rs1609276

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

MAGI2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0048 (1450/29952,GnomAD)
G==0062 (1832/29118,TOPMED)
G==0046 (232/5008,1000G)
G==0018 (71/3854,ALSPAC)
G==0018 (67/3708,TWINSUK)

Position: chr7:79299845 (GRCh38.p7) (7q21.11)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 45 Enhancers around

Promoter: 7 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
MAGI2 transcript variant 2	NM_001301128.1:c.	N/A	Intron Variant
MAGI2 transcript variant 1	NM_012301.3:c.	N/A	Intron Variant
MAGI2 transcript variant X6	XM_011516718.1:c.	N/A	Intron Variant
MAGI2 transcript variant X1	XM_017012840.1:c.	N/A	Intron Variant
MAGI2 transcript variant X2	XM_017012841.1:c.	N/A	Intron Variant
MAGI2 transcript variant X3	XM_017012842.1:c.	N/A	Intron Variant
MAGI2 transcript variant X4	XM_017012843.1:c.	N/A	Intron Variant
MAGI2 transcript variant X5	XM_017012844.1:c.	N/A	Intron Variant
MAGI2 transcript variant X7	XM_017012845.1:c.	N/A	Intron Variant
MAGI2 transcript variant X8	XM_017012846.1:c.	N/A	Intron Variant
MAGI2 transcript variant X14	XM_017012850.1:c.	N/A	Intron Variant
MAGI2 transcript variant X15	XM_017012851.1:c.	N/A	Intron Variant
MAGI2 transcript variant X16	XM_017012852.1:c.	N/A	Intron Variant
MAGI2 transcript variant X9	XM_011516719.2:c.	N/A	Genic Upstream Transcript Variant
MAGI2 transcript variant X10	XM_011516720.2:c.	N/A	Genic Upstream Transcript Variant
MAGI2 transcript variant X17	XM_011516726.2:c.	N/A	Genic Upstream Transcript Variant
MAGI2 transcript variant X19	XM_011516728.1:c.	N/A	Genic Upstream Transcript Variant
MAGI2 transcript variant X11	XM_017012847.1:c.	N/A	Genic Upstream Transcript Variant
MAGI2 transcript variant X12	XM_017012848.1:c.	N/A	Genic Upstream Transcript Variant
MAGI2 transcript variant X13	XM_017012849.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.109	C=0.891
1000Genomes	American	Sub	694	G=0.020	C=0.980
1000Genomes	East Asian	Sub	1008	G=0.033	C=0.967
1000Genomes	Europe	Sub	1006	G=0.025	C=0.975
1000Genomes	Global	Study-wide	5008	G=0.046	C=0.954
1000Genomes	South Asian	Sub	978	G=0.020	C=0.980
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.018	C=0.982
The Genome Aggregation Database	African	Sub	8712	G=0.104	C=0.896
The Genome Aggregation Database	American	Sub	836	G=0.040	C=0.960
The Genome Aggregation Database	East Asian	Sub	1618	G=0.030	C=0.970
The Genome Aggregation Database	Europe	Sub	18484	G=0.024	C=0.975
The Genome Aggregation Database	Global	Study-wide	29952	G=0.048	C=0.951
The Genome Aggregation Database	Other	Sub	302	G=0.020	C=0.980
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.062	C=0.937
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.018	C=0.982

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

SNP ID	p-value	Traits	Study
rs1609276	0.00093	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr7	78910557	78910622	E067	-18539
chr7	78910663	78910723	E067	-18438
chr7	78910804	78910844	E067	-18317
chr7	78910883	78910955	E067	-18206
chr7	78911088	78911128	E067	-18033
chr7	78922189	78922229	E067	-6932
chr7	78922290	78922451	E067	-6710
chr7	78922569	78922619	E067	-6542
chr7	78946929	78947426	E067	17768
chr7	78967418	78967592	E067	38257
chr7	78971311	78971446	E067	42150
chr7	78971311	78971446	E068	42150
chr7	78911433	78911832	E069	-17329
chr7	78911973	78912106	E069	-17055
chr7	78917403	78917559	E069	-11602
chr7	78967418	78967592	E069	38257
chr7	78911433	78911832	E071	-17329
chr7	78918269	78918319	E071	-10842
chr7	78920261	78920461	E071	-8700
chr7	78920597	78920794	E071	-8367
chr7	78922189	78922229	E071	-6932
chr7	78922290	78922451	E071	-6710
chr7	78922569	78922619	E071	-6542
chr7	78930002	78930190	E071	841
chr7	78937534	78937798	E071	8373
chr7	78946929	78947426	E071	17768
chr7	78970945	78970995	E071	41784
chr7	78971311	78971446	E071	42150
chr7	78899495	78899575	E072	-29586
chr7	78911433	78911832	E072	-17329
chr7	78911973	78912106	E072	-17055
chr7	78912164	78912956	E072	-16205
chr7	78967418	78967592	E072	38257
chr7	78968076	78968193	E072	38915
chr7	78971311	78971446	E072	42150
chr7	78896246	78896316	E074	-32845
chr7	78897714	78897894	E074	-31267
chr7	78917403	78917559	E074	-11602
chr7	78918269	78918319	E074	-10842
chr7	78922189	78922229	E074	-6932
chr7	78946929	78947426	E074	17768
chr7	78966184	78966234	E074	37023
chr7	78967418	78967592	E074	38257
chr7	78969694	78969767	E074	40533
chr7	78971311	78971446	E074	42150

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	78967124	78967271	E067	37963
chr7	78967124	78967271	E068	37963
chr7	78967124	78967271	E069	37963
chr7	78967124	78967271	E071	37963
chr7	78967124	78967271	E072	37963
chr7	78967124	78967271	E073	37963
chr7	78967124	78967271	E074	37963