rs1897339

Homo sapiens
T>G
B3GALT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0106 (3201/29952,GnomAD)
G=0096 (2811/29118,TOPMED)
G=0148 (739/5008,1000G)
G=0054 (208/3854,ALSPAC)
G=0053 (198/3708,TWINSUK)
chr2:167551928 (GRCh38.p7) (2q24.3)
AD
GWASdb2
1   publication(s)
See rs on genome
24 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.167551928T>G
GRCh37.p13 chr 2NC_000002.11:g.168408438T>G

Gene: B3GALT1, beta-1,3-galactosyltransferase 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
B3GALT1 transcriptNM_020981.3:c.N/AGenic Upstream Transcript Variant
B3GALT1 transcript variant X1XM_005246931.3:c.N/AIntron Variant
B3GALT1 transcript variant X2XM_011512085.2:c.N/AIntron Variant
B3GALT1 transcript variant X3XM_006712819.3:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.844G=0.156
1000GenomesAmericanSub694T=0.910G=0.090
1000GenomesEast AsianSub1008T=0.688G=0.312
1000GenomesEuropeSub1006T=0.934G=0.066
1000GenomesGlobalStudy-wide5008T=0.852G=0.148
1000GenomesSouth AsianSub978T=0.910G=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.946G=0.054
The Genome Aggregation DatabaseAfricanSub8708T=0.869G=0.131
The Genome Aggregation DatabaseAmericanSub838T=0.930G=0.070
The Genome Aggregation DatabaseEast AsianSub1618T=0.678G=0.322
The Genome Aggregation DatabaseEuropeSub18486T=0.921G=0.078
The Genome Aggregation DatabaseGlobalStudy-wide29952T=0.893G=0.106
The Genome Aggregation DatabaseOtherSub302T=0.930G=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.903G=0.096
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.947G=0.053
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
rs18973390.00035alcohol dependence20201924

eQTL of rs1897339 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 rs1897339 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 )
chr2168366094168366519E067-41919
chr2168366534168367228E067-41210
chr2168448865168449470E06740427
chr2168438060168438154E06829622
chr2168438253168438303E06829815
chr2168448865168449470E06840427
chr2168366094168366519E069-41919
chr2168439329168439764E06930891
chr2168448865168449470E06940427
chr2168438060168438154E07029622
chr2168438253168438303E07029815
chr2168439329168439764E07030891
chr2168366094168366519E071-41919
chr2168438060168438154E07129622
chr2168439329168439764E07130891
chr2168448865168449470E07140427
chr2168366534168367228E072-41210
chr2168448865168449470E07240427
chr2168448865168449470E07440427
chr2168438060168438154E08129622
chr2168438253168438303E08129815
chr2168428768168428846E08220330
chr2168428876168429086E08220438
chr2168438060168438154E08229622