rs6466241

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

MAGI2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0302 (9010/29818,GnomAD)
C=0318 (9274/29118,TOPMED)
C=0323 (1617/5008,1000G)
C=0252 (972/3854,ALSPAC)
C=0239 (886/3708,TWINSUK)

Position: chr7:78475159 (GRCh38.p7) (7q21.11)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 307 Enhancers around

Promoter: 52 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.78475159T>C
GRCh37.p13 chr 7	NC_000007.13:g.78104476T>C
MAGI2 RefSeqGene	NG_011487.1:g.983415A>G

Gene: MAGI2, membrane associated guanylate kinase, WW and PDZ domain containing 2(minus strand)

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 X9	XM_011516719.2:c.	N/A	Intron Variant
MAGI2 transcript variant X10	XM_011516720.2:c.	N/A	Intron Variant
MAGI2 transcript variant X17	XM_011516726.2:c.	N/A	Intron Variant
MAGI2 transcript variant X19	XM_011516728.1: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 X11	XM_017012847.1:c.	N/A	Intron Variant
MAGI2 transcript variant X12	XM_017012848.1:c.	N/A	Intron Variant
MAGI2 transcript variant X13	XM_017012849.1: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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.458	C=0.542
1000Genomes	American	Sub	694	T=0.830	C=0.170
1000Genomes	East Asian	Sub	1008	T=0.765	C=0.235
1000Genomes	Europe	Sub	1006	T=0.772	C=0.228
1000Genomes	Global	Study-wide	5008	T=0.677	C=0.323
1000Genomes	South Asian	Sub	978	T=0.670	C=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.748	C=0.252
The Genome Aggregation Database	African	Sub	8704	T=0.527	C=0.473
The Genome Aggregation Database	American	Sub	834	T=0.860	C=0.140
The Genome Aggregation Database	East Asian	Sub	1550	T=0.780	C=0.220
The Genome Aggregation Database	Europe	Sub	18428	T=0.763	C=0.236
The Genome Aggregation Database	Global	Study-wide	29818	T=0.697	C=0.302
The Genome Aggregation Database	Other	Sub	302	T=0.770	C=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.681	C=0.318
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.761	C=0.239

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
rs6466241	0.00087	alcohol dependence	20201924

eQTL of rs6466241 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 rs6466241 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 )
chr7	78064225	78064328	E067	-40148
chr7	78064340	78064390	E067	-40086
chr7	78064678	78065196	E067	-39280
chr7	78067791	78067851	E067	-36625
chr7	78067967	78068197	E067	-36279
chr7	78071194	78071344	E067	-33132
chr7	78071428	78071509	E067	-32967
chr7	78071720	78071770	E067	-32706
chr7	78071901	78071951	E067	-32525
chr7	78072509	78072681	E067	-31795
chr7	78079663	78079892	E067	-24584
chr7	78079963	78080343	E067	-24133
chr7	78080366	78080548	E067	-23928
chr7	78095317	78095560	E067	-8916
chr7	78096023	78096203	E067	-8273
chr7	78096448	78096529	E067	-7947
chr7	78099312	78099406	E067	-5070
chr7	78106229	78106618	E067	1753
chr7	78119984	78120073	E067	15508
chr7	78120074	78120213	E067	15598
chr7	78120596	78120665	E067	16120
chr7	78120752	78120812	E067	16276
chr7	78120987	78121045	E067	16511
chr7	78121092	78121160	E067	16616
chr7	78121269	78121378	E067	16793
chr7	78121428	78121498	E067	16952
chr7	78122145	78122195	E067	17669
chr7	78122633	78122731	E067	18157
chr7	78122862	78123040	E067	18386
chr7	78123175	78123219	E067	18699
chr7	78125879	78126182	E067	21403
chr7	78064225	78064328	E068	-40148
chr7	78064340	78064390	E068	-40086
chr7	78064678	78065196	E068	-39280
chr7	78066427	78067012	E068	-37464
chr7	78067644	78067771	E068	-36705
chr7	78067791	78067851	E068	-36625
chr7	78067967	78068197	E068	-36279
chr7	78071194	78071344	E068	-33132
chr7	78071428	78071509	E068	-32967
chr7	78071720	78071770	E068	-32706
chr7	78071901	78071951	E068	-32525
chr7	78072509	78072681	E068	-31795
chr7	78073105	78073155	E068	-31321
chr7	78073305	78073397	E068	-31079
chr7	78079663	78079892	E068	-24584
chr7	78079963	78080343	E068	-24133
chr7	78082455	78082735	E068	-21741
chr7	78095317	78095560	E068	-8916
chr7	78096023	78096203	E068	-8273
chr7	78096448	78096529	E068	-7947
chr7	78098070	78098162	E068	-6314
chr7	78098188	78098238	E068	-6238
chr7	78098361	78098411	E068	-6065
chr7	78098523	78098563	E068	-5913
chr7	78098681	78098758	E068	-5718
chr7	78099312	78099406	E068	-5070
chr7	78101954	78102131	E068	-2345
chr7	78102178	78102263	E068	-2213
chr7	78102431	78102634	E068	-1842
chr7	78102659	78103204	E068	-1272
chr7	78103276	78103431	E068	-1045
chr7	78104439	78104572	E068	0
chr7	78105077	78105150	E068	601
chr7	78105454	78105549	E068	978
chr7	78106088	78106146	E068	1612
chr7	78114637	78114702	E068	10161
chr7	78116140	78116190	E068	11664
chr7	78116197	78116247	E068	11721
chr7	78120596	78120665	E068	16120
chr7	78120752	78120812	E068	16276
chr7	78120987	78121045	E068	16511
chr7	78121092	78121160	E068	16616
chr7	78121269	78121378	E068	16793
chr7	78121428	78121498	E068	16952
chr7	78122145	78122195	E068	17669
chr7	78123175	78123219	E068	18699
chr7	78123350	78123514	E068	18874
chr7	78123986	78124060	E068	19510
chr7	78124199	78124239	E068	19723
chr7	78124737	78124814	E068	20261
chr7	78125047	78125095	E068	20571
chr7	78125227	78125319	E068	20751
chr7	78125879	78126182	E068	21403
chr7	78126750	78126859	E068	22274
chr7	78144095	78144205	E068	39619
chr7	78144220	78144396	E068	39744
chr7	78146057	78146111	E068	41581
chr7	78064225	78064328	E069	-40148
chr7	78064340	78064390	E069	-40086
chr7	78064678	78065196	E069	-39280
chr7	78065260	78065316	E069	-39160
chr7	78065463	78065695	E069	-38781
chr7	78065721	78065763	E069	-38713
chr7	78066427	78067012	E069	-37464
chr7	78072509	78072681	E069	-31795
chr7	78073105	78073155	E069	-31321
chr7	78078560	78078715	E069	-25761
chr7	78078763	78078818	E069	-25658
chr7	78078887	78079021	E069	-25455
chr7	78099312	78099406	E069	-5070
chr7	78104439	78104572	E069	0
chr7	78105077	78105150	E069	601
chr7	78105454	78105549	E069	978
chr7	78106088	78106146	E069	1612
chr7	78106229	78106618	E069	1753
chr7	78114637	78114702	E069	10161
chr7	78120074	78120213	E069	15598
chr7	78120596	78120665	E069	16120
chr7	78120752	78120812	E069	16276
chr7	78120987	78121045	E069	16511
chr7	78121092	78121160	E069	16616
chr7	78121269	78121378	E069	16793
chr7	78121428	78121498	E069	16952
chr7	78122145	78122195	E069	17669
chr7	78122633	78122731	E069	18157
chr7	78122862	78123040	E069	18386
chr7	78123175	78123219	E069	18699
chr7	78123350	78123514	E069	18874
chr7	78126750	78126859	E069	22274
chr7	78065463	78065695	E070	-38781
chr7	78065721	78065763	E070	-38713
chr7	78092914	78093147	E070	-11329
chr7	78119522	78119666	E070	15046
chr7	78119984	78120073	E070	15508
chr7	78120074	78120213	E070	15598
chr7	78120596	78120665	E070	16120
chr7	78120752	78120812	E070	16276
chr7	78120987	78121045	E070	16511
chr7	78121092	78121160	E070	16616
chr7	78121269	78121378	E070	16793
chr7	78121428	78121498	E070	16952
chr7	78144095	78144205	E070	39619
chr7	78144220	78144396	E070	39744
chr7	78063685	78063872	E071	-40604
chr7	78064225	78064328	E071	-40148
chr7	78064340	78064390	E071	-40086
chr7	78064678	78065196	E071	-39280
chr7	78065260	78065316	E071	-39160
chr7	78065463	78065695	E071	-38781
chr7	78065721	78065763	E071	-38713
chr7	78066427	78067012	E071	-37464
chr7	78067644	78067771	E071	-36705
chr7	78067791	78067851	E071	-36625
chr7	78067967	78068197	E071	-36279
chr7	78071194	78071344	E071	-33132
chr7	78071428	78071509	E071	-32967
chr7	78071720	78071770	E071	-32706
chr7	78071901	78071951	E071	-32525
chr7	78072509	78072681	E071	-31795
chr7	78077734	78077892	E071	-26584
chr7	78082455	78082735	E071	-21741
chr7	78092831	78092871	E071	-11605
chr7	78092914	78093147	E071	-11329
chr7	78093581	78093664	E071	-10812
chr7	78095317	78095560	E071	-8916
chr7	78096023	78096203	E071	-8273
chr7	78098681	78098758	E071	-5718
chr7	78099312	78099406	E071	-5070
chr7	78101954	78102131	E071	-2345
chr7	78102178	78102263	E071	-2213
chr7	78102431	78102634	E071	-1842
chr7	78102659	78103204	E071	-1272
chr7	78103276	78103431	E071	-1045
chr7	78104439	78104572	E071	0
chr7	78105077	78105150	E071	601
chr7	78105454	78105549	E071	978
chr7	78119522	78119666	E071	15046
chr7	78119984	78120073	E071	15508
chr7	78120074	78120213	E071	15598
chr7	78120596	78120665	E071	16120
chr7	78120752	78120812	E071	16276
chr7	78120987	78121045	E071	16511
chr7	78121092	78121160	E071	16616
chr7	78121269	78121378	E071	16793
chr7	78121428	78121498	E071	16952
chr7	78122145	78122195	E071	17669
chr7	78122633	78122731	E071	18157
chr7	78122862	78123040	E071	18386
chr7	78123175	78123219	E071	18699
chr7	78123350	78123514	E071	18874
chr7	78123986	78124060	E071	19510
chr7	78126750	78126859	E071	22274
chr7	78139959	78140302	E071	35483
chr7	78056259	78056309	E072	-48167
chr7	78064678	78065196	E072	-39280
chr7	78066427	78067012	E072	-37464
chr7	78067644	78067771	E072	-36705
chr7	78067791	78067851	E072	-36625
chr7	78067967	78068197	E072	-36279
chr7	78071428	78071509	E072	-32967
chr7	78071720	78071770	E072	-32706
chr7	78071901	78071951	E072	-32525
chr7	78072509	78072681	E072	-31795
chr7	78073105	78073155	E072	-31321
chr7	78073305	78073397	E072	-31079
chr7	78079963	78080343	E072	-24133
chr7	78080366	78080548	E072	-23928
chr7	78082455	78082735	E072	-21741
chr7	78092914	78093147	E072	-11329
chr7	78099312	78099406	E072	-5070
chr7	78102178	78102263	E072	-2213
chr7	78102659	78103204	E072	-1272
chr7	78103276	78103431	E072	-1045
chr7	78120074	78120213	E072	15598
chr7	78120752	78120812	E072	16276
chr7	78120987	78121045	E072	16511
chr7	78121092	78121160	E072	16616
chr7	78121269	78121378	E072	16793
chr7	78121428	78121498	E072	16952
chr7	78122145	78122195	E072	17669
chr7	78122633	78122731	E072	18157
chr7	78122862	78123040	E072	18386
chr7	78123175	78123219	E072	18699
chr7	78123350	78123514	E072	18874
chr7	78123986	78124060	E072	19510
chr7	78124199	78124239	E072	19723
chr7	78124737	78124814	E072	20261
chr7	78064225	78064328	E073	-40148
chr7	78064340	78064390	E073	-40086
chr7	78064678	78065196	E073	-39280
chr7	78065260	78065316	E073	-39160
chr7	78065463	78065695	E073	-38781
chr7	78065721	78065763	E073	-38713
chr7	78066427	78067012	E073	-37464
chr7	78102431	78102634	E073	-1842
chr7	78102659	78103204	E073	-1272
chr7	78103276	78103431	E073	-1045
chr7	78108790	78108946	E073	4314
chr7	78119522	78119666	E073	15046
chr7	78119984	78120073	E073	15508
chr7	78120074	78120213	E073	15598
chr7	78120596	78120665	E073	16120
chr7	78120752	78120812	E073	16276
chr7	78120987	78121045	E073	16511
chr7	78121092	78121160	E073	16616
chr7	78121269	78121378	E073	16793
chr7	78121428	78121498	E073	16952
chr7	78144095	78144205	E073	39619
chr7	78144220	78144396	E073	39744
chr7	78146309	78146360	E073	41833
chr7	78064225	78064328	E074	-40148
chr7	78064340	78064390	E074	-40086
chr7	78064678	78065196	E074	-39280
chr7	78065260	78065316	E074	-39160
chr7	78067967	78068197	E074	-36279
chr7	78071428	78071509	E074	-32967
chr7	78071720	78071770	E074	-32706
chr7	78071901	78071951	E074	-32525
chr7	78072509	78072681	E074	-31795
chr7	78078091	78078558	E074	-25918
chr7	78078560	78078715	E074	-25761
chr7	78078763	78078818	E074	-25658
chr7	78082455	78082735	E074	-21741
chr7	78082874	78082999	E074	-21477
chr7	78092418	78092458	E074	-12018
chr7	78092831	78092871	E074	-11605
chr7	78092914	78093147	E074	-11329
chr7	78093581	78093664	E074	-10812
chr7	78096023	78096203	E074	-8273
chr7	78096448	78096529	E074	-7947
chr7	78099312	78099406	E074	-5070
chr7	78101954	78102131	E074	-2345
chr7	78102178	78102263	E074	-2213
chr7	78102431	78102634	E074	-1842
chr7	78102659	78103204	E074	-1272
chr7	78106088	78106146	E074	1612
chr7	78116140	78116190	E074	11664
chr7	78116197	78116247	E074	11721
chr7	78119522	78119666	E074	15046
chr7	78119984	78120073	E074	15508
chr7	78120074	78120213	E074	15598
chr7	78120596	78120665	E074	16120
chr7	78120752	78120812	E074	16276
chr7	78120987	78121045	E074	16511
chr7	78121092	78121160	E074	16616
chr7	78121269	78121378	E074	16793
chr7	78121428	78121498	E074	16952
chr7	78122145	78122195	E074	17669
chr7	78122633	78122731	E074	18157
chr7	78122862	78123040	E074	18386
chr7	78123175	78123219	E074	18699
chr7	78123350	78123514	E074	18874
chr7	78123986	78124060	E074	19510
chr7	78124199	78124239	E074	19723
chr7	78124737	78124814	E074	20261
chr7	78125047	78125095	E074	20571
chr7	78125227	78125319	E074	20751
chr7	78125879	78126182	E074	21403
chr7	78126750	78126859	E074	22274
chr7	78127495	78127652	E074	23019
chr7	78127653	78127849	E074	23177
chr7	78120074	78120213	E081	15598
chr7	78120596	78120665	E081	16120
chr7	78120752	78120812	E081	16276
chr7	78120987	78121045	E081	16511
chr7	78121092	78121160	E081	16616
chr7	78121269	78121378	E081	16793
chr7	78121428	78121498	E081	16952
chr7	78067644	78067771	E082	-36705
chr7	78067791	78067851	E082	-36625
chr7	78067967	78068197	E082	-36279
chr7	78098188	78098238	E082	-6238
chr7	78098361	78098411	E082	-6065
chr7	78098523	78098563	E082	-5913
chr7	78098681	78098758	E082	-5718
chr7	78102431	78102634	E082	-1842

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	78116760	78117013	E067	12284
chr7	78118170	78118283	E067	13694
chr7	78118548	78118598	E067	14072
chr7	78118735	78119024	E067	14259
chr7	78119082	78119509	E067	14606
chr7	78116760	78117013	E068	12284
chr7	78117955	78118024	E068	13479
chr7	78118083	78118133	E068	13607
chr7	78118170	78118283	E068	13694
chr7	78118548	78118598	E068	14072
chr7	78118735	78119024	E068	14259
chr7	78119082	78119509	E068	14606
chr7	78125515	78125873	E068	21039
chr7	78116760	78117013	E069	12284
chr7	78118735	78119024	E069	14259
chr7	78119082	78119509	E069	14606
chr7	78125515	78125873	E069	21039
chr7	78118170	78118283	E070	13694
chr7	78118548	78118598	E070	14072
chr7	78118735	78119024	E070	14259
chr7	78119082	78119509	E070	14606
chr7	78117955	78118024	E071	13479
chr7	78118083	78118133	E071	13607
chr7	78118170	78118283	E071	13694
chr7	78118548	78118598	E071	14072
chr7	78118735	78119024	E071	14259
chr7	78119082	78119509	E071	14606
chr7	78125515	78125873	E071	21039
chr7	78116760	78117013	E072	12284
chr7	78117955	78118024	E072	13479
chr7	78118083	78118133	E072	13607
chr7	78118170	78118283	E072	13694
chr7	78118548	78118598	E072	14072
chr7	78118735	78119024	E072	14259
chr7	78119082	78119509	E072	14606
chr7	78125515	78125873	E072	21039
chr7	78118170	78118283	E073	13694
chr7	78118548	78118598	E073	14072
chr7	78118735	78119024	E073	14259
chr7	78119082	78119509	E073	14606
chr7	78117955	78118024	E074	13479
chr7	78118083	78118133	E074	13607
chr7	78118170	78118283	E074	13694
chr7	78118548	78118598	E074	14072
chr7	78118735	78119024	E074	14259
chr7	78119082	78119509	E074	14606
chr7	78117955	78118024	E082	13479
chr7	78118083	78118133	E082	13607
chr7	78118170	78118283	E082	13694
chr7	78118548	78118598	E082	14072
chr7	78118735	78119024	E082	14259
chr7	78119082	78119509	E082	14606