rs2411042

Homo sapiens
G>T
MGAT5B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0066 (2004/29966,GnomAD)
T=0074 (2166/29118,TOPMED)
T=0100 (503/5008,1000G)
T=0037 (143/3854,ALSPAC)
T=0036 (135/3708,TWINSUK)
chr17:76917855 (GRCh38.p7) (17q25.2)
AD
GWASdb2
1   publication(s)
See rs on genome
211 Enhancers around
36 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.76917855G>T
GRCh37.p13 chr 17NC_000017.10:g.74913937G>T

Gene: MGAT5B, mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MGAT5B transcript variant 3NM_001199172.1:c.N/AIntron Variant
MGAT5B transcript variant 1NM_144677.2:c.N/AIntron Variant
MGAT5B transcript variant 2NM_198955.1:c.N/AIntron Variant
MGAT5B transcript variant X2XM_006721707.3:c.N/AIntron Variant
MGAT5B transcript variant X1XM_011524350.2:c.N/AIntron Variant
MGAT5B transcript variant X4XM_011524352.2:c.N/AIntron Variant
MGAT5B transcript variant X3XM_017024200.1:c.N/AIntron Variant
MGAT5B transcript variant X6XM_011524354.2:c.N/AGenic Downstream Transcript Variant
MGAT5B transcript variant X5XR_934377.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.887T=0.113
1000GenomesAmericanSub694G=0.920T=0.080
1000GenomesEast AsianSub1008G=0.806T=0.194
1000GenomesEuropeSub1006G=0.968T=0.032
1000GenomesGlobalStudy-wide5008G=0.900T=0.100
1000GenomesSouth AsianSub978G=0.930T=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.963T=0.037
The Genome Aggregation DatabaseAfricanSub8716G=0.907T=0.093
The Genome Aggregation DatabaseAmericanSub838G=0.930T=0.070
The Genome Aggregation DatabaseEast AsianSub1620G=0.801T=0.199
The Genome Aggregation DatabaseEuropeSub18490G=0.957T=0.042
The Genome Aggregation DatabaseGlobalStudy-wide29966G=0.933T=0.066
The Genome Aggregation DatabaseOtherSub302G=0.900T=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.925T=0.074
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.964T=0.036
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs24110420.000342alcohol dependence21314694

eQTL of rs2411042 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 rs2411042 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 )
chr177490648574906535E067-7402
chr177490669874906752E067-7185
chr177490717574907259E067-6678
chr177490733274907382E067-6555
chr177490745574907662E067-6275
chr177490783074908040E067-5897
chr177491403674914252E06799
chr177491427174914321E067334
chr177491489974914952E067962
chr177491495674915042E0671019
chr177491660074916669E0672663
chr177491668874916738E0672751
chr177492055074920692E0676613
chr177492077474920844E0676837
chr177492100974921066E0677072
chr177492108674921194E0677149
chr177492132374921452E0677386
chr177492149174921915E0677554
chr177493080974930911E06716872
chr177493093174931313E06716994
chr177494465174944759E06730714
chr177486947374869667E068-44270
chr177486972374869790E068-44147
chr177487965374879703E068-34234
chr177487987874880098E068-33839
chr177488920674889254E068-24683
chr177488935774889499E068-24438
chr177488970274889914E068-24023
chr177489002174890256E068-23681
chr177489641974896479E068-17458
chr177489650474896554E068-17383
chr177489769174897927E068-16010
chr177489797574898124E068-15813
chr177489817974898312E068-15625
chr177490594474906314E068-7623
chr177490633574906381E068-7556
chr177490648574906535E068-7402
chr177490669874906752E068-7185
chr177490717574907259E068-6678
chr177490733274907382E068-6555
chr177490745574907662E068-6275
chr177490783074908040E068-5897
chr177490836974908426E068-5511
chr177490858574908635E068-5302
chr177491403674914252E06899
chr177491427174914321E068334
chr177491489974914952E068962
chr177491495674915042E0681019
chr177491507274915122E0681135
chr177491513974915252E0681202
chr177491542074915474E0681483
chr177491585574915915E0681918
chr177491700474917102E0683067
chr177491716374917223E0683226
chr177491743174917515E0683494
chr177491815774918228E0684220
chr177491875274918812E0684815
chr177491920274919292E0685265
chr177491952074919570E0685583
chr177491971374919763E0685776
chr177491976774919827E0685830
chr177491988574919935E0685948
chr177492132374921452E0687386
chr177492149174921915E0687554
chr177492210674922156E0688169
chr177494485874945069E06830921
chr177494514774945236E06831210
chr177494562874945703E06831691
chr177494574774945837E06831810
chr177495473974954894E06840802
chr177486707674867154E069-46783
chr177486717374867261E069-46676
chr177487965374879703E069-34234
chr177487987874880098E069-33839
chr177488123074881298E069-32639
chr177488130374881549E069-32388
chr177488157074881936E069-32001
chr177488920674889254E069-24683
chr177488935774889499E069-24438
chr177492149174921915E0697554
chr177495024374950347E06936306
chr177495361174953718E06939674
chr177495372774954606E06939790
chr177486707674867154E070-46783
chr177486717374867261E070-46676
chr177486741974867553E070-46384
chr177487447874874562E070-39375
chr177488920674889254E070-24683
chr177488935774889499E070-24438
chr177488970274889914E070-24023
chr177490745574907662E070-6275
chr177490783074908040E070-5897
chr177492149174921915E0707554
chr177495352774953581E07039590
chr177495361174953718E07039674
chr177495473974954894E07040802
chr177495496874955055E07041031
chr177495511974955185E07041182
chr177496239374962433E07048456
chr177496262774962677E07048690
chr177496268274962732E07048745
chr177496274974962818E07048812
chr177496297274963045E07049035
chr177496307974963129E07049142
chr177496344674963548E07049509
chr177496374774963863E07049810
chr177486707674867154E071-46783
chr177486717374867261E071-46676
chr177490836974908426E071-5511
chr177490858574908635E071-5302
chr177491403674914252E07199
chr177491427174914321E071334
chr177494289074942930E07128953
chr177494433874944504E07130401
chr177495361174953718E07139674
chr177495372774954606E07139790
chr177486707674867154E072-46783
chr177486717374867261E072-46676
chr177486914374869467E072-44470
chr177486947374869667E072-44270
chr177486972374869790E072-44147
chr177487309674873146E072-40791
chr177487965374879703E072-34234
chr177488123074881298E072-32639
chr177488130374881549E072-32388
chr177488157074881936E072-32001
chr177488197774882049E072-31888
chr177488909174889171E072-24766
chr177488920674889254E072-24683
chr177488935774889499E072-24438
chr177490648574906535E072-7402
chr177490669874906752E072-7185
chr177490836974908426E072-5511
chr177490858574908635E072-5302
chr177490868474908927E072-5010
chr177491403674914252E07299
chr177491427174914321E072334
chr177491585574915915E0721918
chr177491625574916315E0722318
chr177492055074920692E0726613
chr177492132374921452E0727386
chr177492149174921915E0727554
chr177495024374950347E07236306
chr177486741974867553E073-46384
chr177486818974869105E073-44832
chr177486914374869467E073-44470
chr177486947374869667E073-44270
chr177486972374869790E073-44147
chr177486983574869931E073-44006
chr177487654274876694E073-37243
chr177487672474876778E073-37159
chr177488909174889171E073-24766
chr177488920674889254E073-24683
chr177488935774889499E073-24438
chr177488970274889914E073-24023
chr177489002174890256E073-23681
chr177489029974890360E073-23577
chr177490648574906535E073-7402
chr177490669874906752E073-7185
chr177490717574907259E073-6678
chr177490733274907382E073-6555
chr177490745574907662E073-6275
chr177490783074908040E073-5897
chr177490836974908426E073-5511
chr177490942674909524E073-4413
chr177491403674914252E07399
chr177491427174914321E073334
chr177492100974921066E0737072
chr177492108674921194E0737149
chr177492132374921452E0737386
chr177492149174921915E0737554
chr177492210674922156E0738169
chr177492233874922388E0738401
chr177493017974930229E07316242
chr177493080974930911E07316872
chr177493093174931313E07316994
chr177494433874944504E07330401
chr177494455974944609E07330622
chr177494465174944759E07330714
chr177494485874945069E07330921
chr177488909174889171E074-24766
chr177488920674889254E074-24683
chr177488935774889499E074-24438
chr177486707674867154E081-46783
chr177486717374867261E081-46676
chr177486741974867553E081-46384
chr177486784674868095E081-45842
chr177488130374881549E081-32388
chr177490745574907662E081-6275
chr177490783074908040E081-5897
chr177493890274939134E08124965
chr177495352774953581E08139590
chr177495361174953718E08139674
chr177495372774954606E08139790
chr177495473974954894E08140802
chr177495496874955055E08141031
chr177495511974955185E08141182
chr177495521674955266E08141279
chr177495529974955379E08141362
chr177496374774963863E08149810
chr177486784674868095E082-45842
chr177486818974869105E082-44832
chr177486914374869467E082-44470
chr177486947374869667E082-44270
chr177486972374869790E082-44147
chr177486983574869931E082-44006
chr177495352774953581E08239590
chr177495361174953718E08239674
chr177495372774954606E08239790
chr177495473974954894E08240802
chr177495496874955055E08241031










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr177486537774865480E067-48457
chr177486556274865631E067-48306
chr177486564974865891E067-48046
chr177486599074866094E067-47843
chr177486610474866407E067-47530
chr177486657674866721E067-47216
chr177486537774865480E068-48457
chr177486556274865631E068-48306
chr177486564974865891E068-48046
chr177486599074866094E068-47843
chr177486610474866407E068-47530
chr177486657674866721E068-47216
chr177486537774865480E069-48457
chr177486556274865631E069-48306
chr177486564974865891E069-48046
chr177486599074866094E069-47843
chr177486610474866407E069-47530
chr177486657674866721E069-47216
chr177486564974865891E071-48046
chr177486599074866094E071-47843
chr177486610474866407E071-47530
chr177486657674866721E071-47216
chr177486537774865480E072-48457
chr177486556274865631E072-48306
chr177486564974865891E072-48046
chr177486599074866094E072-47843
chr177486610474866407E072-47530
chr177486657674866721E072-47216
chr177486537774865480E073-48457
chr177486556274865631E073-48306
chr177486564974865891E073-48046
chr177486599074866094E073-47843
chr177486610474866407E073-47530
chr177486657674866721E073-47216
chr177486610474866407E082-47530
chr177486657674866721E082-47216