rs13242509

Homo sapiens
T>C
MAGI2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0109 (3286/29956,GnomAD)
C=0119 (3480/29118,TOPMED)
C=0085 (425/5008,1000G)
C=0109 (419/3854,ALSPAC)
C=0098 (363/3708,TWINSUK)
chr7:78560896 (GRCh38.p7) (7q21.11)
AD
GWASdb2
1   publication(s)
See rs on genome
219 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.78560896T>C
GRCh37.p13 chr 7NC_000007.13:g.78190213T>C
MAGI2 RefSeqGeneNG_011487.1:g.897678A>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 2NM_001301128.1:c.N/AIntron Variant
MAGI2 transcript variant 1NM_012301.3:c.N/AIntron Variant
MAGI2 transcript variant X6XM_011516718.1:c.N/AIntron Variant
MAGI2 transcript variant X9XM_011516719.2:c.N/AIntron Variant
MAGI2 transcript variant X10XM_011516720.2:c.N/AIntron Variant
MAGI2 transcript variant X1XM_017012840.1:c.N/AIntron Variant
MAGI2 transcript variant X2XM_017012841.1:c.N/AIntron Variant
MAGI2 transcript variant X3XM_017012842.1:c.N/AIntron Variant
MAGI2 transcript variant X4XM_017012843.1:c.N/AIntron Variant
MAGI2 transcript variant X5XM_017012844.1:c.N/AIntron Variant
MAGI2 transcript variant X7XM_017012845.1:c.N/AIntron Variant
MAGI2 transcript variant X8XM_017012846.1:c.N/AIntron Variant
MAGI2 transcript variant X11XM_017012847.1:c.N/AIntron Variant
MAGI2 transcript variant X12XM_017012848.1:c.N/AIntron Variant
MAGI2 transcript variant X13XM_017012849.1:c.N/AIntron Variant
MAGI2 transcript variant X14XM_017012850.1:c.N/AIntron Variant
MAGI2 transcript variant X15XM_017012851.1:c.N/AIntron Variant
MAGI2 transcript variant X16XM_017012852.1:c.N/AIntron Variant
MAGI2 transcript variant X17XM_011516726.2:c.N/AGenic Upstream Transcript Variant
MAGI2 transcript variant X19XM_011516728.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.865C=0.135
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=0.987C=0.013
1000GenomesEuropeSub1006T=0.886C=0.114
1000GenomesGlobalStudy-wide5008T=0.915C=0.085
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.891C=0.109
The Genome Aggregation DatabaseAfricanSub8720T=0.868C=0.132
The Genome Aggregation DatabaseAmericanSub838T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1620T=0.998C=0.002
The Genome Aggregation DatabaseEuropeSub18476T=0.888C=0.111
The Genome Aggregation DatabaseGlobalStudy-wide29956T=0.890C=0.109
The Genome Aggregation DatabaseOtherSub302T=0.920C=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.880C=0.119
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.902C=0.098
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs132425090.000204alcohol consumption23743675

eQTL of rs13242509 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 rs13242509 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 )
chr77815967978160010E067-30203
chr77816032878160378E067-29835
chr77817053078170587E067-19626
chr77817095778171007E067-19206
chr77817189778172029E067-18184
chr77817205178172101E067-18112
chr77817217878172237E067-17976
chr77819098978191476E067776
chr77819158278192072E0671369
chr77819210378192189E0671890
chr77819253178192949E0672318
chr77819798078198053E0677767
chr77819808578198334E0677872
chr77819998878200038E0679775
chr77820033978200389E06710126
chr77822329778223577E06733084
chr77822358578223760E06733372
chr77822377178223852E06733558
chr77823114778231374E06740934
chr77823675078237305E06746537
chr77823766678237716E06747453
chr77823824778238297E06748034
chr77814409578144205E068-46008
chr77814422078144396E068-45817
chr77814605778146111E068-44102
chr77816032878160378E068-29835
chr77817095778171007E068-19206
chr77817189778172029E068-18184
chr77817205178172101E068-18112
chr77817217878172237E068-17976
chr77817232778172669E068-17544
chr77819098978191476E068776
chr77819158278192072E0681369
chr77819210378192189E0681890
chr77819253178192949E0682318
chr77819540578195483E0685192
chr77819591778195959E0685704
chr77819669378196779E0686480
chr77819680478196858E0686591
chr77819698778197027E0686774
chr77819727078197598E0687057
chr77819771078197852E0687497
chr77819798078198053E0687767
chr77819976078199952E0689547
chr77819998878200038E0689775
chr77820033978200389E06810126
chr77820041078200460E06810197
chr77820047178200511E06810258
chr77820065478200778E06810441
chr77820789378208472E06817680
chr77822329778223577E06833084
chr77822358578223760E06833372
chr77823265378232791E06842440
chr77823642078236645E06846207
chr77823675078237305E06846537
chr77815545078155500E069-34713
chr77815967978160010E069-30203
chr77816032878160378E069-29835
chr77817053078170587E069-19626
chr77817095778171007E069-19206
chr77817167978171733E069-18480
chr77817189778172029E069-18184
chr77817205178172101E069-18112
chr77817217878172237E069-17976
chr77817232778172669E069-17544
chr77818671578186812E069-3401
chr77818685778187087E069-3126
chr77818762278187711E069-2502
chr77818777978188132E069-2081
chr77818953978189800E069-413
chr77819017078190230E0690
chr77819098978191476E069776
chr77819158278192072E0691369
chr77819210378192189E0691890
chr77819253178192949E0692318
chr77819512978195179E0694916
chr77819540578195483E0695192
chr77819620578196316E0695992
chr77819669378196779E0696480
chr77819680478196858E0696591
chr77819698778197027E0696774
chr77819727078197598E0697057
chr77819771078197852E0697497
chr77819808578198334E0697872
chr77821593278216325E06925719
chr77821673178216775E06926518
chr77822329778223577E06933084
chr77822358578223760E06933372
chr77823675078237305E06946537
chr77814409578144205E070-46008
chr77814422078144396E070-45817
chr77817053078170587E070-19626
chr77817095778171007E070-19206
chr77819158278192072E0701369
chr77819210378192189E0701890
chr77819253178192949E0702318
chr77816032878160378E071-29835
chr77817053078170587E071-19626
chr77817095778171007E071-19206
chr77817167978171733E071-18480
chr77817189778172029E071-18184
chr77817205178172101E071-18112
chr77817217878172237E071-17976
chr77817232778172669E071-17544
chr77817307278173112E071-17101
chr77817873678178806E071-11407
chr77818685778187087E071-3126
chr77818762278187711E071-2502
chr77818777978188132E071-2081
chr77818953978189800E071-413
chr77819017078190230E0710
chr77819061378190684E071400
chr77819082978190909E071616
chr77819098978191476E071776
chr77819158278192072E0711369
chr77819210378192189E0711890
chr77819540578195483E0715192
chr77819591778195959E0715704
chr77819620578196316E0715992
chr77819669378196779E0716480
chr77819771078197852E0717497
chr77819798078198053E0717767
chr77819808578198334E0717872
chr77819945578199508E0719242
chr77819976078199952E0719547
chr77819998878200038E0719775
chr77820033978200389E07110126
chr77820041078200460E07110197
chr77820047178200511E07110258
chr77820789378208472E07117680
chr77821773778218013E07127524
chr77823642078236645E07146207
chr77823675078237305E07146537
chr77815855578158646E072-31567
chr77815887578158971E072-31242
chr77815967978160010E072-30203
chr77816032878160378E072-29835
chr77817053078170587E072-19626
chr77817095778171007E072-19206
chr77817167978171733E072-18480
chr77817189778172029E072-18184
chr77817205178172101E072-18112
chr77817217878172237E072-17976
chr77817232778172669E072-17544
chr77817574978175793E072-14420
chr77817718178177231E072-12982
chr77818671578186812E072-3401
chr77818685778187087E072-3126
chr77818762278187711E072-2502
chr77818953978189800E072-413
chr77819098978191476E072776
chr77819158278192072E0721369
chr77819210378192189E0721890
chr77819253178192949E0722318
chr77819540578195483E0725192
chr77819669378196779E0726480
chr77819680478196858E0726591
chr77819698778197027E0726774
chr77819727078197598E0727057
chr77819771078197852E0727497
chr77819798078198053E0727767
chr77819808578198334E0727872
chr77819976078199952E0729547
chr77819998878200038E0729775
chr77821747978217529E07227266
chr77822197678222102E07231763
chr77823374478233860E07243531
chr77814409578144205E073-46008
chr77814422078144396E073-45817
chr77814630978146360E073-43853
chr77819540578195483E0735192
chr77819976078199952E0739547
chr77819998878200038E0739775
chr77815855578158646E074-31567
chr77815887578158971E074-31242
chr77816032878160378E074-29835
chr77817053078170587E074-19626
chr77817095778171007E074-19206
chr77817167978171733E074-18480
chr77817189778172029E074-18184
chr77817205178172101E074-18112
chr77817217878172237E074-17976
chr77817232778172669E074-17544
chr77818671578186812E074-3401
chr77818685778187087E074-3126
chr77819017078190230E0740
chr77819061378190684E074400
chr77819082978190909E074616
chr77819098978191476E074776
chr77819158278192072E0741369
chr77819210378192189E0741890
chr77819540578195483E0745192
chr77819591778195959E0745704
chr77819856978198619E0748356
chr77819870778198757E0748494
chr77819911178199161E0748898
chr77819945578199508E0749242
chr77819976078199952E0749547
chr77819998878200038E0749775
chr77821500878215094E07424795
chr77821526678215379E07425053
chr77821540278215512E07425189
chr77821747978217529E07427266
chr77821773778218013E07427524
chr77822292978223056E07432716
chr77822329778223577E07433084
chr77822358578223760E07433372
chr77822377178223852E07433558
chr77823114778231374E07440934
chr77823675078237305E07446537
chr77818953978189800E081-413
chr77819098978191476E081776
chr77819158278192072E0811369
chr77819210378192189E0811890
chr77819253178192949E0812318
chr77819098978191476E082776
chr77819158278192072E0821369
chr77819210378192189E0821890
chr77819253178192949E0822318