rs1143006

Homo sapiens
G>A
B3GNTL1 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0288 (34981/121356,ExAC)
A=0279 (8361/29924,GnomAD)
A=0260 (7583/29118,TOPMED)
G==0265 (3453/13006,GO-ESP)
A=0286 (1430/5008,1000G)
A=0270 (1042/3854,ALSPAC)
A=0260 (963/3708,TWINSUK)
chr17:83048511 (GRCh38.p7) (17q25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
83 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.83048511G>A
GRCh37.p13 chr 17NC_000017.10:g.81006387G>A
GRCh38.p7 chr 17 alt locus HSCHR17_1_CTG9NT_187612.1:g.54428C>T

Gene: B3GNTL1, UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
B3GNTL1 transcript variant 3NM_001320743.1:c.N/AGenic Upstream Transcript Variant
B3GNTL1 transcript variant 2NM_001320742.1:c....NM_001320742.1:c.195C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform bNP_001307671.1:p....NP_001307671.1:p.His65=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant 1NM_001009905.2:c....NM_001009905.2:c.237C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform aNP_001009905.1:p....NP_001009905.1:p.His79=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant 4NR_135465.1:n.251C>TC>TNon Coding Transcript Variant
B3GNTL1 transcript variant 5NR_135466.1:n.N/AGenic Upstream Transcript Variant
B3GNTL1 transcript variant X10XM_011523535.1:c.N/AGenic Upstream Transcript Variant
B3GNTL1 transcript variant X11XM_017024206.1:c.N/AGenic Upstream Transcript Variant
B3GNTL1 transcript variant X13XM_006722274.2:c....XM_006722274.2:c.237C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform X3XP_006722337.2:p....XP_006722337.2:p.His79=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant X3XM_006722272.3:c....XM_006722272.3:c.237C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform X1XP_006722335.1:p....XP_006722335.1:p.His79=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant X11XM_011523532.2:c....XM_011523532.2:c.237C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform X2XP_011521834.1:p....XP_011521834.1:p.His79=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant X6XM_017024205.1:c....XM_017024205.1:c.237C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform X3XP_016879694.1:p....XP_016879694.1:p.His79=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant X19XM_017024207.1:c....XM_017024207.1:c.237C>TH [CAC]> H [CAT]Coding Sequence Variant
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like protein 1 isoform X4XP_016879696.1:p....XP_016879696.1:p.His79=H [His]> H [His]Synonymous Variant
B3GNTL1 transcript variant X6XR_933927.2:n.285C>TC>TNon Coding Transcript Variant
B3GNTL1 transcript variant X8XR_933928.2:n.285C>TC>TNon Coding Transcript Variant
B3GNTL1 transcript variant X9XR_001752429.1:n....XR_001752429.1:n.285C>TC>TNon Coding Transcript Variant
B3GNTL1 transcript variant X15XR_001752430.1:n....XR_001752430.1:n.285C>TC>TNon Coding Transcript Variant
B3GNTL1 transcript variant X16XR_001752431.1:n....XR_001752431.1:n.285C>TC>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.746A=0.254
1000GenomesAmericanSub694G=0.730A=0.270
1000GenomesEast AsianSub1008G=0.634A=0.366
1000GenomesEuropeSub1006G=0.704A=0.296
1000GenomesGlobalStudy-wide5008G=0.714A=0.286
1000GenomesSouth AsianSub978G=0.760A=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.730A=0.270
The Exome Aggregation ConsortiumAmericanSub21968G=0.748A=0.251
The Exome Aggregation ConsortiumAsianSub25152G=0.703A=0.297
The Exome Aggregation ConsortiumEuropeSub73330G=0.704A=0.295
The Exome Aggregation ConsortiumGlobalStudy-wide121356G=0.711A=0.288
The Exome Aggregation ConsortiumOtherSub906G=0.670A=0.330
The Genome Aggregation DatabaseAfricanSub8696G=0.753A=0.247
The Genome Aggregation DatabaseAmericanSub838G=0.740A=0.260
The Genome Aggregation DatabaseEast AsianSub1610G=0.579A=0.421
The Genome Aggregation DatabaseEuropeSub18478G=0.718A=0.281
The Genome Aggregation DatabaseGlobalStudy-wide29924G=0.720A=0.279
The Genome Aggregation DatabaseOtherSub302G=0.630A=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.739A=0.260
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.740A=0.260
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs11430060.000612alcohol dependence24277619

eQTL of rs1143006 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr17:81006387B3GNTL1ENSG00000175711.4G>A4.9401e-12-3299Cerebellum

meQTL of rs1143006 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 )
chr178102098881021506E06814601
chr178102766881027778E06821281
chr178102858381028708E06822196
chr178102878881028875E06822401
chr178102888381029102E06822496
chr178102098881021506E06914601
chr178102152981021683E06915142
chr178102858381028708E06922196
chr178102878881028875E06922401
chr178102888381029102E06922496
chr178103539681035632E06929009
chr178101081181010884E0704424
chr178101092581011862E0704538
chr178101187081012866E0705483
chr178102098881021506E07114601
chr178102152981021683E07115142
chr178101081181010884E0724424
chr178101092581011862E0724538
chr178102098881021506E07214601
chr178102858381028708E07222196
chr178102878881028875E07222401
chr178102888381029102E07222496
chr178103539681035632E07229009
chr178104821981050231E07241832
chr178102098881021506E07314601
chr178103539681035632E07329009
chr178104513081045264E07338743
chr178101081181010884E0744424
chr178102098881021506E07414601
chr178102152981021683E07415142
chr178102858381028708E07422196
chr178102878881028875E07422401
chr178102888381029102E07422496
chr178096370080963740E081-42647
chr178096416380964241E081-42146
chr178096433880964388E081-41999
chr178096463580965392E081-40995
chr178096542780965532E081-40855
chr178096553980965702E081-40685
chr178096585480966012E081-40375
chr178096614780966329E081-40058
chr178096657280966704E081-39683
chr178096685380966912E081-39475
chr178096763280967761E081-38626
chr178096780780967859E081-38528
chr178096804180968546E081-37841
chr178096856880968787E081-37600
chr178096947480969880E081-36507
chr178097137080971424E081-34963
chr178097143480971484E081-34903
chr178097149980971550E081-34837
chr178097199280972050E081-34337
chr178097233280972407E081-33980
chr178097252880972568E081-33819
chr178097266780972717E081-33670
chr178097281580973510E081-32877
chr178097358680973824E081-32563
chr178097418580974245E081-32142
chr178097446280974543E081-31844
chr178097476680974816E081-31571
chr178100429681004346E081-2041
chr178100437581004868E081-1519
chr178101081181010884E0814424
chr178101092581011862E0814538
chr178103772981043033E08131342
chr178096585480966012E082-40375
chr178096614780966329E082-40058
chr178096657280966704E082-39683
chr178096685380966912E082-39475
chr178096763280967761E082-38626
chr178096780780967859E082-38528
chr178096804180968546E082-37841
chr178096856880968787E082-37600
chr178096947480969880E082-36507
chr178097137080971424E082-34963
chr178097143480971484E082-34903
chr178097149980971550E082-34837
chr178097199280972050E082-34337
chr178097233280972407E082-33980
chr178097252880972568E082-33819
chr178097266780972717E082-33670
chr178101081181010884E0824424
chr178101092581011862E0824538









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr178100846181010511E0672074
chr178103581181037708E06729424
chr178100846181010511E0682074
chr178103581181037708E06829424
chr178100846181010511E0692074
chr178103581181037708E06929424
chr178100846181010511E0702074
chr178100846181010511E0712074
chr178103581181037708E07129424
chr178100846181010511E0722074
chr178103581181037708E07229424
chr178100846181010511E0732074
chr178103581181037708E07329424
chr178100846181010511E0742074
chr178100846181010511E0822074
chr178103581181037708E08229424