rs682654

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

PTP4A2 : 500B Downstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0281 (8423/29950,GnomAD)
A=0349 (10170/29118,TOPMED)
A=0384 (1921/5008,1000G)
A=0144 (556/3854,ALSPAC)
A=0138 (511/3708,TWINSUK)

Position: chr1:31905922 (GRCh38.p7) (1p35.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 298 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.31905922C>A
GRCh37.p13 chr 1	NC_000001.10:g.32371523C>A

Gene: PTP4A2, protein tyrosine phosphatase type IVA, member 2(minus strand): 500B Downstream Variant

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.365	A=0.635
1000Genomes	American	Sub	694	C=0.690	A=0.310
1000Genomes	East Asian	Sub	1008	C=0.605	A=0.395
1000Genomes	Europe	Sub	1006	C=0.864	A=0.136
1000Genomes	Global	Study-wide	5008	C=0.616	A=0.384
1000Genomes	South Asian	Sub	978	C=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.856	A=0.144
The Genome Aggregation Database	African	Sub	8714	C=0.425	A=0.575
The Genome Aggregation Database	American	Sub	838	C=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1614	C=0.627	A=0.373
The Genome Aggregation Database	Europe	Sub	18482	C=0.859	A=0.140
The Genome Aggregation Database	Global	Study-wide	29950	C=0.718	A=0.281
The Genome Aggregation Database	Other	Sub	302	C=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.650	A=0.349
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=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
rs682654	2.36E-06	alcohol consumption	23953852

eQTL of rs682654 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 rs682654 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	32326252	32326630	E067	-44893
chr1	32370412	32370729	E067	-794
chr1	32371284	32371398	E067	-125
chr1	32378578	32378622	E067	7055
chr1	32378643	32378693	E067	7120
chr1	32379604	32379667	E067	8081
chr1	32380100	32380170	E067	8577
chr1	32389492	32389989	E067	17969
chr1	32389994	32390099	E067	18471
chr1	32390599	32391077	E067	19076
chr1	32391998	32392108	E067	20475
chr1	32392120	32392281	E067	20597
chr1	32392433	32392473	E067	20910
chr1	32392517	32392752	E067	20994
chr1	32392886	32393536	E067	21363
chr1	32394326	32394681	E067	22803
chr1	32395089	32395201	E067	23566
chr1	32395427	32395613	E067	23904
chr1	32395854	32395894	E067	24331
chr1	32395972	32396093	E067	24449
chr1	32396155	32396359	E067	24632
chr1	32396361	32396900	E067	24838
chr1	32396911	32397116	E067	25388
chr1	32397184	32397575	E067	25661
chr1	32397704	32397807	E067	26181
chr1	32398074	32398522	E067	26551
chr1	32398649	32398882	E067	27126
chr1	32399423	32399582	E067	27900
chr1	32399678	32399766	E067	28155
chr1	32399937	32400151	E067	28414
chr1	32400344	32400648	E067	28821
chr1	32401468	32401590	E067	29945
chr1	32401685	32401769	E067	30162
chr1	32420141	32421206	E067	48618
chr1	32376634	32376863	E068	5111
chr1	32377790	32377851	E068	6267
chr1	32377947	32378272	E068	6424
chr1	32379604	32379667	E068	8081
chr1	32380100	32380170	E068	8577
chr1	32386600	32386853	E068	15077
chr1	32386890	32387077	E068	15367
chr1	32387152	32387271	E068	15629
chr1	32387286	32387420	E068	15763
chr1	32387608	32387706	E068	16085
chr1	32387791	32387839	E068	16268
chr1	32388070	32388176	E068	16547
chr1	32388230	32388527	E068	16707
chr1	32388658	32388740	E068	17135
chr1	32388809	32388905	E068	17286
chr1	32389492	32389989	E068	17969
chr1	32389994	32390099	E068	18471
chr1	32390599	32391077	E068	19076
chr1	32391998	32392108	E068	20475
chr1	32392120	32392281	E068	20597
chr1	32392433	32392473	E068	20910
chr1	32392517	32392752	E068	20994
chr1	32392886	32393536	E068	21363
chr1	32393617	32393701	E068	22094
chr1	32394138	32394227	E068	22615
chr1	32394326	32394681	E068	22803
chr1	32395089	32395201	E068	23566
chr1	32395427	32395613	E068	23904
chr1	32395854	32395894	E068	24331
chr1	32395972	32396093	E068	24449
chr1	32396155	32396359	E068	24632
chr1	32396361	32396900	E068	24838
chr1	32396911	32397116	E068	25388
chr1	32397184	32397575	E068	25661
chr1	32397704	32397807	E068	26181
chr1	32398074	32398522	E068	26551
chr1	32398649	32398882	E068	27126
chr1	32398932	32399040	E068	27409
chr1	32399107	32399159	E068	27584
chr1	32399318	32399418	E068	27795
chr1	32399423	32399582	E068	27900
chr1	32400344	32400648	E068	28821
chr1	32401468	32401590	E068	29945
chr1	32401685	32401769	E068	30162
chr1	32404662	32404728	E068	33139
chr1	32404811	32404882	E068	33288
chr1	32420141	32421206	E068	48618
chr1	32326252	32326630	E069	-44893
chr1	32376634	32376863	E069	5111
chr1	32377790	32377851	E069	6267
chr1	32377947	32378272	E069	6424
chr1	32378484	32378545	E069	6961
chr1	32378578	32378622	E069	7055
chr1	32379604	32379667	E069	8081
chr1	32386600	32386853	E069	15077
chr1	32386890	32387077	E069	15367
chr1	32387152	32387271	E069	15629
chr1	32387286	32387420	E069	15763
chr1	32387608	32387706	E069	16085
chr1	32387791	32387839	E069	16268
chr1	32388070	32388176	E069	16547
chr1	32389492	32389989	E069	17969
chr1	32389994	32390099	E069	18471
chr1	32390599	32391077	E069	19076
chr1	32392120	32392281	E069	20597
chr1	32392433	32392473	E069	20910
chr1	32392517	32392752	E069	20994
chr1	32392886	32393536	E069	21363
chr1	32393617	32393701	E069	22094
chr1	32393972	32394019	E069	22449
chr1	32394138	32394227	E069	22615
chr1	32394326	32394681	E069	22803
chr1	32396155	32396359	E069	24632
chr1	32396361	32396900	E069	24838
chr1	32396911	32397116	E069	25388
chr1	32397184	32397575	E069	25661
chr1	32397704	32397807	E069	26181
chr1	32398074	32398522	E069	26551
chr1	32398649	32398882	E069	27126
chr1	32398932	32399040	E069	27409
chr1	32399107	32399159	E069	27584
chr1	32399678	32399766	E069	28155
chr1	32399937	32400151	E069	28414
chr1	32400344	32400648	E069	28821
chr1	32401468	32401590	E069	29945
chr1	32401685	32401769	E069	30162
chr1	32404662	32404728	E069	33139
chr1	32420141	32421206	E069	48618
chr1	32421453	32421518	E069	49930
chr1	32392120	32392281	E070	20597
chr1	32392433	32392473	E070	20910
chr1	32392517	32392752	E070	20994
chr1	32392886	32393536	E070	21363
chr1	32326252	32326630	E071	-44893
chr1	32332083	32332288	E071	-39235
chr1	32332349	32332389	E071	-39134
chr1	32369499	32369666	E071	-1857
chr1	32369794	32369887	E071	-1636
chr1	32376634	32376863	E071	5111
chr1	32377790	32377851	E071	6267
chr1	32377947	32378272	E071	6424
chr1	32378484	32378545	E071	6961
chr1	32378578	32378622	E071	7055
chr1	32378643	32378693	E071	7120
chr1	32378746	32378820	E071	7223
chr1	32379604	32379667	E071	8081
chr1	32386600	32386853	E071	15077
chr1	32386890	32387077	E071	15367
chr1	32387152	32387271	E071	15629
chr1	32388230	32388527	E071	16707
chr1	32388658	32388740	E071	17135
chr1	32388809	32388905	E071	17286
chr1	32389492	32389989	E071	17969
chr1	32389994	32390099	E071	18471
chr1	32390599	32391077	E071	19076
chr1	32391666	32391716	E071	20143
chr1	32391775	32391972	E071	20252
chr1	32391998	32392108	E071	20475
chr1	32393617	32393701	E071	22094
chr1	32394326	32394681	E071	22803
chr1	32395089	32395201	E071	23566
chr1	32395427	32395613	E071	23904
chr1	32395854	32395894	E071	24331
chr1	32395972	32396093	E071	24449
chr1	32396155	32396359	E071	24632
chr1	32396361	32396900	E071	24838
chr1	32397704	32397807	E071	26181
chr1	32398074	32398522	E071	26551
chr1	32398649	32398882	E071	27126
chr1	32398932	32399040	E071	27409
chr1	32399107	32399159	E071	27584
chr1	32399318	32399418	E071	27795
chr1	32399423	32399582	E071	27900
chr1	32399678	32399766	E071	28155
chr1	32399937	32400151	E071	28414
chr1	32400344	32400648	E071	28821
chr1	32401468	32401590	E071	29945
chr1	32401685	32401769	E071	30162
chr1	32404811	32404882	E071	33288
chr1	32405016	32406047	E071	33493
chr1	32410828	32410878	E071	39305
chr1	32411119	32411163	E071	39596
chr1	32411272	32411334	E071	39749
chr1	32411385	32411487	E071	39862
chr1	32420141	32421206	E071	48618
chr1	32421453	32421518	E071	49930
chr1	32325414	32325583	E072	-45940
chr1	32326252	32326630	E072	-44893
chr1	32332083	32332288	E072	-39235
chr1	32332349	32332389	E072	-39134
chr1	32332403	32332654	E072	-38869
chr1	32345880	32346059	E072	-25464
chr1	32346126	32346176	E072	-25347
chr1	32346311	32346377	E072	-25146
chr1	32346649	32347484	E072	-24039
chr1	32379604	32379667	E072	8081
chr1	32386890	32387077	E072	15367
chr1	32387152	32387271	E072	15629
chr1	32387286	32387420	E072	15763
chr1	32389492	32389989	E072	17969
chr1	32389994	32390099	E072	18471
chr1	32390599	32391077	E072	19076
chr1	32392433	32392473	E072	20910
chr1	32392517	32392752	E072	20994
chr1	32392886	32393536	E072	21363
chr1	32393617	32393701	E072	22094
chr1	32394326	32394681	E072	22803
chr1	32395089	32395201	E072	23566
chr1	32395427	32395613	E072	23904
chr1	32395854	32395894	E072	24331
chr1	32395972	32396093	E072	24449
chr1	32396155	32396359	E072	24632
chr1	32396361	32396900	E072	24838
chr1	32397184	32397575	E072	25661
chr1	32398074	32398522	E072	26551
chr1	32398649	32398882	E072	27126
chr1	32398932	32399040	E072	27409
chr1	32399107	32399159	E072	27584
chr1	32399318	32399418	E072	27795
chr1	32399423	32399582	E072	27900
chr1	32399678	32399766	E072	28155
chr1	32399937	32400151	E072	28414
chr1	32400344	32400648	E072	28821
chr1	32401468	32401590	E072	29945
chr1	32401685	32401769	E072	30162
chr1	32420141	32421206	E072	48618
chr1	32421453	32421518	E072	49930
chr1	32389492	32389989	E073	17969
chr1	32389994	32390099	E073	18471
chr1	32390599	32391077	E073	19076
chr1	32392433	32392473	E073	20910
chr1	32392517	32392752	E073	20994
chr1	32392886	32393536	E073	21363
chr1	32395427	32395613	E073	23904
chr1	32395854	32395894	E073	24331
chr1	32395972	32396093	E073	24449
chr1	32396155	32396359	E073	24632
chr1	32396361	32396900	E073	24838
chr1	32398074	32398522	E073	26551
chr1	32404662	32404728	E073	33139
chr1	32420141	32421206	E073	48618
chr1	32326252	32326630	E074	-44893
chr1	32377790	32377851	E074	6267
chr1	32379604	32379667	E074	8081
chr1	32380100	32380170	E074	8577
chr1	32386600	32386853	E074	15077
chr1	32386890	32387077	E074	15367
chr1	32387152	32387271	E074	15629
chr1	32387286	32387420	E074	15763
chr1	32389492	32389989	E074	17969
chr1	32389994	32390099	E074	18471
chr1	32390599	32391077	E074	19076
chr1	32391998	32392108	E074	20475
chr1	32392120	32392281	E074	20597
chr1	32392433	32392473	E074	20910
chr1	32392517	32392752	E074	20994
chr1	32393617	32393701	E074	22094
chr1	32394326	32394681	E074	22803
chr1	32395089	32395201	E074	23566
chr1	32395427	32395613	E074	23904
chr1	32395854	32395894	E074	24331
chr1	32395972	32396093	E074	24449
chr1	32396155	32396359	E074	24632
chr1	32396361	32396900	E074	24838
chr1	32396911	32397116	E074	25388
chr1	32397184	32397575	E074	25661
chr1	32397704	32397807	E074	26181
chr1	32398074	32398522	E074	26551
chr1	32398649	32398882	E074	27126
chr1	32398932	32399040	E074	27409
chr1	32399107	32399159	E074	27584
chr1	32399318	32399418	E074	27795
chr1	32399423	32399582	E074	27900
chr1	32399678	32399766	E074	28155
chr1	32399937	32400151	E074	28414
chr1	32400344	32400648	E074	28821
chr1	32401468	32401590	E074	29945
chr1	32401685	32401769	E074	30162
chr1	32404662	32404728	E074	33139
chr1	32404811	32404882	E074	33288
chr1	32405016	32406047	E074	33493
chr1	32420141	32421206	E074	48618
chr1	32421453	32421518	E074	49930
chr1	32332083	32332288	E081	-39235
chr1	32332349	32332389	E081	-39134
chr1	32332403	32332654	E081	-38869
chr1	32333569	32333721	E081	-37802
chr1	32334806	32334968	E081	-36555
chr1	32335021	32335378	E081	-36145
chr1	32335415	32335455	E081	-36068
chr1	32335834	32335954	E081	-35569
chr1	32335995	32336039	E081	-35484
chr1	32336089	32336196	E081	-35327
chr1	32346649	32347484	E081	-24039
chr1	32399678	32399766	E081	28155
chr1	32399937	32400151	E081	28414
chr1	32400344	32400648	E081	28821
chr1	32401468	32401590	E081	29945
chr1	32401685	32401769	E081	30162
chr1	32345880	32346059	E082	-25464
chr1	32346126	32346176	E082	-25347
chr1	32346311	32346377	E082	-25146
chr1	32401468	32401590	E082	29945
chr1	32401685	32401769	E082	30162

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	32402218	32404616	E067	30695
chr1	32402218	32404616	E068	30695
chr1	32402218	32404616	E069	30695
chr1	32402218	32404616	E070	30695
chr1	32402218	32404616	E071	30695
chr1	32402218	32404616	E072	30695
chr1	32402218	32404616	E073	30695
chr1	32402218	32404616	E074	30695
chr1	32402218	32404616	E082	30695