rs639233

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PTP4A2 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0284 (8505/29928,GnomAD)
T=0351 (10228/29118,TOPMED)
T=0386 (1934/5008,1000G)
T=0144 (556/3854,ALSPAC)
T=0138 (512/3708,TWINSUK)

Position: chr1:31907280 (GRCh38.p7) (1p35.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 303 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.31907280C>T
GRCh37.p13 chr 1	NC_000001.10:g.32372881C>T

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	3 Prime UTR Variant
PTP4A2 transcript variant 3	NM_001195100.1:c.	N/A	3 Prime UTR Variant
PTP4A2 transcript variant 4	NM_001195101.1:c.	N/A	3 Prime UTR Variant
PTP4A2 transcript variant X2	XM_005271231.3:c.	N/A	3 Prime UTR Variant
PTP4A2 transcript variant X3	XM_005271232.3:c.	N/A	3 Prime UTR Variant
PTP4A2 transcript variant X4	XM_017002401.1:c.	N/A	3 Prime UTR Variant
PTP4A2 transcript variant X1	XR_946766.2:n.295...XR_946766.2:n.2955G>A	G>A	Non Coding Transcript Variant
PTP4A2 transcript variant X2	XR_001737441.1:n....XR_001737441.1:n.2882G>A	G>A	Non Coding Transcript Variant
PTP4A2 transcript variant X3	XR_001737442.1:n....XR_001737442.1:n.2832G>A	G>A	Non Coding Transcript Variant
PTP4A2 transcript variant X4	XR_001737443.1:n....XR_001737443.1:n.2700G>A	G>A	Non Coding Transcript Variant
PTP4A2 transcript variant X5	XR_001737444.1:n....XR_001737444.1:n.2634G>A	G>A	Non Coding Transcript Variant
PTP4A2 transcript variant X6	XR_001737445.1:n....XR_001737445.1:n.2744G>A	G>A	Non Coding Transcript Variant
PTP4A2 transcript variant X7	XR_001737446.1:n....XR_001737446.1:n.2690G>A	G>A	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.358	T=0.642
1000Genomes	American	Sub	694	C=0.690	T=0.310
1000Genomes	East Asian	Sub	1008	C=0.604	T=0.396
1000Genomes	Europe	Sub	1006	C=0.864	T=0.136
1000Genomes	Global	Study-wide	5008	C=0.614	T=0.386
1000Genomes	South Asian	Sub	978	C=0.660	T=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.856	T=0.144
The Genome Aggregation Database	African	Sub	8708	C=0.416	T=0.584
The Genome Aggregation Database	American	Sub	834	C=0.800	T=0.200
The Genome Aggregation Database	East Asian	Sub	1602	C=0.624	T=0.376
The Genome Aggregation Database	Europe	Sub	18482	C=0.859	T=0.140
The Genome Aggregation Database	Global	Study-wide	29928	C=0.715	T=0.284
The Genome Aggregation Database	Other	Sub	302	C=0.820	T=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.648	T=0.351
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.862	T=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
rs639233	2.06E-06	alcohol consumption	23953852

eQTL of rs639233 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 rs639233 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	-46251
chr1	32370412	32370729	E067	-2152
chr1	32371284	32371398	E067	-1483
chr1	32378578	32378622	E067	5697
chr1	32378643	32378693	E067	5762
chr1	32379604	32379667	E067	6723
chr1	32380100	32380170	E067	7219
chr1	32389492	32389989	E067	16611
chr1	32389994	32390099	E067	17113
chr1	32390599	32391077	E067	17718
chr1	32391998	32392108	E067	19117
chr1	32392120	32392281	E067	19239
chr1	32392433	32392473	E067	19552
chr1	32392517	32392752	E067	19636
chr1	32392886	32393536	E067	20005
chr1	32394326	32394681	E067	21445
chr1	32395089	32395201	E067	22208
chr1	32395427	32395613	E067	22546
chr1	32395854	32395894	E067	22973
chr1	32395972	32396093	E067	23091
chr1	32396155	32396359	E067	23274
chr1	32396361	32396900	E067	23480
chr1	32396911	32397116	E067	24030
chr1	32397184	32397575	E067	24303
chr1	32397704	32397807	E067	24823
chr1	32398074	32398522	E067	25193
chr1	32398649	32398882	E067	25768
chr1	32399423	32399582	E067	26542
chr1	32399678	32399766	E067	26797
chr1	32399937	32400151	E067	27056
chr1	32400344	32400648	E067	27463
chr1	32401468	32401590	E067	28587
chr1	32401685	32401769	E067	28804
chr1	32420141	32421206	E067	47260
chr1	32376634	32376863	E068	3753
chr1	32377790	32377851	E068	4909
chr1	32377947	32378272	E068	5066
chr1	32379604	32379667	E068	6723
chr1	32380100	32380170	E068	7219
chr1	32386600	32386853	E068	13719
chr1	32386890	32387077	E068	14009
chr1	32387152	32387271	E068	14271
chr1	32387286	32387420	E068	14405
chr1	32387608	32387706	E068	14727
chr1	32387791	32387839	E068	14910
chr1	32388070	32388176	E068	15189
chr1	32388230	32388527	E068	15349
chr1	32388658	32388740	E068	15777
chr1	32388809	32388905	E068	15928
chr1	32389492	32389989	E068	16611
chr1	32389994	32390099	E068	17113
chr1	32390599	32391077	E068	17718
chr1	32391998	32392108	E068	19117
chr1	32392120	32392281	E068	19239
chr1	32392433	32392473	E068	19552
chr1	32392517	32392752	E068	19636
chr1	32392886	32393536	E068	20005
chr1	32393617	32393701	E068	20736
chr1	32394138	32394227	E068	21257
chr1	32394326	32394681	E068	21445
chr1	32395089	32395201	E068	22208
chr1	32395427	32395613	E068	22546
chr1	32395854	32395894	E068	22973
chr1	32395972	32396093	E068	23091
chr1	32396155	32396359	E068	23274
chr1	32396361	32396900	E068	23480
chr1	32396911	32397116	E068	24030
chr1	32397184	32397575	E068	24303
chr1	32397704	32397807	E068	24823
chr1	32398074	32398522	E068	25193
chr1	32398649	32398882	E068	25768
chr1	32398932	32399040	E068	26051
chr1	32399107	32399159	E068	26226
chr1	32399318	32399418	E068	26437
chr1	32399423	32399582	E068	26542
chr1	32400344	32400648	E068	27463
chr1	32401468	32401590	E068	28587
chr1	32401685	32401769	E068	28804
chr1	32404662	32404728	E068	31781
chr1	32404811	32404882	E068	31930
chr1	32420141	32421206	E068	47260
chr1	32421557	32422224	E068	48676
chr1	32326252	32326630	E069	-46251
chr1	32376634	32376863	E069	3753
chr1	32377790	32377851	E069	4909
chr1	32377947	32378272	E069	5066
chr1	32378484	32378545	E069	5603
chr1	32378578	32378622	E069	5697
chr1	32379604	32379667	E069	6723
chr1	32386600	32386853	E069	13719
chr1	32386890	32387077	E069	14009
chr1	32387152	32387271	E069	14271
chr1	32387286	32387420	E069	14405
chr1	32387608	32387706	E069	14727
chr1	32387791	32387839	E069	14910
chr1	32388070	32388176	E069	15189
chr1	32389492	32389989	E069	16611
chr1	32389994	32390099	E069	17113
chr1	32390599	32391077	E069	17718
chr1	32392120	32392281	E069	19239
chr1	32392433	32392473	E069	19552
chr1	32392517	32392752	E069	19636
chr1	32392886	32393536	E069	20005
chr1	32393617	32393701	E069	20736
chr1	32393972	32394019	E069	21091
chr1	32394138	32394227	E069	21257
chr1	32394326	32394681	E069	21445
chr1	32396155	32396359	E069	23274
chr1	32396361	32396900	E069	23480
chr1	32396911	32397116	E069	24030
chr1	32397184	32397575	E069	24303
chr1	32397704	32397807	E069	24823
chr1	32398074	32398522	E069	25193
chr1	32398649	32398882	E069	25768
chr1	32398932	32399040	E069	26051
chr1	32399107	32399159	E069	26226
chr1	32399678	32399766	E069	26797
chr1	32399937	32400151	E069	27056
chr1	32400344	32400648	E069	27463
chr1	32401468	32401590	E069	28587
chr1	32401685	32401769	E069	28804
chr1	32404662	32404728	E069	31781
chr1	32420141	32421206	E069	47260
chr1	32421453	32421518	E069	48572
chr1	32421557	32422224	E069	48676
chr1	32392120	32392281	E070	19239
chr1	32392433	32392473	E070	19552
chr1	32392517	32392752	E070	19636
chr1	32392886	32393536	E070	20005
chr1	32326252	32326630	E071	-46251
chr1	32332083	32332288	E071	-40593
chr1	32332349	32332389	E071	-40492
chr1	32369499	32369666	E071	-3215
chr1	32369794	32369887	E071	-2994
chr1	32376634	32376863	E071	3753
chr1	32377790	32377851	E071	4909
chr1	32377947	32378272	E071	5066
chr1	32378484	32378545	E071	5603
chr1	32378578	32378622	E071	5697
chr1	32378643	32378693	E071	5762
chr1	32378746	32378820	E071	5865
chr1	32379604	32379667	E071	6723
chr1	32386600	32386853	E071	13719
chr1	32386890	32387077	E071	14009
chr1	32387152	32387271	E071	14271
chr1	32388230	32388527	E071	15349
chr1	32388658	32388740	E071	15777
chr1	32388809	32388905	E071	15928
chr1	32389492	32389989	E071	16611
chr1	32389994	32390099	E071	17113
chr1	32390599	32391077	E071	17718
chr1	32391666	32391716	E071	18785
chr1	32391775	32391972	E071	18894
chr1	32391998	32392108	E071	19117
chr1	32393617	32393701	E071	20736
chr1	32394326	32394681	E071	21445
chr1	32395089	32395201	E071	22208
chr1	32395427	32395613	E071	22546
chr1	32395854	32395894	E071	22973
chr1	32395972	32396093	E071	23091
chr1	32396155	32396359	E071	23274
chr1	32396361	32396900	E071	23480
chr1	32397704	32397807	E071	24823
chr1	32398074	32398522	E071	25193
chr1	32398649	32398882	E071	25768
chr1	32398932	32399040	E071	26051
chr1	32399107	32399159	E071	26226
chr1	32399318	32399418	E071	26437
chr1	32399423	32399582	E071	26542
chr1	32399678	32399766	E071	26797
chr1	32399937	32400151	E071	27056
chr1	32400344	32400648	E071	27463
chr1	32401468	32401590	E071	28587
chr1	32401685	32401769	E071	28804
chr1	32404811	32404882	E071	31930
chr1	32405016	32406047	E071	32135
chr1	32410828	32410878	E071	37947
chr1	32411119	32411163	E071	38238
chr1	32411272	32411334	E071	38391
chr1	32411385	32411487	E071	38504
chr1	32420141	32421206	E071	47260
chr1	32421453	32421518	E071	48572
chr1	32421557	32422224	E071	48676
chr1	32325414	32325583	E072	-47298
chr1	32326252	32326630	E072	-46251
chr1	32332083	32332288	E072	-40593
chr1	32332349	32332389	E072	-40492
chr1	32332403	32332654	E072	-40227
chr1	32345880	32346059	E072	-26822
chr1	32346126	32346176	E072	-26705
chr1	32346311	32346377	E072	-26504
chr1	32346649	32347484	E072	-25397
chr1	32379604	32379667	E072	6723
chr1	32386890	32387077	E072	14009
chr1	32387152	32387271	E072	14271
chr1	32387286	32387420	E072	14405
chr1	32389492	32389989	E072	16611
chr1	32389994	32390099	E072	17113
chr1	32390599	32391077	E072	17718
chr1	32392433	32392473	E072	19552
chr1	32392517	32392752	E072	19636
chr1	32392886	32393536	E072	20005
chr1	32393617	32393701	E072	20736
chr1	32394326	32394681	E072	21445
chr1	32395089	32395201	E072	22208
chr1	32395427	32395613	E072	22546
chr1	32395854	32395894	E072	22973
chr1	32395972	32396093	E072	23091
chr1	32396155	32396359	E072	23274
chr1	32396361	32396900	E072	23480
chr1	32397184	32397575	E072	24303
chr1	32398074	32398522	E072	25193
chr1	32398649	32398882	E072	25768
chr1	32398932	32399040	E072	26051
chr1	32399107	32399159	E072	26226
chr1	32399318	32399418	E072	26437
chr1	32399423	32399582	E072	26542
chr1	32399678	32399766	E072	26797
chr1	32399937	32400151	E072	27056
chr1	32400344	32400648	E072	27463
chr1	32401468	32401590	E072	28587
chr1	32401685	32401769	E072	28804
chr1	32420141	32421206	E072	47260
chr1	32421453	32421518	E072	48572
chr1	32421557	32422224	E072	48676
chr1	32389492	32389989	E073	16611
chr1	32389994	32390099	E073	17113
chr1	32390599	32391077	E073	17718
chr1	32392433	32392473	E073	19552
chr1	32392517	32392752	E073	19636
chr1	32392886	32393536	E073	20005
chr1	32395427	32395613	E073	22546
chr1	32395854	32395894	E073	22973
chr1	32395972	32396093	E073	23091
chr1	32396155	32396359	E073	23274
chr1	32396361	32396900	E073	23480
chr1	32398074	32398522	E073	25193
chr1	32404662	32404728	E073	31781
chr1	32420141	32421206	E073	47260
chr1	32326252	32326630	E074	-46251
chr1	32377790	32377851	E074	4909
chr1	32379604	32379667	E074	6723
chr1	32380100	32380170	E074	7219
chr1	32386600	32386853	E074	13719
chr1	32386890	32387077	E074	14009
chr1	32387152	32387271	E074	14271
chr1	32387286	32387420	E074	14405
chr1	32389492	32389989	E074	16611
chr1	32389994	32390099	E074	17113
chr1	32390599	32391077	E074	17718
chr1	32391998	32392108	E074	19117
chr1	32392120	32392281	E074	19239
chr1	32392433	32392473	E074	19552
chr1	32392517	32392752	E074	19636
chr1	32393617	32393701	E074	20736
chr1	32394326	32394681	E074	21445
chr1	32395089	32395201	E074	22208
chr1	32395427	32395613	E074	22546
chr1	32395854	32395894	E074	22973
chr1	32395972	32396093	E074	23091
chr1	32396155	32396359	E074	23274
chr1	32396361	32396900	E074	23480
chr1	32396911	32397116	E074	24030
chr1	32397184	32397575	E074	24303
chr1	32397704	32397807	E074	24823
chr1	32398074	32398522	E074	25193
chr1	32398649	32398882	E074	25768
chr1	32398932	32399040	E074	26051
chr1	32399107	32399159	E074	26226
chr1	32399318	32399418	E074	26437
chr1	32399423	32399582	E074	26542
chr1	32399678	32399766	E074	26797
chr1	32399937	32400151	E074	27056
chr1	32400344	32400648	E074	27463
chr1	32401468	32401590	E074	28587
chr1	32401685	32401769	E074	28804
chr1	32404662	32404728	E074	31781
chr1	32404811	32404882	E074	31930
chr1	32405016	32406047	E074	32135
chr1	32420141	32421206	E074	47260
chr1	32421453	32421518	E074	48572
chr1	32421557	32422224	E074	48676
chr1	32332083	32332288	E081	-40593
chr1	32332349	32332389	E081	-40492
chr1	32332403	32332654	E081	-40227
chr1	32333569	32333721	E081	-39160
chr1	32334806	32334968	E081	-37913
chr1	32335021	32335378	E081	-37503
chr1	32335415	32335455	E081	-37426
chr1	32335834	32335954	E081	-36927
chr1	32335995	32336039	E081	-36842
chr1	32336089	32336196	E081	-36685
chr1	32346649	32347484	E081	-25397
chr1	32399678	32399766	E081	26797
chr1	32399937	32400151	E081	27056
chr1	32400344	32400648	E081	27463
chr1	32401468	32401590	E081	28587
chr1	32401685	32401769	E081	28804
chr1	32345880	32346059	E082	-26822
chr1	32346126	32346176	E082	-26705
chr1	32346311	32346377	E082	-26504
chr1	32401468	32401590	E082	28587
chr1	32401685	32401769	E082	28804

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	32402218	32404616	E067	29337
chr1	32402218	32404616	E068	29337
chr1	32402218	32404616	E069	29337
chr1	32402218	32404616	E070	29337
chr1	32402218	32404616	E071	29337
chr1	32402218	32404616	E072	29337
chr1	32402218	32404616	E073	29337
chr1	32402218	32404616	E074	29337
chr1	32402218	32404616	E082	29337