rs1394289

Homo sapiens
T>C
SH3BGRL2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0167 (5006/29966,GnomAD)
C=0165 (4810/29118,TOPMED)
C=0177 (885/5008,1000G)
C=0190 (732/3854,ALSPAC)
C=0194 (718/3708,TWINSUK)
chr6:79601644 (GRCh38.p7) (6q14.1)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.79601644T>C
GRCh37.p13 chr 6NC_000006.11:g.80311361T>C

Gene: SH3BGRL2, SH3 domain binding glutamate rich protein like 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SH3BGRL2 transcriptNM_031469.3:c.N/AGenic Upstream Transcript Variant
LOC112267857 transcript variant X1XM_011536282.2:c.N/AIntron Variant
SH3BGRL2 transcript variant X2XM_017011344.1:c.N/AIntron Variant
LOC112267857 transcript variant X2XM_017011345.1:c.N/AIntron Variant
SH3BGRL2 transcript variant X1XM_011536165.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.892C=0.108
1000GenomesAmericanSub694T=0.760C=0.240
1000GenomesEast AsianSub1008T=0.846C=0.154
1000GenomesEuropeSub1006T=0.811C=0.189
1000GenomesGlobalStudy-wide5008T=0.823C=0.177
1000GenomesSouth AsianSub978T=0.760C=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.810C=0.190
The Genome Aggregation DatabaseAfricanSub8732T=0.889C=0.111
The Genome Aggregation DatabaseAmericanSub832T=0.780C=0.220
The Genome Aggregation DatabaseEast AsianSub1616T=0.832C=0.168
The Genome Aggregation DatabaseEuropeSub18484T=0.808C=0.191
The Genome Aggregation DatabaseGlobalStudy-wide29966T=0.832C=0.167
The Genome Aggregation DatabaseOtherSub302T=0.870C=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.834C=0.165
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.806C=0.194
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs13942890.00079alcohol dependence20201924

eQTL of rs1394289 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 rs1394289 in Fetal Brain

Probe ID Position Gene beta p-value
cg20980108chr6:80316821-0.04409896670661983.1290e-12

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 )
chr68030964580309865E067-1496
chr68031001080310241E067-1120
chr68031237780312464E0671016
chr68031269780312845E0671336
chr68032226680322475E06710905
chr68032263380323002E06711272
chr68034992180350027E06738560
chr68035012680350304E06738765
chr68035030580350359E06738944
chr68035036780350454E06739006
chr68035313580353229E06741774
chr68035818680358384E06746825
chr68035890780358980E06747546
chr68035936380359683E06748002
chr68035981980360022E06748458
chr68030964580309865E068-1496
chr68031001080310241E068-1120
chr68031039680310472E068-889
chr68031054680311005E068-356
chr68031237780312464E0681016
chr68031269780312845E0681336
chr68031294780313071E0681586
chr68031677280316948E0685411
chr68031699080317084E0685629
chr68031725880317308E0685897
chr68031797880318065E0686617
chr68031819380318315E0686832
chr68034434380344448E06832982
chr68034451680344699E06833155
chr68034992180350027E06838560
chr68035012680350304E06838765
chr68035030580350359E06838944
chr68035036780350454E06839006
chr68035053480350574E06839173
chr68035076980350842E06839408
chr68035224880352340E06840887
chr68035313580353229E06841774
chr68035890780358980E06847546
chr68035936380359683E06848002
chr68031237780312464E0691016
chr68032226680322475E06910905
chr68032263380323002E06911272
chr68032310780323157E06911746
chr68033998780340242E06928626
chr68034992180350027E06938560
chr68035012680350304E06938765
chr68035030580350359E06938944
chr68035036780350454E06939006
chr68035053480350574E06939173
chr68035076980350842E06939408
chr68035313580353229E06941774
chr68032226680322475E07010905
chr68032263380323002E07011272
chr68031677280316948E0715411
chr68031699080317084E0715629
chr68034451680344699E07133155
chr68034992180350027E07138560
chr68035012680350304E07138765
chr68035030580350359E07138944
chr68035036780350454E07139006
chr68035053480350574E07139173
chr68035313580353229E07141774
chr68032226680322475E07210905
chr68032263380323002E07211272
chr68034481180345274E07233450
chr68034992180350027E07238560
chr68035012680350304E07238765
chr68035224880352340E07240887
chr68035313580353229E07241774
chr68035818680358384E07246825
chr68027989380280957E073-30404
chr68030964580309865E073-1496
chr68031039680310472E073-889
chr68031237780312464E0731016
chr68031269780312845E0731336
chr68031294780313071E0731586
chr68032226680322475E07410905
chr68034992180350027E07438560
chr68035012680350304E07438765
chr68035030580350359E07438944
chr68035036780350454E07439006
chr68035053480350574E07439173
chr68035076980350842E07439408
chr68035313580353229E07441774
chr68035981980360022E07448458
chr68027884880279052E081-32309
chr68027908980279171E081-32190
chr68027928980279406E081-31955
chr68027948480279546E081-31815
chr68027958080279819E081-31542
chr68027989380280957E081-30404
chr68031237780312464E0811016
chr68031269780312845E0811336
chr68034434380344448E08132982
chr68034451680344699E08133155
chr68034992180350027E08138560
chr68035012680350304E08138765
chr68035030580350359E08138944
chr68035036780350454E08139006
chr68035053480350574E08139173
chr68035076980350842E08139408
chr68027446280274832E082-36529
chr68028102980281079E082-30282
chr68031237780312464E0821016
chr68031269780312845E0821336
chr68031294780313071E0821586
chr68034434380344448E08232982
chr68034451680344699E08233155
chr68034481180345274E08233450
chr68034992180350027E08238560
chr68035012680350304E08238765
chr68035030580350359E08238944
chr68035036780350454E08239006










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr68034046480341763E06729103
chr68034243980342580E06731078
chr68034276980342854E06731408
chr68034046480341763E06829103
chr68034243980342580E06831078
chr68034276980342854E06831408
chr68034046480341763E06929103
chr68034046480341763E07029103
chr68034046480341763E07129103
chr68034243980342580E07131078
chr68034046480341763E07229103
chr68034243980342580E07231078
chr68034276980342854E07231408
chr68034046480341763E07329103
chr68034243980342580E07331078
chr68034276980342854E07331408
chr68034046480341763E07429103
chr68034046480341763E08129103
chr68034046480341763E08229103
chr68034243980342580E08231078
chr68034276980342854E08231408