886	32393536	E069	-7630
chr1	32393617	32393701	E069	-7465
chr1	32393972	32394019	E069	-7147
chr1	32394138	32394227	E069	-6939
chr1	32394326	32394681	E069	-6485
chr1	32396155	32396359	E069	-4807
chr1	32396361	32396900	E069	-4266
chr1	32396911	32397116	E069	-4050
chr1	32397184	32397575	E069	-3591
chr1	32397704	32397807	E069	-3359
chr1	32398074	32398522	E069	-2644
chr1	32398649	32398882	E069	-2284
chr1	32398932	32399040	E069	-2126
chr1	32399107	32399159	E069	-2007
chr1	32399678	32399766	E069	-1400
chr1	32399937	32400151	E069	-1015
chr1	32400344	32400648	E069	-518
chr1	32401468	32401590	E069	302
chr1	32401685	32401769	E069	519
chr1	32404662	32404728	E069	3496
chr1	32420141	32421206	E069	18975
chr1	32421453	32421518	E069	20287
chr1	32421557	32422224	E069	20391
chr1	32429629	32430220	E069	28463
chr1	32430278	32430328	E069	29112
chr1	32430332	32430376	E069	29166
chr1	32392120	32392281	E070	-8885
chr1	32392433	32392473	E070	-8693
chr1	32392517	32392752	E070	-8414
chr1	32392886	32393536	E070	-7630
chr1	32446430	32446504	E070	45264
chr1	32446576	32446706	E070	45410
chr1	32447056	32447515	E070	45890
chr1	32447616	32447944	E070	46450
chr1	32369499	32369666	E071	-31500
chr1	32369794	32369887	E071	-31279
chr1	32376634	32376863	E071	-24303
chr1	32377790	32377851	E071	-23315
chr1	32377947	32378272	E071	-22894
chr1	32378484	32378545	E071	-22621
chr1	32378578	32378622	E071	-22544
chr1	32378643	32378693	E071	-22473
chr1	32378746	32378820	E071	-22346
chr1	32379604	32379667	E071	-21499
chr1	32386600	32386853	E071	-14313
chr1	32386890	32387077	E071	-14089
chr1	32387152	32387271	E071	-13895
chr1	32388230	32388527	E071	-12639
chr1	32388658	32388740	E071	-12426
chr1	32388809	32388905	E071	-12261
chr1	32389492	32389989	E071	-11177
chr1	32389994	32390099	E071	-11067
chr1	32390599	32391077	E071	-10089
chr1	32391666	32391716	E071	-9450
chr1	32391775	32391972	E071	-9194
chr1	32391998	32392108	E071	-9058
chr1	32393617	32393701	E071	-7465
chr1	32394326	32394681	E071	-6485
chr1	32395089	32395201	E071	-5965
chr1	32395427	32395613	E071	-5553
chr1	32395854	32395894	E071	-5272
chr1	32395972	32396093	E071	-5073
chr1	32396155	32396359	E071	-4807
chr1	32396361	32396900	E071	-4266
chr1	32397704	32397807	E071	-3359
chr1	32398074	32398522	E071	-2644
chr1	32398649	32398882	E071	-2284
chr1	32398932	32399040	E071	-2126
chr1	32399107	32399159	E071	-2007
chr1	32399318	32399418	E071	-1748
chr1	32399423	32399582	E071	-1584
chr1	32399678	32399766	E071	-1400
chr1	32399937	32400151	E071	-1015
chr1	32400344	32400648	E071	-518
chr1	32401468	32401590	E071	302
chr1	32401685	32401769	E071	519
chr1	32404811	32404882	E071	3645
chr1	32405016	32406047	E071	3850
chr1	32410828	32410878	E071	9662
chr1	32411119	32411163	E071	9953
chr1	32411272	32411334	E071	10106
chr1	32411385	32411487	E071	10219
chr1	32420141	32421206	E071	18975
chr1	32421453	32421518	E071	20287
chr1	32421557	32422224	E071	20391
chr1	32429629	32430220	E071	28463
chr1	32430278	32430328	E071	29112
chr1	32430332	32430376	E071	29166
chr1	32446237	32446309	E071	45071
chr1	32446369	32446409	E071	45203
chr1	32446430	32446504	E071	45264
chr1	32446576	32446706	E071	45410
chr1	32379604	32379667	E072	-21499
chr1	32386890	32387077	E072	-14089
chr1	32387152	32387271	E072	-13895
chr1	32387286	32387420	E072	-13746
chr1	32389492	32389989	E072	-11177
chr1	32389994	32390099	E072	-11067
chr1	32390599	32391077	E072	-10089
chr1	32392433	32392473	E072	-8693
chr1	32392517	32392752	E072	-8414
chr1	32392886	32393536	E072	-7630
chr1	32393617	32393701	E072	-7465
chr1	32394326	32394681	E072	-6485
chr1	32395089	32395201	E072	-5965
chr1	32395427	32395613	E072	-5553
chr1	32395854	32395894	E072	-5272
chr1	32395972	32396093	E072	-5073
chr1	32396155	32396359	E072	-4807
chr1	32396361	32396900	E072	-4266
chr1	32397184	32397575	E072	-3591
chr1	32398074	32398522	E072	-2644
chr1	32398649	32398882	E072	-2284
chr1	32398932	32399040	E072	-2126
chr1	32399107	32399159	E072	-2007
chr1	32399318	32399418	E072	-1748
chr1	32399423	32399582	E072	-1584
chr1	32399678	32399766	E072	-1400
chr1	32399937	32400151	E072	-1015
chr1	32400344	32400648	E072	-518
chr1	32401468	32401590	E072	302
chr1	32401685	32401769	E072	519
chr1	32420141	32421206	E072	18975
chr1	32421453	32421518	E072	20287
chr1	32421557	32422224	E072	20391
chr1	32429629	32430220	E072	28463
chr1	32389492	32389989	E073	-11177
chr1	32389994	32390099	E073	-11067
chr1	32390599	32391077	E073	-10089
chr1	32392433	32392473	E073	-8693
chr1	32392517	32392752	E073	-8414
chr1	32392886	32393536	E073	-7630
chr1	32395427	32395613	E073	-5553
chr1	32395854	32395894	E073	-5272
chr1	32395972	32396093	E073	-5073
chr1	32396155	32396359	E073	-4807
chr1	32396361	32396900	E073	-4266
chr1	32398074	32398522	E073	-2644
chr1	32404662	32404728	E073	3496
chr1	32420141	32421206	E073	18975
chr1	32429629	32430220	E073	28463
chr1	32377790	32377851	E074	-23315
chr1	32379604	32379667	E074	-21499
chr1	32380100	32380170	E074	-20996
chr1	32386600	32386853	E074	-14313
chr1	32386890	32387077	E074	-14089
chr1	32387152	32387271	E074	-13895
chr1	32387286	32387420	E074	-13746
chr1	32389492	32389989	E074	-11177
chr1	32389994	32390099	E074	-11067
chr1	32390599	32391077	E074	-10089
chr1	32391998	32392108	E074	-9058
chr1	32392120	32392281	E074	-8885
chr1	32392433	32392473	E074	-8693
chr1	32392517	32392752	E074	-8414
chr1	32393617	32393701	E074	-7465
chr1	32394326	32394681	E074	-6485
chr1	32395089	32395201	E074	-5965
chr1	32395427	32395613	E074	-5553
chr1	32395854	32395894	E074	-5272
chr1	32395972	32396093	E074	-5073
chr1	32396155	32396359	E074	-4807
chr1	32396361	32396900	E074	-4266
chr1	32396911	32397116	E074	-4050
chr1	32397184	32397575	E074	-3591
chr1	32397704	32397807	E074	-3359
chr1	32398074	32398522	E074	-2644
chr1	32398649	32398882	E074	-2284
chr1	32398932	32399040	E074	-2126
chr1	32399107	32399159	E074	-2007
chr1	32399318	32399418	E074	-1748
chr1	32399423	32399582	E074	-1584
chr1	32399678	32399766	E074	-1400
chr1	32399937	32400151	E074	-1015
chr1	32400344	32400648	E074	-518
chr1	32401468	32401590	E074	302
chr1	32401685	32401769	E074	519
chr1	32404662	32404728	E074	3496
chr1	32404811	32404882	E074	3645
chr1	32405016	32406047	E074	3850
chr1	32420141	32421206	E074	18975
chr1	32421453	32421518	E074	20287
chr1	32421557	32422224	E074	20391
chr1	32429629	32430220	E074	28463
chr1	32399678	32399766	E081	-1400
chr1	32399937	32400151	E081	-1015
chr1	32400344	32400648	E081	-518
chr1	32401468	32401590	E081	302
chr1	32401685	32401769	E081	519
chr1	32425225	32425609	E081	24059
chr1	32425633	32425827	E081	24467
chr1	32446760	32446888	E081	45594
chr1	32447056	32447515	E081	45890
chr1	32447616	32447944	E081	46450
chr1	32401468	32401590	E082	302
chr1	32401685	32401769	E082	519
chr1	32425225	32425609	E082	24059
chr1	32425633	32425827	E082	24467
chr1	32426930	32426996	E082	25764
chr1	32430278	32430328	E082	29112
chr1	32430332	32430376	E082	29166
chr1	32446237	32446309	E082	45071
chr1	32446369	32446409	E082	45203
chr1	32446430	32446504	E082	45264
chr1	32446576	32446706	E082	45410
chr1	32446760	32446888	E082	45594
chr1	32447056	32447515	E082	45890

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	32402218	32404616	E067	1052
chr1	32402218	32404616	E068	1052
chr1	32402218	32404616	E069	1052
chr1	32402218	32404616	E070	1052
chr1	32402218	32404616	E071	1052
chr1	32402218	32404616	E072	1052
chr1	32402218	32404616	E073	1052
chr1	32402218	32404616	E074	1052
chr1	32402218	32404616	E082	1052