rs17150722

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

MAGI2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0108 (3228/29870,GnomAD)
T=0126 (3679/29118,TOPMED)
T=0087 (435/5008,1000G)
T=0116 (447/3854,ALSPAC)
T=0123 (456/3708,TWINSUK)

Position: chr7:78429448 (GRCh38.p7) (7q21.11)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 327 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.78429448A>T
GRCh37.p13 chr 7	NC_000007.13:g.78058765A>T
MAGI2 RefSeqGene	NG_011487.1:g.1029126T>A

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	A=0.864	T=0.136
1000Genomes	American	Sub	694	A=0.920	T=0.080
1000Genomes	East Asian	Sub	1008	A=0.996	T=0.004
1000Genomes	Europe	Sub	1006	A=0.887	T=0.113
1000Genomes	Global	Study-wide	5008	A=0.913	T=0.087
1000Genomes	South Asian	Sub	978	A=0.920	T=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.884	T=0.116
The Genome Aggregation Database	African	Sub	8686	A=0.855	T=0.145
The Genome Aggregation Database	American	Sub	832	A=0.930	T=0.070
The Genome Aggregation Database	East Asian	Sub	1596	A=0.999	T=0.001
The Genome Aggregation Database	Europe	Sub	18456	A=0.898	T=0.102
The Genome Aggregation Database	Global	Study-wide	29870	A=0.891	T=0.108
The Genome Aggregation Database	Other	Sub	300	A=0.930	T=0.070
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.873	T=0.126
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.877	T=0.123

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs17150722	0.000641	nicotine smoking	19268276

eQTL of rs17150722 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 rs17150722 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	78022631	78022701	E067	-36064
chr7	78022754	78022804	E067	-35961
chr7	78022883	78023241	E067	-35524
chr7	78023599	78023649	E067	-35116
chr7	78023750	78023868	E067	-34897
chr7	78035557	78035633	E067	-23132
chr7	78035735	78036388	E067	-22377
chr7	78047434	78047488	E067	-11277
chr7	78047782	78047832	E067	-10933
chr7	78048746	78048797	E067	-9968
chr7	78048833	78048884	E067	-9881
chr7	78049125	78049212	E067	-9553
chr7	78049259	78049368	E067	-9397
chr7	78049519	78049675	E067	-9090
chr7	78050222	78050446	E067	-8319
chr7	78050531	78050617	E067	-8148
chr7	78051059	78051099	E067	-7666
chr7	78051256	78051296	E067	-7469
chr7	78051415	78051465	E067	-7300
chr7	78051478	78051532	E067	-7233
chr7	78064225	78064328	E067	5460
chr7	78064340	78064390	E067	5575
chr7	78064678	78065196	E067	5913
chr7	78067791	78067851	E067	9026
chr7	78067967	78068197	E067	9202
chr7	78071194	78071344	E067	12429
chr7	78071428	78071509	E067	12663
chr7	78071720	78071770	E067	12955
chr7	78071901	78071951	E067	13136
chr7	78072509	78072681	E067	13744
chr7	78079663	78079892	E067	20898
chr7	78079963	78080343	E067	21198
chr7	78080366	78080548	E067	21601
chr7	78095317	78095560	E067	36552
chr7	78096023	78096203	E067	37258
chr7	78096448	78096529	E067	37683
chr7	78099312	78099406	E067	40547
chr7	78106229	78106618	E067	47464
chr7	78018537	78018666	E068	-40099
chr7	78018718	78018768	E068	-39997
chr7	78025153	78025246	E068	-33519
chr7	78025653	78025870	E068	-32895
chr7	78025960	78026010	E068	-32755
chr7	78026993	78027137	E068	-31628
chr7	78027397	78027706	E068	-31059
chr7	78028308	78028417	E068	-30348
chr7	78028478	78028540	E068	-30225
chr7	78028547	78028957	E068	-29808
chr7	78045485	78045578	E068	-13187
chr7	78046652	78046702	E068	-12063
chr7	78047434	78047488	E068	-11277
chr7	78047782	78047832	E068	-10933
chr7	78048746	78048797	E068	-9968
chr7	78048833	78048884	E068	-9881
chr7	78049125	78049212	E068	-9553
chr7	78049259	78049368	E068	-9397
chr7	78049519	78049675	E068	-9090
chr7	78050222	78050446	E068	-8319
chr7	78050531	78050617	E068	-8148
chr7	78051059	78051099	E068	-7666
chr7	78051256	78051296	E068	-7469
chr7	78051415	78051465	E068	-7300
chr7	78051478	78051532	E068	-7233
chr7	78052003	78052211	E068	-6554
chr7	78064225	78064328	E068	5460
chr7	78064340	78064390	E068	5575
chr7	78064678	78065196	E068	5913
chr7	78066427	78067012	E068	7662
chr7	78067644	78067771	E068	8879
chr7	78067791	78067851	E068	9026
chr7	78067967	78068197	E068	9202
chr7	78071194	78071344	E068	12429
chr7	78071428	78071509	E068	12663
chr7	78071720	78071770	E068	12955
chr7	78071901	78071951	E068	13136
chr7	78072509	78072681	E068	13744
chr7	78073105	78073155	E068	14340
chr7	78073305	78073397	E068	14540
chr7	78079663	78079892	E068	20898
chr7	78079963	78080343	E068	21198
chr7	78082455	78082735	E068	23690
chr7	78095317	78095560	E068	36552
chr7	78096023	78096203	E068	37258
chr7	78096448	78096529	E068	37683
chr7	78098070	78098162	E068	39305
chr7	78098188	78098238	E068	39423
chr7	78098361	78098411	E068	39596
chr7	78098523	78098563	E068	39758
chr7	78098681	78098758	E068	39916
chr7	78099312	78099406	E068	40547
chr7	78101954	78102131	E068	43189
chr7	78102178	78102263	E068	43413
chr7	78102431	78102634	E068	43666
chr7	78102659	78103204	E068	43894
chr7	78103276	78103431	E068	44511
chr7	78104439	78104572	E068	45674
chr7	78105077	78105150	E068	46312
chr7	78105454	78105549	E068	46689
chr7	78106088	78106146	E068	47323
chr7	78012156	78012222	E069	-46543
chr7	78012530	78012841	E069	-45924
chr7	78022631	78022701	E069	-36064
chr7	78022754	78022804	E069	-35961
chr7	78024720	78024883	E069	-33882
chr7	78029180	78029463	E069	-29302
chr7	78045485	78045578	E069	-13187
chr7	78047434	78047488	E069	-11277
chr7	78047782	78047832	E069	-10933
chr7	78048746	78048797	E069	-9968
chr7	78048833	78048884	E069	-9881
chr7	78049125	78049212	E069	-9553
chr7	78049259	78049368	E069	-9397
chr7	78049519	78049675	E069	-9090
chr7	78050222	78050446	E069	-8319
chr7	78050531	78050617	E069	-8148
chr7	78051059	78051099	E069	-7666
chr7	78051256	78051296	E069	-7469
chr7	78051415	78051465	E069	-7300
chr7	78051478	78051532	E069	-7233
chr7	78064225	78064328	E069	5460
chr7	78064340	78064390	E069	5575
chr7	78064678	78065196	E069	5913
chr7	78065260	78065316	E069	6495
chr7	78065463	78065695	E069	6698
chr7	78065721	78065763	E069	6956
chr7	78066427	78067012	E069	7662
chr7	78072509	78072681	E069	13744
chr7	78073105	78073155	E069	14340
chr7	78078560	78078715	E069	19795
chr7	78078763	78078818	E069	19998
chr7	78078887	78079021	E069	20122
chr7	78099312	78099406	E069	40547
chr7	78104439	78104572	E069	45674
chr7	78105077	78105150	E069	46312
chr7	78105454	78105549	E069	46689
chr7	78106088	78106146	E069	47323
chr7	78106229	78106618	E069	47464
chr7	78048746	78048797	E070	-9968
chr7	78048833	78048884	E070	-9881
chr7	78049125	78049212	E070	-9553
chr7	78049259	78049368	E070	-9397
chr7	78049519	78049675	E070	-9090
chr7	78050222	78050446	E070	-8319
chr7	78065463	78065695	E070	6698
chr7	78065721	78065763	E070	6956
chr7	78092914	78093147	E070	34149
chr7	78014303	78014357	E071	-44408
chr7	78018537	78018666	E071	-40099
chr7	78018718	78018768	E071	-39997
chr7	78022754	78022804	E071	-35961
chr7	78022883	78023241	E071	-35524
chr7	78027935	78028244	E071	-30521
chr7	78028308	78028417	E071	-30348
chr7	78028478	78028540	E071	-30225
chr7	78028547	78028957	E071	-29808
chr7	78047434	78047488	E071	-11277
chr7	78047782	78047832	E071	-10933
chr7	78048746	78048797	E071	-9968
chr7	78048833	78048884	E071	-9881
chr7	78049125	78049212	E071	-9553
chr7	78049259	78049368	E071	-9397
chr7	78049519	78049675	E071	-9090
chr7	78050222	78050446	E071	-8319
chr7	78050531	78050617	E071	-8148
chr7	78051059	78051099	E071	-7666
chr7	78051256	78051296	E071	-7469
chr7	78051415	78051465	E071	-7300
chr7	78051478	78051532	E071	-7233
chr7	78053288	78053348	E071	-5417
chr7	78053428	78053496	E071	-5269
chr7	78063685	78063872	E071	4920
chr7	78064225	78064328	E071	5460
chr7	78064340	78064390	E071	5575
chr7	78064678	78065196	E071	5913
chr7	78065260	78065316	E071	6495
chr7	78065463	78065695	E071	6698
chr7	78065721	78065763	E071	6956
chr7	78066427	78067012	E071	7662
chr7	78067644	78067771	E071	8879
chr7	78067791	78067851	E071	9026
chr7	78067967	78068197	E071	9202
chr7	78071194	78071344	E071	12429
chr7	78071428	78071509	E071	12663
chr7	78071720	78071770	E071	12955
chr7	78071901	78071951	E071	13136
chr7	78072509	78072681	E071	13744
chr7	78077734	78077892	E071	18969
chr7	78082455	78082735	E071	23690
chr7	78092831	78092871	E071	34066
chr7	78092914	78093147	E071	34149
chr7	78093581	78093664	E071	34816
chr7	78095317	78095560	E071	36552
chr7	78096023	78096203	E071	37258
chr7	78098681	78098758	E071	39916
chr7	78099312	78099406	E071	40547
chr7	78101954	78102131	E071	43189
chr7	78102178	78102263	E071	43413
chr7	78102431	78102634	E071	43666
chr7	78102659	78103204	E071	43894
chr7	78103276	78103431	E071	44511
chr7	78104439	78104572	E071	45674
chr7	78105077	78105150	E071	46312
chr7	78105454	78105549	E071	46689
chr7	78018537	78018666	E072	-40099
chr7	78018718	78018768	E072	-39997
chr7	78018814	78018869	E072	-39896
chr7	78026993	78027137	E072	-31628
chr7	78027397	78027706	E072	-31059
chr7	78027935	78028244	E072	-30521
chr7	78028308	78028417	E072	-30348
chr7	78028478	78028540	E072	-30225
chr7	78028547	78028957	E072	-29808
chr7	78045485	78045578	E072	-13187
chr7	78047434	78047488	E072	-11277
chr7	78047782	78047832	E072	-10933
chr7	78048746	78048797	E072	-9968
chr7	78048833	78048884	E072	-9881
chr7	78049125	78049212	E072	-9553
chr7	78049259	78049368	E072	-9397
chr7	78049519	78049675	E072	-9090
chr7	78050222	78050446	E072	-8319
chr7	78050531	78050617	E072	-8148
chr7	78051059	78051099	E072	-7666
chr7	78051256	78051296	E072	-7469
chr7	78051415	78051465	E072	-7300
chr7	78051478	78051532	E072	-7233
chr7	78056259	78056309	E072	-2456
chr7	78064678	78065196	E072	5913
chr7	78066427	78067012	E072	7662
chr7	78067644	78067771	E072	8879
chr7	78067791	78067851	E072	9026
chr7	78067967	78068197	E072	9202
chr7	78071428	78071509	E072	12663
chr7	78071720	78071770	E072	12955
chr7	78071901	78071951	E072	13136
chr7	78072509	78072681	E072	13744
chr7	78073105	78073155	E072	14340
chr7	78073305	78073397	E072	14540
chr7	78079963	78080343	E072	21198
chr7	78080366	78080548	E072	21601
chr7	78082455	78082735	E072	23690
chr7	78092914	78093147	E072	34149
chr7	78099312	78099406	E072	40547
chr7	78102178	78102263	E072	43413
chr7	78102659	78103204	E072	43894
chr7	78103276	78103431	E072	44511
chr7	78022631	78022701	E073	-36064
chr7	78022754	78022804	E073	-35961
chr7	78047434	78047488	E073	-11277
chr7	78047782	78047832	E073	-10933
chr7	78048833	78048884	E073	-9881
chr7	78049125	78049212	E073	-9553
chr7	78049259	78049368	E073	-9397
chr7	78049519	78049675	E073	-9090
chr7	78050222	78050446	E073	-8319
chr7	78064225	78064328	E073	5460
chr7	78064340	78064390	E073	5575
chr7	78064678	78065196	E073	5913
chr7	78065260	78065316	E073	6495
chr7	78065463	78065695	E073	6698
chr7	78065721	78065763	E073	6956
chr7	78066427	78067012	E073	7662
chr7	78102431	78102634	E073	43666
chr7	78102659	78103204	E073	43894
chr7	78103276	78103431	E073	44511
chr7	78014303	78014357	E074	-44408
chr7	78015670	78015995	E074	-42770
chr7	78016169	78016232	E074	-42533
chr7	78022754	78022804	E074	-35961
chr7	78022883	78023241	E074	-35524
chr7	78023599	78023649	E074	-35116
chr7	78023750	78023868	E074	-34897
chr7	78026993	78027137	E074	-31628
chr7	78027397	78027706	E074	-31059
chr7	78027935	78028244	E074	-30521
chr7	78028308	78028417	E074	-30348
chr7	78028478	78028540	E074	-30225
chr7	78028547	78028957	E074	-29808
chr7	78045485	78045578	E074	-13187
chr7	78047434	78047488	E074	-11277
chr7	78047782	78047832	E074	-10933
chr7	78048746	78048797	E074	-9968
chr7	78048833	78048884	E074	-9881
chr7	78049125	78049212	E074	-9553
chr7	78049259	78049368	E074	-9397
chr7	78049519	78049675	E074	-9090
chr7	78050222	78050446	E074	-8319
chr7	78050531	78050617	E074	-8148
chr7	78051415	78051465	E074	-7300
chr7	78051478	78051532	E074	-7233
chr7	78064225	78064328	E074	5460
chr7	78064340	78064390	E074	5575
chr7	78064678	78065196	E074	5913
chr7	78065260	78065316	E074	6495
chr7	78067967	78068197	E074	9202
chr7	78071428	78071509	E074	12663
chr7	78071720	78071770	E074	12955
chr7	78071901	78071951	E074	13136
chr7	78072509	78072681	E074	13744
chr7	78078091	78078558	E074	19326
chr7	78078560	78078715	E074	19795
chr7	78078763	78078818	E074	19998
chr7	78082455	78082735	E074	23690
chr7	78082874	78082999	E074	24109
chr7	78092418	78092458	E074	33653
chr7	78092831	78092871	E074	34066
chr7	78092914	78093147	E074	34149
chr7	78093581	78093664	E074	34816
chr7	78096023	78096203	E074	37258
chr7	78096448	78096529	E074	37683
chr7	78099312	78099406	E074	40547
chr7	78101954	78102131	E074	43189
chr7	78102178	78102263	E074	43413
chr7	78102431	78102634	E074	43666
chr7	78102659	78103204	E074	43894
chr7	78106088	78106146	E074	47323
chr7	78028308	78028417	E081	-30348
chr7	78028478	78028540	E081	-30225
chr7	78028547	78028957	E081	-29808
chr7	78067644	78067771	E082	8879
chr7	78067791	78067851	E082	9026
chr7	78067967	78068197	E082	9202
chr7	78098188	78098238	E082	39423
chr7	78098361	78098411	E082	39596
chr7	78098523	78098563	E082	39758
chr7	78098681	78098758	E082	39916
chr7	78102431	78102634	E082	43666