rs6668685

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

GLMN : Intron Variant
RPAP2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0136 (4075/29956,GnomAD)
G==0116 (3405/29118,TOPMED)
G==0068 (342/5008,1000G)
G==0198 (764/3854,ALSPAC)
G==0195 (723/3708,TWINSUK)

Position: chr1:92326255 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 13 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.92326255G>T
GRCh37.p13 chr 1	NC_000001.10:g.92791812G>T

Gene: RPAP2, RNA polymerase II associated protein 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RPAP2 transcript	NM_024813.2:c.	N/A	Intron Variant
RPAP2 transcript variant X6	XM_005271223.2:c.	N/A	Intron Variant
RPAP2 transcript variant X4	XM_011542167.2:c.	N/A	Intron Variant
RPAP2 transcript variant X2	XM_017002362.1:c.	N/A	Intron Variant
RPAP2 transcript variant X3	XM_017002363.1:c.	N/A	Intron Variant
RPAP2 transcript variant X5	XM_017002364.1:c.	N/A	Intron Variant
RPAP2 transcript variant X1	XR_246295.2:n.	N/A	Intron Variant

Gene: GLMN, glomulin, FKBP associated protein(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GLMN transcript variant 2	NM_001319683.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant 1	NM_053274.2:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant 3	NR_135089.1:n.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X3	XM_011540546.2:c.	N/A	Intron Variant
GLMN transcript variant X7	XM_005270401.3:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X9	XM_006710309.2:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X1	XM_017000137.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X2	XM_017000138.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X4	XM_017000139.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X5	XM_017000140.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X6	XM_017000141.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X10	XM_017000142.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X11	XM_017000143.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X13	XM_017000144.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X8	XR_001736941.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.023	T=0.977
1000Genomes	American	Sub	694	G=0.110	T=0.890
1000Genomes	East Asian	Sub	1008	G=0.002	T=0.998
1000Genomes	Europe	Sub	1006	G=0.194	T=0.806
1000Genomes	Global	Study-wide	5008	G=0.068	T=0.932
1000Genomes	South Asian	Sub	978	G=0.040	T=0.960
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.198	T=0.802
The Genome Aggregation Database	African	Sub	8704	G=0.049	T=0.951
The Genome Aggregation Database	American	Sub	838	G=0.100	T=0.900
The Genome Aggregation Database	East Asian	Sub	1620	G=0.002	T=0.998
The Genome Aggregation Database	Europe	Sub	18492	G=0.191	T=0.808
The Genome Aggregation Database	Global	Study-wide	29956	G=0.136	T=0.864
The Genome Aggregation Database	Other	Sub	302	G=0.090	T=0.910
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.116	T=0.883
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.195	T=0.805

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
rs6668685	3.17E-05	alcohol consumption	23953852

eQTL of rs6668685 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:92791812	RP4-621B10.8	ENSG00000273487.1	G>T	2.7662e-4	137018	Frontal_Cortex_BA9

meQTL of rs6668685 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	92765994	92766180	E067	-25632
chr1	92765994	92766180	E068	-25632
chr1	92765994	92766180	E069	-25632
chr1	92765994	92766180	E070	-25632
chr1	92765994	92766180	E072	-25632
chr1	92765994	92766180	E073	-25632
chr1	92765994	92766180	E074	-25632
chr1	92765994	92766180	E082	-25632

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	92763588	92763688	E067	-28124
chr1	92763733	92765237	E067	-26575
chr1	92763733	92765237	E068	-26575
chr1	92763733	92765237	E069	-26575
chr1	92763588	92763688	E070	-28124
chr1	92763733	92765237	E070	-26575
chr1	92763733	92765237	E071	-26575
chr1	92763733	92765237	E072	-26575
chr1	92763733	92765237	E073	-26575
chr1	92763733	92765237	E074	-26575
chr1	92763733	92765237	E081	-26575
chr1	92763588	92763688	E082	-28124
chr1	92763733	92765237	E082	-26575