rs2287919

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ARHGEF18 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0198 (23052/116134,ExAC)
T=0174 (5231/29914,GnomAD)
T=0159 (4645/29118,TOPMED)
C==0176 (2294/13006,GO-ESP)
T=0155 (777/5008,1000G)
T=0231 (892/3854,ALSPAC)
T=0222 (824/3708,TWINSUK)

Position: chr19:7464529 (GRCh38.p7) (19p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 154 Enhancers around

Promoter: 34 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.7464529C>T
GRCh37.p13 chr 19	NC_000019.9:g.7529415C>T

Gene: ARHGEF18, Rho/Rac guanine nucleotide exchange factor 18(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARHGEF18 transcript variant 2	NM_001130955.1:c.	N/A	Intron Variant
ARHGEF18 transcript variant 1	NM_015318.3:c.	N/A	Intron Variant
ARHGEF18 transcript variant X2	XM_005272464.4:c.	N/A	Intron Variant
ARHGEF18 transcript variant X5	XM_006722705.3:c.	N/A	Intron Variant
ARHGEF18 transcript variant X6	XM_006722706.3:c.	N/A	Intron Variant
ARHGEF18 transcript variant X10	XM_006722708.2:c.	N/A	Intron Variant
ARHGEF18 transcript variant X1	XM_011527835.2:c.	N/A	Intron Variant
ARHGEF18 transcript variant X3	XM_011527836.2:c.	N/A	Intron Variant
ARHGEF18 transcript variant X4	XM_011527837.2:c.	N/A	Intron Variant
ARHGEF18 transcript variant X7	XM_011527838.2:c.	N/A	Intron Variant
ARHGEF18 transcript variant X8	XM_011527839.2:c.	N/A	Intron Variant
ARHGEF18 transcript variant X9	XM_011527840.1:c.	N/A	Intron Variant
ARHGEF18 transcript variant X11	XM_011527841.2:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.917	T=0.083
1000Genomes	American	Sub	694	C=0.790	T=0.210
1000Genomes	East Asian	Sub	1008	C=0.881	T=0.119
1000Genomes	Europe	Sub	1006	C=0.760	T=0.240
1000Genomes	Global	Study-wide	5008	C=0.845	T=0.155
1000Genomes	South Asian	Sub	978	C=0.830	T=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.769	T=0.231
The Exome Aggregation Consortium	American	Sub	21738	C=0.862	T=0.137
The Exome Aggregation Consortium	Asian	Sub	22026	C=0.830	T=0.169
The Exome Aggregation Consortium	Europe	Sub	71526	C=0.774	T=0.226
The Exome Aggregation Consortium	Global	Study-wide	116134	C=0.801	T=0.198
The Exome Aggregation Consortium	Other	Sub	844	C=0.810	T=0.190
The Genome Aggregation Database	African	Sub	8720	C=0.894	T=0.106
The Genome Aggregation Database	American	Sub	836	C=0.830	T=0.170
The Genome Aggregation Database	East Asian	Sub	1614	C=0.885	T=0.115
The Genome Aggregation Database	Europe	Sub	18442	C=0.788	T=0.211
The Genome Aggregation Database	Global	Study-wide	29914	C=0.825	T=0.174
The Genome Aggregation Database	Other	Sub	302	C=0.730	T=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.840	T=0.159
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.778	T=0.222

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2287919	0.0007	alcohol dependence	20201924

eQTL of rs2287919 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 rs2287919 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 )
chr19	7480106	7480215	E067	-49200
chr19	7480424	7480898	E067	-48517
chr19	7480905	7481049	E067	-48366
chr19	7499539	7499589	E067	-29826
chr19	7501559	7501709	E067	-27706
chr19	7505077	7505201	E067	-24214
chr19	7505495	7505991	E067	-23424
chr19	7506383	7506446	E067	-22969
chr19	7506462	7506551	E067	-22864
chr19	7506618	7506668	E067	-22747
chr19	7507439	7507578	E067	-21837
chr19	7507705	7507755	E067	-21660
chr19	7543715	7544047	E067	14300
chr19	7548547	7548994	E067	19132
chr19	7557790	7558014	E067	28375
chr19	7558224	7558268	E067	28809
chr19	7558539	7558583	E067	29124
chr19	7559101	7559845	E067	29686
chr19	7560043	7560102	E067	30628
chr19	7560141	7560186	E067	30726
chr19	7560297	7560359	E067	30882
chr19	7560515	7560555	E067	31100
chr19	7479916	7479991	E068	-49424
chr19	7480063	7480103	E068	-49312
chr19	7480106	7480215	E068	-49200
chr19	7480424	7480898	E068	-48517
chr19	7480905	7481049	E068	-48366
chr19	7506383	7506446	E068	-22969
chr19	7506462	7506551	E068	-22864
chr19	7506618	7506668	E068	-22747
chr19	7543296	7543676	E068	13881
chr19	7543715	7544047	E068	14300
chr19	7548547	7548994	E068	19132
chr19	7557790	7558014	E068	28375
chr19	7558224	7558268	E068	28809
chr19	7558539	7558583	E068	29124
chr19	7560043	7560102	E068	30628
chr19	7560141	7560186	E068	30726
chr19	7560297	7560359	E068	30882
chr19	7561921	7562013	E068	32506
chr19	7562064	7562157	E068	32649
chr19	7562247	7562459	E068	32832
chr19	7480063	7480103	E069	-49312
chr19	7480106	7480215	E069	-49200
chr19	7480424	7480898	E069	-48517
chr19	7480905	7481049	E069	-48366
chr19	7499539	7499589	E069	-29826
chr19	7500181	7500231	E069	-29184
chr19	7500387	7500467	E069	-28948
chr19	7501559	7501709	E069	-27706
chr19	7501801	7501970	E069	-27445
chr19	7506383	7506446	E069	-22969
chr19	7506462	7506551	E069	-22864
chr19	7507439	7507578	E069	-21837
chr19	7547699	7548536	E069	18284
chr19	7548547	7548994	E069	19132
chr19	7560043	7560102	E069	30628
chr19	7560141	7560186	E069	30726
chr19	7560297	7560359	E069	30882
chr19	7561921	7562013	E069	32506
chr19	7562064	7562157	E069	32649
chr19	7562247	7562459	E069	32832
chr19	7562527	7562681	E069	33112
chr19	7547699	7548536	E070	18284
chr19	7548547	7548994	E070	19132
chr19	7480063	7480103	E071	-49312
chr19	7480106	7480215	E071	-49200
chr19	7480424	7480898	E071	-48517
chr19	7480905	7481049	E071	-48366
chr19	7499539	7499589	E071	-29826
chr19	7500181	7500231	E071	-29184
chr19	7500387	7500467	E071	-28948
chr19	7501559	7501709	E071	-27706
chr19	7501801	7501970	E071	-27445
chr19	7506383	7506446	E071	-22969
chr19	7506462	7506551	E071	-22864
chr19	7506618	7506668	E071	-22747
chr19	7507439	7507578	E071	-21837
chr19	7507705	7507755	E071	-21660
chr19	7543296	7543676	E071	13881
chr19	7543715	7544047	E071	14300
chr19	7544102	7544152	E071	14687
chr19	7544334	7545148	E071	14919
chr19	7556833	7557767	E071	27418
chr19	7557790	7558014	E071	28375
chr19	7558224	7558268	E071	28809
chr19	7558539	7558583	E071	29124
chr19	7560043	7560102	E071	30628
chr19	7560141	7560186	E071	30726
chr19	7560297	7560359	E071	30882
chr19	7560515	7560555	E071	31100
chr19	7561921	7562013	E071	32506
chr19	7562064	7562157	E071	32649
chr19	7562247	7562459	E071	32832
chr19	7562527	7562681	E071	33112
chr19	7564998	7565054	E071	35583
chr19	7570218	7572152	E071	40803
chr19	7480063	7480103	E072	-49312
chr19	7480106	7480215	E072	-49200
chr19	7480424	7480898	E072	-48517
chr19	7480905	7481049	E072	-48366
chr19	7482812	7483121	E072	-46294
chr19	7499539	7499589	E072	-29826
chr19	7500181	7500231	E072	-29184
chr19	7500387	7500467	E072	-28948
chr19	7501559	7501709	E072	-27706
chr19	7501801	7501970	E072	-27445
chr19	7502381	7502425	E072	-26990
chr19	7502558	7502608	E072	-26807
chr19	7507439	7507578	E072	-21837
chr19	7507705	7507755	E072	-21660
chr19	7543296	7543676	E072	13881
chr19	7543715	7544047	E072	14300
chr19	7557790	7558014	E072	28375
chr19	7558224	7558268	E072	28809
chr19	7558539	7558583	E072	29124
chr19	7560043	7560102	E072	30628
chr19	7560141	7560186	E072	30726
chr19	7560297	7560359	E072	30882
chr19	7560515	7560555	E072	31100
chr19	7561003	7561047	E072	31588
chr19	7561921	7562013	E072	32506
chr19	7562064	7562157	E072	32649
chr19	7562247	7562459	E072	32832
chr19	7562527	7562681	E072	33112
chr19	7564880	7564930	E072	35465
chr19	7570218	7572152	E072	40803
chr19	7480106	7480215	E073	-49200
chr19	7543296	7543676	E073	13881
chr19	7543715	7544047	E073	14300
chr19	7547330	7547572	E073	17915
chr19	7547578	7547679	E073	18163
chr19	7547699	7548536	E073	18284
chr19	7548547	7548994	E073	19132
chr19	7557790	7558014	E073	28375
chr19	7558224	7558268	E073	28809
chr19	7558539	7558583	E073	29124
chr19	7559101	7559845	E073	29686
chr19	7482812	7483121	E074	-46294
chr19	7501559	7501709	E074	-27706
chr19	7501801	7501970	E074	-27445
chr19	7502381	7502425	E074	-26990
chr19	7502558	7502608	E074	-26807
chr19	7507439	7507578	E074	-21837
chr19	7543296	7543676	E074	13881
chr19	7557790	7558014	E074	28375
chr19	7558224	7558268	E074	28809
chr19	7558539	7558583	E074	29124
chr19	7560043	7560102	E074	30628
chr19	7560141	7560186	E074	30726
chr19	7560297	7560359	E074	30882
chr19	7560515	7560555	E074	31100
chr19	7547699	7548536	E081	18284
chr19	7548547	7548994	E081	19132

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	7553068	7553422	E067	23653
chr19	7553534	7554870	E067	24119
chr19	7565513	7565702	E067	36098
chr19	7565715	7566467	E067	36300
chr19	7553068	7553422	E068	23653
chr19	7553534	7554870	E068	24119
chr19	7565513	7565702	E068	36098
chr19	7565715	7566467	E068	36300
chr19	7553068	7553422	E069	23653
chr19	7553534	7554870	E069	24119
chr19	7565513	7565702	E069	36098
chr19	7565715	7566467	E069	36300
chr19	7553068	7553422	E070	23653
chr19	7553534	7554870	E070	24119
chr19	7565513	7565702	E070	36098
chr19	7565715	7566467	E070	36300
chr19	7553068	7553422	E071	23653
chr19	7553534	7554870	E071	24119
chr19	7565513	7565702	E071	36098
chr19	7565715	7566467	E071	36300
chr19	7553068	7553422	E072	23653
chr19	7553534	7554870	E072	24119
chr19	7565513	7565702	E072	36098
chr19	7565715	7566467	E072	36300
chr19	7553534	7554870	E073	24119
chr19	7565513	7565702	E073	36098
chr19	7565715	7566467	E073	36300
chr19	7553534	7554870	E074	24119
chr19	7565513	7565702	E074	36098
chr19	7565715	7566467	E074	36300
chr19	7553068	7553422	E082	23653
chr19	7553534	7554870	E082	24119
chr19	7565513	7565702	E082	36098
chr19	7565715	7566467	E082	36300