rs6659246

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

MARC2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0250 (7492/29946,GnomAD)
A=0266 (7760/29116,TOPMED)
A=0336 (1683/5008,1000G)
A=0141 (545/3854,ALSPAC)
A=0155 (573/3708,TWINSUK)

Position: chr1:220757885 (GRCh38.p7) (1q41)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 67 Enhancers around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.220757885C>A
GRCh37.p13 chr 1	NC_000001.10:g.220931227C>A

Gene: MARC2, mitochondrial amidoxime reducing component 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MARC2 transcript variant 1	NM_001317338.1:c.	N/A	Intron Variant
MARC2 transcript variant 2	NM_017898.4:c.	N/A	Intron Variant
MARC2 transcript variant X6	XM_006711407.2:c.	N/A	Intron Variant
MARC2 transcript variant X2	XM_011509684.1:c.	N/A	Intron Variant
MARC2 transcript variant X4	XM_017001581.1:c.	N/A	Intron Variant
MARC2 transcript variant X1	XR_001737257.1:n.	N/A	Intron Variant
MARC2 transcript variant X3	XR_001737258.1:n.	N/A	Intron Variant
MARC2 transcript variant X2	XR_247029.4:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.628	A=0.372
1000Genomes	American	Sub	694	C=0.620	A=0.380
1000Genomes	East Asian	Sub	1008	C=0.538	A=0.462
1000Genomes	Europe	Sub	1006	C=0.835	A=0.165
1000Genomes	Global	Study-wide	5008	C=0.664	A=0.336
1000Genomes	South Asian	Sub	978	C=0.700	A=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.859	A=0.141
The Genome Aggregation Database	African	Sub	8708	C=0.655	A=0.345
The Genome Aggregation Database	American	Sub	838	C=0.630	A=0.370
The Genome Aggregation Database	East Asian	Sub	1616	C=0.496	A=0.504
The Genome Aggregation Database	Europe	Sub	18482	C=0.820	A=0.179
The Genome Aggregation Database	Global	Study-wide	29946	C=0.749	A=0.250
The Genome Aggregation Database	Other	Sub	302	C=0.830	A=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.733	A=0.266
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.845	A=0.155

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
rs6659246	0.000237	alcohol dependence	20201924

eQTL of rs6659246 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:220931227	3/2/2018 12:00:00 AM	ENSG00000117791.11	C>A	5.6644e-5	9660	Cerebellum

meQTL of rs6659246 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	220905971	220906038	E067	-25189
chr1	220906086	220907026	E067	-24201
chr1	220924196	220924295	E067	-6932
chr1	220924566	220924756	E067	-6471
chr1	220924760	220924925	E067	-6302
chr1	220924968	220925018	E067	-6209
chr1	220905971	220906038	E068	-25189
chr1	220924002	220924069	E068	-7158
chr1	220924196	220924295	E068	-6932
chr1	220924566	220924756	E068	-6471
chr1	220924760	220924925	E068	-6302
chr1	220949983	220950398	E068	18756
chr1	220964957	220965020	E068	33730
chr1	220924002	220924069	E069	-7158
chr1	220924196	220924295	E069	-6932
chr1	220924566	220924756	E069	-6471
chr1	220924760	220924925	E069	-6302
chr1	220924968	220925018	E069	-6209
chr1	220925119	220925171	E069	-6056
chr1	220948707	220948824	E069	17480
chr1	220959223	220959339	E069	27996
chr1	220923190	220923886	E070	-7341
chr1	220924002	220924069	E070	-7158
chr1	220924196	220924295	E070	-6932
chr1	220924566	220924756	E070	-6471
chr1	220924760	220924925	E070	-6302
chr1	220959223	220959339	E070	27996
chr1	220961418	220961855	E070	30191
chr1	220905971	220906038	E071	-25189
chr1	220924002	220924069	E071	-7158
chr1	220924196	220924295	E071	-6932
chr1	220924566	220924756	E071	-6471
chr1	220949983	220950398	E072	18756
chr1	220961418	220961855	E072	30191
chr1	220964754	220964899	E072	33527
chr1	220964957	220965020	E072	33730
chr1	220906086	220907026	E073	-24201
chr1	220924002	220924069	E073	-7158
chr1	220924196	220924295	E073	-6932
chr1	220924566	220924756	E073	-6471
chr1	220924760	220924925	E073	-6302
chr1	220924968	220925018	E073	-6209
chr1	220925119	220925171	E073	-6056
chr1	220964754	220964899	E073	33527
chr1	220964957	220965020	E073	33730
chr1	220959223	220959339	E074	27996
chr1	220905971	220906038	E081	-25189
chr1	220924196	220924295	E081	-6932
chr1	220924566	220924756	E081	-6471
chr1	220924760	220924925	E081	-6302
chr1	220924968	220925018	E081	-6209
chr1	220925119	220925171	E081	-6056
chr1	220925374	220925452	E081	-5775
chr1	220949983	220950398	E081	18756
chr1	220950424	220950489	E081	19197
chr1	220959223	220959339	E081	27996
chr1	220961418	220961855	E081	30191
chr1	220964365	220964585	E081	33138
chr1	220964754	220964899	E081	33527
chr1	220964957	220965020	E081	33730
chr1	220920704	220920768	E082	-10459
chr1	220924566	220924756	E082	-6471
chr1	220924760	220924925	E082	-6302
chr1	220924968	220925018	E082	-6209
chr1	220925119	220925171	E082	-6056
chr1	220925374	220925452	E082	-5775
chr1	220958994	220959094	E082	27767

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	220920901	220922731	E067	-8496
chr1	220959444	220961072	E067	28217
chr1	220920901	220922731	E068	-8496
chr1	220959444	220961072	E068	28217
chr1	220920901	220922731	E069	-8496
chr1	220959444	220961072	E069	28217
chr1	220920901	220922731	E070	-8496
chr1	220959444	220961072	E070	28217
chr1	220920901	220922731	E071	-8496
chr1	220959444	220961072	E071	28217
chr1	220920901	220922731	E072	-8496
chr1	220959444	220961072	E072	28217
chr1	220920901	220922731	E073	-8496
chr1	220959444	220961072	E073	28217
chr1	220920901	220922731	E074	-8496
chr1	220959444	220961072	E074	28217
chr1	220920901	220922731	E082	-8496
chr1	220959444	220961072	E082	28217