rs17148121

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

RAPGEF1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0246 (7372/29904,GnomAD)
T=0280 (8180/29118,TOPMED)
T=0299 (1498/5008,1000G)
T=0131 (505/3854,ALSPAC)
T=0118 (436/3708,TWINSUK)

Position: chr9:131628423 (GRCh38.p7) (9q34.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 344 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.131628423C>T
GRCh37.p13 chr 9	NC_000009.11:g.134503810C>T

Gene: RAPGEF1, Rap guanine nucleotide exchange factor 1(minus strand)

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.514	T=0.486
1000Genomes	American	Sub	694	C=0.800	T=0.200
1000Genomes	East Asian	Sub	1008	C=0.666	T=0.334
1000Genomes	Europe	Sub	1006	C=0.821	T=0.179
1000Genomes	Global	Study-wide	5008	C=0.701	T=0.299
1000Genomes	South Asian	Sub	978	C=0.800	T=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.869	T=0.131
The Genome Aggregation Database	African	Sub	8694	C=0.549	T=0.451
The Genome Aggregation Database	American	Sub	838	C=0.850	T=0.150
The Genome Aggregation Database	East Asian	Sub	1616	C=0.660	T=0.340
The Genome Aggregation Database	Europe	Sub	18456	C=0.852	T=0.147
The Genome Aggregation Database	Global	Study-wide	29904	C=0.753	T=0.246
The Genome Aggregation Database	Other	Sub	300	C=0.840	T=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.719	T=0.280
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.882	T=0.118

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
rs17148121	8.02E-06	alcohol consumption	23953852

eQTL of rs17148121 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr9:134503810	POMT1	ENSG00000130714.11	C>T	2.5154e-10	125521	Cerebellum

meQTL of rs17148121 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	134483337	134483415	E067	-20395
chr9	134483505	134483738	E067	-20072
chr9	134483741	134485483	E067	-18327
chr9	134485550	134486225	E067	-17585
chr9	134492595	134492677	E067	-11133
chr9	134492739	134492817	E067	-10993
chr9	134492916	134492970	E067	-10840
chr9	134493159	134493848	E067	-9962
chr9	134496339	134496460	E067	-7350
chr9	134496548	134496697	E067	-7113
chr9	134496731	134496857	E067	-6953
chr9	134499780	134501820	E067	-1990
chr9	134508452	134509433	E067	4642
chr9	134509480	134509723	E067	5670
chr9	134515905	134516073	E067	12095
chr9	134525111	134525261	E067	21301
chr9	134525350	134525552	E067	21540
chr9	134525557	134526306	E067	21747
chr9	134530254	134531007	E067	26444
chr9	134531436	134531510	E067	27626
chr9	134531546	134534558	E067	27736
chr9	134535843	134536685	E067	32033
chr9	134543467	134547093	E067	39657
chr9	134547121	134547248	E067	43311
chr9	134547261	134547417	E067	43451
chr9	134550081	134551377	E067	46271
chr9	134460000	134460193	E068	-43617
chr9	134468445	134468528	E068	-35282
chr9	134468542	134468744	E068	-35066
chr9	134468777	134468831	E068	-34979
chr9	134468942	134469028	E068	-34782
chr9	134469155	134469240	E068	-34570
chr9	134469288	134469433	E068	-34377
chr9	134469584	134469814	E068	-33996
chr9	134469833	134469956	E068	-33854
chr9	134470071	134470121	E068	-33689
chr9	134482288	134482328	E068	-21482
chr9	134482373	134482866	E068	-20944
chr9	134482940	134483098	E068	-20712
chr9	134483107	134483321	E068	-20489
chr9	134483337	134483415	E068	-20395
chr9	134483505	134483738	E068	-20072
chr9	134483741	134485483	E068	-18327
chr9	134485550	134486225	E068	-17585
chr9	134486402	134486815	E068	-16995
chr9	134486839	134487407	E068	-16403
chr9	134487455	134487540	E068	-16270
chr9	134487702	134488218	E068	-15592
chr9	134488226	134488717	E068	-15093
chr9	134488777	134488976	E068	-14834
chr9	134491830	134492553	E068	-11257
chr9	134492595	134492677	E068	-11133
chr9	134492739	134492817	E068	-10993
chr9	134492916	134492970	E068	-10840
chr9	134493159	134493848	E068	-9962
chr9	134493864	134493961	E068	-9849
chr9	134496339	134496460	E068	-7350
chr9	134496548	134496697	E068	-7113
chr9	134496731	134496857	E068	-6953
chr9	134496892	134497949	E068	-5861
chr9	134499780	134501820	E068	-1990
chr9	134508452	134509433	E068	4642
chr9	134515246	134515866	E068	11436
chr9	134515905	134516073	E068	12095
chr9	134516232	134516423	E068	12422
chr9	134520377	134521298	E068	16567
chr9	134525557	134526306	E068	21747
chr9	134530140	134530183	E068	26330
chr9	134530254	134531007	E068	26444
chr9	134531436	134531510	E068	27626
chr9	134531546	134534558	E068	27736
chr9	134535506	134535761	E068	31696
chr9	134535843	134536685	E068	32033
chr9	134536801	134536915	E068	32991
chr9	134536939	134536979	E068	33129
chr9	134542690	134543455	E068	38880
chr9	134543467	134547093	E068	39657
chr9	134547775	134548431	E068	43965
chr9	134549712	134549798	E068	45902
chr9	134549842	134550023	E068	46032
chr9	134550081	134551377	E068	46271
chr9	134454941	134455257	E069	-48553
chr9	134455327	134455526	E069	-48284
chr9	134483107	134483321	E069	-20489
chr9	134483337	134483415	E069	-20395
chr9	134483505	134483738	E069	-20072
chr9	134483741	134485483	E069	-18327
chr9	134485550	134486225	E069	-17585
chr9	134486402	134486815	E069	-16995
chr9	134492595	134492677	E069	-11133
chr9	134492739	134492817	E069	-10993
chr9	134492916	134492970	E069	-10840
chr9	134493159	134493848	E069	-9962
chr9	134493864	134493961	E069	-9849
chr9	134496339	134496460	E069	-7350
chr9	134496548	134496697	E069	-7113
chr9	134496731	134496857	E069	-6953
chr9	134499780	134501820	E069	-1990
chr9	134508452	134509433	E069	4642
chr9	134515246	134515866	E069	11436
chr9	134515905	134516073	E069	12095
chr9	134516232	134516423	E069	12422
chr9	134525111	134525261	E069	21301
chr9	134525350	134525552	E069	21540
chr9	134525557	134526306	E069	21747
chr9	134530254	134531007	E069	26444
chr9	134531546	134534558	E069	27736
chr9	134534636	134534723	E069	30826
chr9	134534885	134535226	E069	31075
chr9	134535506	134535761	E069	31696
chr9	134535843	134536685	E069	32033
chr9	134542690	134543455	E069	38880
chr9	134543467	134547093	E069	39657
chr9	134547121	134547248	E069	43311
chr9	134547261	134547417	E069	43451
chr9	134547450	134547538	E069	43640
chr9	134547710	134547760	E069	43900
chr9	134547775	134548431	E069	43965
chr9	134549842	134550023	E069	46032
chr9	134550081	134551377	E069	46271
chr9	134483505	134483738	E070	-20072
chr9	134483741	134485483	E070	-18327
chr9	134493159	134493848	E070	-9962
chr9	134515905	134516073	E070	12095
chr9	134531436	134531510	E070	27626
chr9	134535843	134536685	E070	32033
chr9	134543467	134547093	E070	39657
chr9	134453883	134454768	E071	-49042
chr9	134454769	134454881	E071	-48929
chr9	134454941	134455257	E071	-48553
chr9	134483505	134483738	E071	-20072
chr9	134483741	134485483	E071	-18327
chr9	134485550	134486225	E071	-17585
chr9	134491830	134492553	E071	-11257
chr9	134492595	134492677	E071	-11133
chr9	134492739	134492817	E071	-10993
chr9	134492916	134492970	E071	-10840
chr9	134493159	134493848	E071	-9962
chr9	134496339	134496460	E071	-7350
chr9	134496548	134496697	E071	-7113
chr9	134496731	134496857	E071	-6953
chr9	134496892	134497949	E071	-5861
chr9	134498890	134499078	E071	-4732
chr9	134499145	134499237	E071	-4573
chr9	134499247	134499714	E071	-4096
chr9	134499780	134501820	E071	-1990
chr9	134508452	134509433	E071	4642
chr9	134510216	134510300	E071	6406
chr9	134515246	134515866	E071	11436
chr9	134515905	134516073	E071	12095
chr9	134516232	134516423	E071	12422
chr9	134525557	134526306	E071	21747
chr9	134528046	134528188	E071	24236
chr9	134528827	134528867	E071	25017
chr9	134528870	134528968	E071	25060
chr9	134529046	134529161	E071	25236
chr9	134530254	134531007	E071	26444
chr9	134531436	134531510	E071	27626
chr9	134531546	134534558	E071	27736
chr9	134534636	134534723	E071	30826
chr9	134534885	134535226	E071	31075
chr9	134535506	134535761	E071	31696
chr9	134535843	134536685	E071	32033
chr9	134542247	134542480	E071	38437
chr9	134542690	134543455	E071	38880
chr9	134543467	134547093	E071	39657
chr9	134547121	134547248	E071	43311
chr9	134547261	134547417	E071	43451
chr9	134547450	134547538	E071	43640
chr9	134547710	134547760	E071	43900
chr9	134547775	134548431	E071	43965
chr9	134548463	134548548	E071	44653
chr9	134548676	134548752	E071	44866
chr9	134548831	134548871	E071	45021
chr9	134548988	134549116	E071	45178
chr9	134549121	134549209	E071	45311
chr9	134549226	134549290	E071	45416
chr9	134549712	134549798	E071	45902
chr9	134549842	134550023	E071	46032
chr9	134550081	134551377	E071	46271
chr9	134453883	134454768	E072	-49042
chr9	134454769	134454881	E072	-48929
chr9	134454941	134455257	E072	-48553
chr9	134455327	134455526	E072	-48284
chr9	134455641	134455887	E072	-47923
chr9	134483337	134483415	E072	-20395
chr9	134483505	134483738	E072	-20072
chr9	134483741	134485483	E072	-18327
chr9	134485550	134486225	E072	-17585
chr9	134486402	134486815	E072	-16995
chr9	134486839	134487407	E072	-16403
chr9	134493159	134493848	E072	-9962
chr9	134496339	134496460	E072	-7350
chr9	134496548	134496697	E072	-7113
chr9	134496731	134496857	E072	-6953
chr9	134496892	134497949	E072	-5861
chr9	134498890	134499078	E072	-4732
chr9	134499145	134499237	E072	-4573
chr9	134508452	134509433	E072	4642
chr9	134515246	134515866	E072	11436
chr9	134515905	134516073	E072	12095
chr9	134516232	134516423	E072	12422
chr9	134525557	134526306	E072	21747
chr9	134530254	134531007	E072	26444
chr9	134531436	134531510	E072	27626
chr9	134531546	134534558	E072	27736
chr9	134534636	134534723	E072	30826
chr9	134534885	134535226	E072	31075
chr9	134535506	134535761	E072	31696
chr9	134535843	134536685	E072	32033
chr9	134542690	134543455	E072	38880
chr9	134543467	134547093	E072	39657
chr9	134549842	134550023	E072	46032
chr9	134550081	134551377	E072	46271
chr9	134453883	134454768	E073	-49042
chr9	134454769	134454881	E073	-48929
chr9	134454941	134455257	E073	-48553
chr9	134455327	134455526	E073	-48284
chr9	134455641	134455887	E073	-47923
chr9	134483505	134483738	E073	-20072
chr9	134483741	134485483	E073	-18327
chr9	134485550	134486225	E073	-17585
chr9	134491830	134492553	E073	-11257
chr9	134492595	134492677	E073	-11133
chr9	134492739	134492817	E073	-10993
chr9	134492916	134492970	E073	-10840
chr9	134493159	134493848	E073	-9962
chr9	134496339	134496460	E073	-7350
chr9	134496548	134496697	E073	-7113
chr9	134496731	134496857	E073	-6953
chr9	134499780	134501820	E073	-1990
chr9	134508452	134509433	E073	4642
chr9	134509480	134509723	E073	5670
chr9	134515246	134515866	E073	11436
chr9	134515905	134516073	E073	12095
chr9	134516232	134516423	E073	12422
chr9	134516536	134518492	E073	12726
chr9	134525111	134525261	E073	21301
chr9	134525350	134525552	E073	21540
chr9	134525557	134526306	E073	21747
chr9	134530140	134530183	E073	26330
chr9	134530254	134531007	E073	26444
chr9	134531436	134531510	E073	27626
chr9	134531546	134534558	E073	27736
chr9	134534636	134534723	E073	30826
chr9	134534885	134535226	E073	31075
chr9	134535843	134536685	E073	32033
chr9	134536801	134536915	E073	32991
chr9	134536939	134536979	E073	33129
chr9	134542690	134543455	E073	38880
chr9	134543467	134547093	E073	39657
chr9	134547121	134547248	E073	43311
chr9	134547261	134547417	E073	43451
chr9	134547450	134547538	E073	43640
chr9	134547710	134547760	E073	43900
chr9	134547775	134548431	E073	43965
chr9	134548463	134548548	E073	44653
chr9	134549842	134550023	E073	46032
chr9	134550081	134551377	E073	46271
chr9	134455641	134455887	E074	-47923
chr9	134455890	134455964	E074	-47846
chr9	134483505	134483738	E074	-20072
chr9	134483741	134485483	E074	-18327
chr9	134485550	134486225	E074	-17585
chr9	134492739	134492817	E074	-10993
chr9	134492916	134492970	E074	-10840
chr9	134493159	134493848	E074	-9962
chr9	134493864	134493961	E074	-9849
chr9	134494019	134494101	E074	-9709
chr9	134494116	134494217	E074	-9593
chr9	134496339	134496460	E074	-7350
chr9	134496548	134496697	E074	-7113
chr9	134496731	134496857	E074	-6953
chr9	134496892	134497949	E074	-5861
chr9	134499780	134501820	E074	-1990
chr9	134508452	134509433	E074	4642
chr9	134515246	134515866	E074	11436
chr9	134515905	134516073	E074	12095
chr9	134516232	134516423	E074	12422
chr9	134516536	134518492	E074	12726
chr9	134518614	134518706	E074	14804
chr9	134530254	134531007	E074	26444
chr9	134531546	134534558	E074	27736
chr9	134534636	134534723	E074	30826
chr9	134534885	134535226	E074	31075
chr9	134535506	134535761	E074	31696
chr9	134535843	134536685	E074	32033
chr9	134536801	134536915	E074	32991
chr9	134536939	134536979	E074	33129
chr9	134543467	134547093	E074	39657
chr9	134547121	134547248	E074	43311
chr9	134547261	134547417	E074	43451
chr9	134547450	134547538	E074	43640
chr9	134547710	134547760	E074	43900
chr9	134547775	134548431	E074	43965
chr9	134548463	134548548	E074	44653
chr9	134549712	134549798	E074	45902
chr9	134549842	134550023	E074	46032
chr9	134550081	134551377	E074	46271
chr9	134453883	134454768	E081	-49042
chr9	134454769	134454881	E081	-48929
chr9	134454941	134455257	E081	-48553
chr9	134455327	134455526	E081	-48284
chr9	134455641	134455887	E081	-47923
chr9	134455890	134455964	E081	-47846
chr9	134482373	134482866	E081	-20944
chr9	134482940	134483098	E081	-20712
chr9	134483107	134483321	E081	-20489
chr9	134483337	134483415	E081	-20395
chr9	134483505	134483738	E081	-20072
chr9	134483741	134485483	E081	-18327
chr9	134485550	134486225	E081	-17585
chr9	134486402	134486815	E081	-16995
chr9	134486839	134487407	E081	-16403
chr9	134487455	134487540	E081	-16270
chr9	134487702	134488218	E081	-15592
chr9	134488226	134488717	E081	-15093
chr9	134488777	134488976	E081	-14834
chr9	134489036	134489090	E081	-14720
chr9	134489191	134489284	E081	-14526
chr9	134489336	134489422	E081	-14388
chr9	134489563	134489668	E081	-14142
chr9	134489685	134489727	E081	-14083
chr9	134489760	134489925	E081	-13885
chr9	134496892	134497949	E081	-5861
chr9	134499247	134499714	E081	-4096
chr9	134499780	134501820	E081	-1990
chr9	134501853	134501927	E081	-1883
chr9	134531546	134534558	E081	27736
chr9	134550081	134551377	E081	46271
chr9	134453883	134454768	E082	-49042
chr9	134455641	134455887	E082	-47923
chr9	134455890	134455964	E082	-47846
chr9	134483505	134483738	E082	-20072
chr9	134485550	134486225	E082	-17585
chr9	134486402	134486815	E082	-16995
chr9	134486839	134487407	E082	-16403
chr9	134487702	134488218	E082	-15592
chr9	134488226	134488717	E082	-15093
chr9	134499247	134499714	E082	-4096
chr9	134499780	134501820	E082	-1990
chr9	134531546	134534558	E082	27736
chr9	134543467	134547093	E082	39657
chr9	134550081	134551377	E082	46271