rs7678962

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PIGG : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0150 (16659/110702,ExAC)
A=0186 (5592/29926,GnomAD)
A=0225 (6558/29118,TOPMED)
G==0195 (2548/13006,GO-ESP)
A=0224 (1123/5008,1000G)
A=0118 (453/3854,ALSPAC)
A=0115 (428/3708,TWINSUK)

Position: chr4:523409 (GRCh38.p7) (4p16.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 74 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.523409G>A
GRCh37.p13 chr 4	NC_000004.11:g.517198G>A

Gene: PIGG, phosphatidylinositol glycan anchor biosynthesis class G(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PIGG transcript variant 1	NM_001127178.2:c.	N/A	Intron Variant
PIGG transcript variant 3	NM_001289051.1:c.	N/A	Intron Variant
PIGG transcript variant 4	NM_001289052.1:c.	N/A	Intron Variant
PIGG transcript variant 2	NM_017733.4:c.	N/A	Intron Variant
PIGG transcript variant 5	NM_001289053.1:c.	N/A	Genic Downstream Transcript Variant
PIGG transcript variant 6	NM_001289055.1:c.	N/A	Genic Downstream Transcript Variant
PIGG transcript variant 7	NM_001289057.1:c.	N/A	Genic Downstream Transcript Variant
PIGG transcript variant 8	NR_110293.1:n.	N/A	Intron Variant
PIGG transcript variant X3	XM_005272284.2:c.	N/A	Intron Variant
PIGG transcript variant X2	XM_011513490.2:c.	N/A	Intron Variant
PIGG transcript variant X5	XM_011513491.1:c.	N/A	Intron Variant
PIGG transcript variant X9	XM_011513492.1:c.	N/A	Intron Variant
PIGG transcript variant X6	XM_017008321.1:c.	N/A	Intron Variant
PIGG transcript variant X14	XM_017008322.1:c.	N/A	Intron Variant
PIGG transcript variant X20	XM_017008323.1:c.	N/A	Intron Variant
PIGG transcript variant X27	XM_017008324.1:c.	N/A	Intron Variant
PIGG transcript variant X28	XM_017008325.1:c.	N/A	Intron Variant
PIGG transcript variant X21	XM_011513493.1:c.	N/A	Genic Downstream Transcript Variant
PIGG transcript variant X22	XM_011513494.2:c.	N/A	Genic Downstream Transcript Variant
PIGG transcript variant X31	XM_017008326.1:c.	N/A	Genic Downstream Transcript Variant
PIGG transcript variant X1	XR_001741248.1:n.	N/A	Intron Variant
PIGG transcript variant X7	XR_001741249.1:n.	N/A	Intron Variant
PIGG transcript variant X10	XR_001741250.1:n.	N/A	Intron Variant
PIGG transcript variant X11	XR_001741251.1:n.	N/A	Intron Variant
PIGG transcript variant X13	XR_001741252.1:n.	N/A	Intron Variant
PIGG transcript variant X16	XR_001741253.1:n.	N/A	Intron Variant
PIGG transcript variant X17	XR_001741254.1:n.	N/A	Intron Variant
PIGG transcript variant X18	XR_001741255.1:n.	N/A	Intron Variant
PIGG transcript variant X23	XR_001741256.1:n.	N/A	Intron Variant
PIGG transcript variant X24	XR_001741257.1:n.	N/A	Intron Variant
PIGG transcript variant X25	XR_001741258.1:n.	N/A	Intron Variant
PIGG transcript variant X26	XR_001741259.1:n.	N/A	Intron Variant
PIGG transcript variant X29	XR_001741260.1:n.	N/A	Intron Variant
PIGG transcript variant X30	XR_001741261.1:n.	N/A	Intron Variant
PIGG transcript variant X32	XR_001741262.1:n.	N/A	Intron Variant
PIGG transcript variant X33	XR_001741263.1:n.	N/A	Intron Variant
PIGG transcript variant X34	XR_001741264.1:n.	N/A	Intron Variant
PIGG transcript variant X4	XR_924965.2:n.	N/A	Intron Variant
PIGG transcript variant X8	XR_924966.2:n.	N/A	Intron Variant
PIGG transcript variant X9	XR_924967.2:n.	N/A	Intron Variant
PIGG transcript variant X12	XR_924969.2:n.	N/A	Intron Variant
PIGG transcript variant X19	XR_924972.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.604	A=0.396
1000Genomes	American	Sub	694	G=0.900	A=0.100
1000Genomes	East Asian	Sub	1008	G=0.780	A=0.220
1000Genomes	Europe	Sub	1006	G=0.869	A=0.131
1000Genomes	Global	Study-wide	5008	G=0.776	A=0.224
1000Genomes	South Asian	Sub	978	G=0.820	A=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.882	A=0.118
The Exome Aggregation Consortium	American	Sub	21572	G=0.788	A=0.211
The Exome Aggregation Consortium	Asian	Sub	18006	G=0.816	A=0.183
The Exome Aggregation Consortium	Europe	Sub	70334	G=0.876	A=0.123
The Exome Aggregation Consortium	Global	Study-wide	110702	G=0.849	A=0.150
The Exome Aggregation Consortium	Other	Sub	790	G=0.870	A=0.130
The Genome Aggregation Database	African	Sub	8696	G=0.663	A=0.337
The Genome Aggregation Database	American	Sub	838	G=0.900	A=0.100
The Genome Aggregation Database	East Asian	Sub	1616	G=0.794	A=0.206
The Genome Aggregation Database	Europe	Sub	18474	G=0.881	A=0.118
The Genome Aggregation Database	Global	Study-wide	29926	G=0.813	A=0.186
The Genome Aggregation Database	Other	Sub	302	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.774	A=0.225
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.885	A=0.115

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs7678962	0.000221	alcohol dependence	21314694

eQTL of rs7678962 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr4:517198	RP11-1191J2.2	ENSG00000242686.2	G>A	3.1784e-15	-132236	Cerebellum
Chr4:517198	MFSD7	ENSG00000169026.8	G>A	5.8983e-9	-166032	Cerebellum
Chr4:517198	RP11-1191J2.2	ENSG00000242686.2	G>A	0.0000e+0	-132236	Cortex
Chr4:517198	MFSD7	ENSG00000169026.8	G>A	2.2514e-4	-166032	Cortex
Chr4:517198	PIGG	ENSG00000174227.11	G>A	9.6644e-5	24209	Caudate_basal_ganglia
Chr4:517198	RP11-1191J2.2	ENSG00000242686.2	G>A	1.4355e-15	-132236	Caudate_basal_ganglia
Chr4:517198	PIGG	ENSG00000174227.11	G>A	4.7407e-3	24209	Brain_Spinal_cord_cervical
Chr4:517198	RP11-1191J2.2	ENSG00000242686.2	G>A	1.4274e-12	-132236	Hippocampus
Chr4:517198	RP11-1191J2.2	ENSG00000242686.2	G>A	1.6853e-10	-132236	Putamen_basal_ganglia
Chr4:517198	RP11-1191J2.2	ENSG00000242686.2	G>A	8.9143e-20	-132236	Nucleus_accumbens_basal_ganglia

meQTL of rs7678962 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg12958093	chr4:629037	PDE6B	0.0538608280652102	3.3980e-11

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 )
chr4	491120	491194	E067	-26004
chr4	491120	491194	E069	-26004
chr4	491568	491630	E069	-25568
chr4	554533	554659	E071	37335
chr4	491120	491194	E072	-26004
chr4	491568	491630	E072	-25568
chr4	498731	498787	E073	-18411
chr4	490061	490158	E074	-27040
chr4	490211	490309	E074	-26889

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	467610	468333	E067	-48865
chr4	468382	468453	E067	-48745
chr4	492067	492182	E067	-25016
chr4	492222	492300	E067	-24898
chr4	492335	492585	E067	-24613
chr4	492635	492694	E067	-24504
chr4	492768	493293	E067	-23905
chr4	493306	493975	E067	-23223
chr4	467610	468333	E068	-48865
chr4	468382	468453	E068	-48745
chr4	492222	492300	E068	-24898
chr4	492335	492585	E068	-24613
chr4	492635	492694	E068	-24504
chr4	492768	493293	E068	-23905
chr4	493306	493975	E068	-23223
chr4	467610	468333	E069	-48865
chr4	468382	468453	E069	-48745
chr4	492222	492300	E069	-24898
chr4	492335	492585	E069	-24613
chr4	492635	492694	E069	-24504
chr4	492768	493293	E069	-23905
chr4	493306	493975	E069	-23223
chr4	467610	468333	E070	-48865
chr4	468382	468453	E070	-48745
chr4	492067	492182	E070	-25016
chr4	492222	492300	E070	-24898
chr4	492335	492585	E070	-24613
chr4	492635	492694	E070	-24504
chr4	492768	493293	E070	-23905
chr4	493306	493975	E070	-23223
chr4	467610	468333	E071	-48865
chr4	468382	468453	E071	-48745
chr4	492222	492300	E071	-24898
chr4	492335	492585	E071	-24613
chr4	492635	492694	E071	-24504
chr4	492768	493293	E071	-23905
chr4	493306	493975	E071	-23223
chr4	467610	468333	E072	-48865
chr4	468382	468453	E072	-48745
chr4	492222	492300	E072	-24898
chr4	492335	492585	E072	-24613
chr4	492635	492694	E072	-24504
chr4	492768	493293	E072	-23905
chr4	493306	493975	E072	-23223
chr4	467610	468333	E073	-48865
chr4	468382	468453	E073	-48745
chr4	492067	492182	E073	-25016
chr4	492222	492300	E073	-24898
chr4	492335	492585	E073	-24613
chr4	492635	492694	E073	-24504
chr4	492768	493293	E073	-23905
chr4	493306	493975	E073	-23223
chr4	467610	468333	E074	-48865
chr4	468382	468453	E074	-48745
chr4	492222	492300	E074	-24898
chr4	492335	492585	E074	-24613
chr4	492635	492694	E074	-24504
chr4	492768	493293	E074	-23905
chr4	493306	493975	E074	-23223
chr4	467610	468333	E081	-48865
chr4	468382	468453	E081	-48745
chr4	492222	492300	E081	-24898
chr4	492335	492585	E081	-24613
chr4	492635	492694	E081	-24504
chr4	492768	493293	E081	-23905
chr4	493306	493975	E081	-23223
chr4	467610	468333	E082	-48865
chr4	468382	468453	E082	-48745
chr4	492067	492182	E082	-25016
chr4	492222	492300	E082	-24898
chr4	492335	492585	E082	-24613
chr4	492635	492694	E082	-24504
chr4	492768	493293	E082	-23905
chr4	493306	493975	E082	-23223