rs1041264

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

RAPGEF1 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0233 (6937/29700,GnomAD)
T=0259 (7548/29118,TOPMED)
T=0328 (1642/5008,1000G)
T=0132 (510/3854,ALSPAC)
T=0119 (443/3708,TWINSUK)

Position: chr9:131741953 (GRCh38.p7) (9q34.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 358 Enhancers around

Promoter: 4 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.131741953C>T
GRCh37.p13 chr 9	NC_000009.11:g.134617340C>T

Gene: RAPGEF1, Rap guanine nucleotide exchange factor 1(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RAPGEF1 transcript variant 3	NM_001304275.1:c.	N/A	N/A
RAPGEF1 transcript variant 1	NM_005312.3:c.	N/A	N/A
RAPGEF1 transcript variant 2	NM_198679.1:c.	N/A	N/A
RAPGEF1 transcript variant X6	XM_005272186.4:c.	N/A	Upstream Transcript Variant
RAPGEF1 transcript variant X15	XM_005272191.3:c.	N/A	Upstream Transcript Variant
RAPGEF1 transcript variant X5	XM_006717067.3:c.	N/A	N/A
RAPGEF1 transcript variant X14	XM_006717072.3:c.	N/A	N/A
RAPGEF1 transcript variant X23	XM_006717074.3:c.	N/A	N/A
RAPGEF1 transcript variant X1	XM_011518569.2:c.	N/A	N/A
RAPGEF1 transcript variant X2	XM_011518570.2:c.	N/A	N/A
RAPGEF1 transcript variant X3	XM_011518571.2:c.	N/A	N/A
RAPGEF1 transcript variant X4	XM_011518572.2:c.	N/A	N/A
RAPGEF1 transcript variant X7	XM_011518573.2:c.	N/A	N/A
RAPGEF1 transcript variant X9	XM_011518574.2:c.	N/A	N/A
RAPGEF1 transcript variant X10	XM_011518575.2:c.	N/A	N/A
RAPGEF1 transcript variant X19	XM_011518576.2:c.	N/A	N/A
RAPGEF1 transcript variant X20	XM_011518577.2:c.	N/A	N/A
RAPGEF1 transcript variant X21	XM_011518578.2:c.	N/A	N/A
RAPGEF1 transcript variant X22	XM_011518579.2:c.	N/A	N/A
RAPGEF1 transcript variant X27	XM_011518580.2:c.	N/A	N/A
RAPGEF1 transcript variant X28	XM_011518581.2:c.	N/A	N/A
RAPGEF1 transcript variant X29	XM_011518582.2:c.	N/A	N/A
RAPGEF1 transcript variant X8	XM_017014633.1:c.	N/A	N/A
RAPGEF1 transcript variant X11	XM_017014634.1:c.	N/A	N/A
RAPGEF1 transcript variant X12	XM_017014635.1:c.	N/A	N/A
RAPGEF1 transcript variant X13	XM_017014636.1:c.	N/A	N/A
RAPGEF1 transcript variant X16	XM_017014637.1:c.	N/A	N/A
RAPGEF1 transcript variant X17	XM_017014638.1:c.	N/A	N/A
RAPGEF1 transcript variant X18	XM_017014639.1:c.	N/A	N/A
RAPGEF1 transcript variant X24	XM_017014640.1:c.	N/A	N/A
RAPGEF1 transcript variant X26	XM_017014641.1:c.	N/A	N/A
RAPGEF1 transcript variant X25	XR_001746282.1:n.	N/A	N/A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.591	T=0.409
1000Genomes	American	Sub	694	C=0.760	T=0.240
1000Genomes	East Asian	Sub	1008	C=0.560	T=0.440
1000Genomes	Europe	Sub	1006	C=0.820	T=0.180
1000Genomes	Global	Study-wide	5008	C=0.672	T=0.328
1000Genomes	South Asian	Sub	978	C=0.680	T=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.868	T=0.132
The Genome Aggregation Database	African	Sub	8646	C=0.633	T=0.367
The Genome Aggregation Database	American	Sub	830	C=0.780	T=0.220
The Genome Aggregation Database	East Asian	Sub	1610	C=0.537	T=0.463
The Genome Aggregation Database	Europe	Sub	18312	C=0.848	T=0.151
The Genome Aggregation Database	Global	Study-wide	29700	C=0.766	T=0.233
The Genome Aggregation Database	Other	Sub	302	C=0.820	T=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.740	T=0.259
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.881	T=0.119

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
rs1041264	3.07E-06	alcohol consumption	23953852

eQTL of rs1041264 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 rs1041264 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 )
chr9	134570643	134570940	E067	-46400
chr9	134570993	134571081	E067	-46259
chr9	134571208	134571318	E067	-46022
chr9	134571340	134571414	E067	-45926
chr9	134571429	134571547	E067	-45793
chr9	134571573	134571703	E067	-45637
chr9	134572371	134573124	E067	-44216
chr9	134573222	134574436	E067	-42904
chr9	134579536	134580126	E067	-37214
chr9	134580194	134580351	E067	-36989
chr9	134580378	134580446	E067	-36894
chr9	134580464	134580585	E067	-36755
chr9	134580621	134580719	E067	-36621
chr9	134580824	134581877	E067	-35463
chr9	134582052	134582223	E067	-35117
chr9	134582537	134582602	E067	-34738
chr9	134582806	134582886	E067	-34454
chr9	134582889	134582953	E067	-34387
chr9	134583114	134584077	E067	-33263
chr9	134602669	134605270	E067	-12070
chr9	134606114	134608087	E067	-9253
chr9	134608088	134610126	E067	-7214
chr9	134610457	134611652	E067	-5688
chr9	134611701	134611751	E067	-5589
chr9	134611843	134612361	E067	-4979
chr9	134612400	134612469	E067	-4871
chr9	134612488	134612694	E067	-4646
chr9	134612703	134612885	E067	-4455
chr9	134612894	134613028	E067	-4312
chr9	134637506	134637669	E067	20166
chr9	134637675	134638289	E067	20335
chr9	134638393	134638495	E067	21053
chr9	134567529	134567579	E068	-49761
chr9	134567729	134567942	E068	-49398
chr9	134567946	134568335	E068	-49005
chr9	134568477	134568531	E068	-48809
chr9	134568902	134568969	E068	-48371
chr9	134568985	134569845	E068	-47495
chr9	134570643	134570940	E068	-46400
chr9	134570993	134571081	E068	-46259
chr9	134571208	134571318	E068	-46022
chr9	134571340	134571414	E068	-45926
chr9	134571429	134571547	E068	-45793
chr9	134571573	134571703	E068	-45637
chr9	134572371	134573124	E068	-44216
chr9	134573222	134574436	E068	-42904
chr9	134574541	134574610	E068	-42730
chr9	134574968	134575076	E068	-42264
chr9	134575101	134575155	E068	-42185
chr9	134575410	134575460	E068	-41880
chr9	134575492	134575542	E068	-41798
chr9	134576084	134576149	E068	-41191
chr9	134576169	134576219	E068	-41121
chr9	134579087	134579336	E068	-38004
chr9	134579358	134579472	E068	-37868
chr9	134579536	134580126	E068	-37214
chr9	134580194	134580351	E068	-36989
chr9	134580378	134580446	E068	-36894
chr9	134580464	134580585	E068	-36755
chr9	134580621	134580719	E068	-36621
chr9	134580824	134581877	E068	-35463
chr9	134582052	134582223	E068	-35117
chr9	134582537	134582602	E068	-34738
chr9	134582806	134582886	E068	-34454
chr9	134582889	134582953	E068	-34387
chr9	134583114	134584077	E068	-33263
chr9	134584178	134584241	E068	-33099
chr9	134584817	134586127	E068	-31213
chr9	134588542	134588739	E068	-28601
chr9	134588820	134589089	E068	-28251
chr9	134590148	134590238	E068	-27102
chr9	134590386	134590495	E068	-26845
chr9	134590577	134590627	E068	-26713
chr9	134590738	134590788	E068	-26552
chr9	134591607	134591853	E068	-25487
chr9	134592303	134592413	E068	-24927
chr9	134592540	134592690	E068	-24650
chr9	134592727	134592777	E068	-24563
chr9	134593468	134593863	E068	-23477
chr9	134594152	134595264	E068	-22076
chr9	134595338	134595411	E068	-21929
chr9	134595758	134595941	E068	-21399
chr9	134602495	134602622	E068	-14718
chr9	134602669	134605270	E068	-12070
chr9	134606114	134608087	E068	-9253
chr9	134608088	134610126	E068	-7214
chr9	134610141	134610425	E068	-6915
chr9	134610457	134611652	E068	-5688
chr9	134611701	134611751	E068	-5589
chr9	134611843	134612361	E068	-4979
chr9	134612400	134612469	E068	-4871
chr9	134612488	134612694	E068	-4646
chr9	134612703	134612885	E068	-4455
chr9	134612894	134613028	E068	-4312
chr9	134622606	134623099	E068	5266
chr9	134630950	134631305	E068	13610
chr9	134631329	134631479	E068	13989
chr9	134567729	134567942	E069	-49398
chr9	134567946	134568335	E069	-49005
chr9	134568477	134568531	E069	-48809
chr9	134572371	134573124	E069	-44216
chr9	134573222	134574436	E069	-42904
chr9	134574541	134574610	E069	-42730
chr9	134574968	134575076	E069	-42264
chr9	134575101	134575155	E069	-42185
chr9	134575410	134575460	E069	-41880
chr9	134575492	134575542	E069	-41798
chr9	134579536	134580126	E069	-37214
chr9	134580194	134580351	E069	-36989
chr9	134580378	134580446	E069	-36894
chr9	134580464	134580585	E069	-36755
chr9	134580621	134580719	E069	-36621
chr9	134582052	134582223	E069	-35117
chr9	134582537	134582602	E069	-34738
chr9	134582806	134582886	E069	-34454
chr9	134582889	134582953	E069	-34387
chr9	134583114	134584077	E069	-33263
chr9	134595758	134595941	E069	-21399
chr9	134595968	134596014	E069	-21326
chr9	134602669	134605270	E069	-12070
chr9	134606114	134608087	E069	-9253
chr9	134608088	134610126	E069	-7214
chr9	134610141	134610425	E069	-6915
chr9	134610457	134611652	E069	-5688
chr9	134611701	134611751	E069	-5589
chr9	134611843	134612361	E069	-4979
chr9	134612400	134612469	E069	-4871
chr9	134612488	134612694	E069	-4646
chr9	134572371	134573124	E070	-44216
chr9	134579536	134580126	E070	-37214
chr9	134580194	134580351	E070	-36989
chr9	134580378	134580446	E070	-36894
chr9	134580464	134580585	E070	-36755
chr9	134580621	134580719	E070	-36621
chr9	134580824	134581877	E070	-35463
chr9	134597562	134598017	E070	-19323
chr9	134606114	134608087	E070	-9253
chr9	134660645	134660748	E070	43305
chr9	134567729	134567942	E071	-49398
chr9	134567946	134568335	E071	-49005
chr9	134570643	134570940	E071	-46400
chr9	134570993	134571081	E071	-46259
chr9	134571208	134571318	E071	-46022
chr9	134571340	134571414	E071	-45926
chr9	134571429	134571547	E071	-45793
chr9	134571573	134571703	E071	-45637
chr9	134572135	134572185	E071	-45155
chr9	134572371	134573124	E071	-44216
chr9	134573222	134574436	E071	-42904
chr9	134574541	134574610	E071	-42730
chr9	134574968	134575076	E071	-42264
chr9	134575101	134575155	E071	-42185
chr9	134575410	134575460	E071	-41880
chr9	134575492	134575542	E071	-41798
chr9	134576084	134576149	E071	-41191
chr9	134576169	134576219	E071	-41121
chr9	134576318	134576404	E071	-40936
chr9	134578990	134579047	E071	-38293
chr9	134579087	134579336	E071	-38004
chr9	134579358	134579472	E071	-37868
chr9	134579536	134580126	E071	-37214
chr9	134580194	134580351	E071	-36989
chr9	134580378	134580446	E071	-36894
chr9	134580464	134580585	E071	-36755
chr9	134580621	134580719	E071	-36621
chr9	134580824	134581877	E071	-35463
chr9	134582052	134582223	E071	-35117
chr9	134582537	134582602	E071	-34738
chr9	134582806	134582886	E071	-34454
chr9	134582889	134582953	E071	-34387
chr9	134583114	134584077	E071	-33263
chr9	134587450	134587646	E071	-29694
chr9	134587756	134588070	E071	-29270
chr9	134593295	134593421	E071	-23919
chr9	134593468	134593863	E071	-23477
chr9	134594152	134595264	E071	-22076
chr9	134599980	134601091	E071	-16249
chr9	134602669	134605270	E071	-12070
chr9	134608088	134610126	E071	-7214
chr9	134610141	134610425	E071	-6915
chr9	134610457	134611652	E071	-5688
chr9	134611701	134611751	E071	-5589
chr9	134612703	134612885	E071	-4455
chr9	134612894	134613028	E071	-4312
chr9	134618587	134619278	E071	1247
chr9	134622606	134623099	E071	5266
chr9	134572371	134573124	E072	-44216
chr9	134573222	134574436	E072	-42904
chr9	134574541	134574610	E072	-42730
chr9	134574968	134575076	E072	-42264
chr9	134575101	134575155	E072	-42185
chr9	134579536	134580126	E072	-37214
chr9	134580194	134580351	E072	-36989
chr9	134580378	134580446	E072	-36894
chr9	134580464	134580585	E072	-36755
chr9	134583114	134584077	E072	-33263
chr9	134593468	134593863	E072	-23477
chr9	134594152	134595264	E072	-22076
chr9	134599980	134601091	E072	-16249
chr9	134602669	134605270	E072	-12070
chr9	134606114	134608087	E072	-9253
chr9	134611701	134611751	E072	-5589
chr9	134612400	134612469	E072	-4871
chr9	134612488	134612694	E072	-4646
chr9	134612703	134612885	E072	-4455
chr9	134612894	134613028	E072	-4312
chr9	134567946	134568335	E073	-49005
chr9	134570415	134570602	E073	-46738
chr9	134570643	134570940	E073	-46400
chr9	134570993	134571081	E073	-46259
chr9	134573222	134574436	E073	-42904
chr9	134574541	134574610	E073	-42730
chr9	134579536	134580126	E073	-37214
chr9	134580194	134580351	E073	-36989
chr9	134580378	134580446	E073	-36894
chr9	134580464	134580585	E073	-36755
chr9	134580621	134580719	E073	-36621
chr9	134583114	134584077	E073	-33263
chr9	134588542	134588739	E073	-28601
chr9	134588820	134589089	E073	-28251
chr9	134590148	134590238	E073	-27102
chr9	134590386	134590495	E073	-26845
chr9	134590577	134590627	E073	-26713
chr9	134590738	134590788	E073	-26552
chr9	134593468	134593863	E073	-23477
chr9	134602669	134605270	E073	-12070
chr9	134606114	134608087	E073	-9253
chr9	134608088	134610126	E073	-7214
chr9	134610141	134610425	E073	-6915
chr9	134610457	134611652	E073	-5688
chr9	134611701	134611751	E073	-5589
chr9	134611843	134612361	E073	-4979
chr9	134612400	134612469	E073	-4871
chr9	134612488	134612694	E073	-4646
chr9	134612703	134612885	E073	-4455
chr9	134637675	134638289	E073	20335
chr9	134567729	134567942	E074	-49398
chr9	134567946	134568335	E074	-49005
chr9	134572371	134573124	E074	-44216
chr9	134573222	134574436	E074	-42904
chr9	134574541	134574610	E074	-42730
chr9	134574968	134575076	E074	-42264
chr9	134575101	134575155	E074	-42185
chr9	134582537	134582602	E074	-34738
chr9	134582806	134582886	E074	-34454
chr9	134582889	134582953	E074	-34387
chr9	134583114	134584077	E074	-33263
chr9	134591385	134591606	E074	-25734
chr9	134591607	134591853	E074	-25487
chr9	134592303	134592413	E074	-24927
chr9	134592540	134592690	E074	-24650
chr9	134592727	134592777	E074	-24563
chr9	134593171	134593279	E074	-24061
chr9	134593295	134593421	E074	-23919
chr9	134593468	134593863	E074	-23477
chr9	134594152	134595264	E074	-22076
chr9	134595338	134595411	E074	-21929
chr9	134595758	134595941	E074	-21399
chr9	134595968	134596014	E074	-21326
chr9	134596057	134596144	E074	-21196
chr9	134596507	134596608	E074	-20732
chr9	134596688	134596776	E074	-20564
chr9	134596788	134596964	E074	-20376
chr9	134596978	134597095	E074	-20245
chr9	134602669	134605270	E074	-12070
chr9	134606114	134608087	E074	-9253
chr9	134608088	134610126	E074	-7214
chr9	134610141	134610425	E074	-6915
chr9	134610457	134611652	E074	-5688
chr9	134611701	134611751	E074	-5589
chr9	134611843	134612361	E074	-4979
chr9	134612400	134612469	E074	-4871
chr9	134612488	134612694	E074	-4646
chr9	134612703	134612885	E074	-4455
chr9	134637506	134637669	E074	20166
chr9	134637675	134638289	E074	20335
chr9	134638393	134638495	E074	21053
chr9	134570993	134571081	E081	-46259
chr9	134571208	134571318	E081	-46022
chr9	134571340	134571414	E081	-45926
chr9	134571429	134571547	E081	-45793
chr9	134571573	134571703	E081	-45637
chr9	134572135	134572185	E081	-45155
chr9	134572371	134573124	E081	-44216
chr9	134573222	134574436	E081	-42904
chr9	134579358	134579472	E081	-37868
chr9	134579536	134580126	E081	-37214
chr9	134580194	134580351	E081	-36989
chr9	134580378	134580446	E081	-36894
chr9	134580464	134580585	E081	-36755
chr9	134580621	134580719	E081	-36621
chr9	134580824	134581877	E081	-35463
chr9	134595758	134595941	E081	-21399
chr9	134595968	134596014	E081	-21326
chr9	134596057	134596144	E081	-21196
chr9	134596507	134596608	E081	-20732
chr9	134596688	134596776	E081	-20564
chr9	134596788	134596964	E081	-20376
chr9	134596978	134597095	E081	-20245
chr9	134597562	134598017	E081	-19323
chr9	134598039	134598143	E081	-19197
chr9	134599062	134599279	E081	-18061
chr9	134599530	134599620	E081	-17720
chr9	134599633	134599704	E081	-17636
chr9	134599980	134601091	E081	-16249
chr9	134601486	134601555	E081	-15785
chr9	134601614	134601677	E081	-15663
chr9	134601706	134601888	E081	-15452
chr9	134601982	134602365	E081	-14975
chr9	134602495	134602622	E081	-14718
chr9	134602669	134605270	E081	-12070
chr9	134606114	134608087	E081	-9253
chr9	134608088	134610126	E081	-7214
chr9	134610457	134611652	E081	-5688
chr9	134611701	134611751	E081	-5589
chr9	134611843	134612361	E081	-4979
chr9	134612400	134612469	E081	-4871
chr9	134612488	134612694	E081	-4646
chr9	134612703	134612885	E081	-4455
chr9	134612894	134613028	E081	-4312
chr9	134613419	134613537	E081	-3803
chr9	134630950	134631305	E081	13610
chr9	134637506	134637669	E081	20166
chr9	134637675	134638289	E081	20335
chr9	134638393	134638495	E081	21053
chr9	134567946	134568335	E082	-49005
chr9	134570643	134570940	E082	-46400
chr9	134570993	134571081	E082	-46259
chr9	134571208	134571318	E082	-46022
chr9	134571340	134571414	E082	-45926
chr9	134571429	134571547	E082	-45793
chr9	134571573	134571703	E082	-45637
chr9	134572135	134572185	E082	-45155
chr9	134572371	134573124	E082	-44216
chr9	134579536	134580126	E082	-37214
chr9	134580194	134580351	E082	-36989
chr9	134580378	134580446	E082	-36894
chr9	134580464	134580585	E082	-36755
chr9	134580621	134580719	E082	-36621
chr9	134580824	134581877	E082	-35463
chr9	134582052	134582223	E082	-35117
chr9	134596507	134596608	E082	-20732
chr9	134596688	134596776	E082	-20564
chr9	134596788	134596964	E082	-20376
chr9	134596978	134597095	E082	-20245
chr9	134597562	134598017	E082	-19323
chr9	134598039	134598143	E082	-19197
chr9	134598610	134598666	E082	-18674
chr9	134598717	134598875	E082	-18465
chr9	134599062	134599279	E082	-18061
chr9	134599530	134599620	E082	-17720
chr9	134599633	134599704	E082	-17636
chr9	134599980	134601091	E082	-16249
chr9	134602669	134605270	E082	-12070
chr9	134606114	134608087	E082	-9253
chr9	134610141	134610425	E082	-6915
chr9	134660645	134660748	E082	43305
chr9	134660779	134660856	E082	43439

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	134614129	134616002	E068	-1338
chr9	134614129	134616002	E070	-1338
chr9	134614129	134616002	E073	-1338
chr9	134614129	134616002	E074	-1338