rs12086347

Homo sapiens
G>A / G>T
GALNT2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0276 (8164/29494,GnomAD)
A=0301 (8774/29116,TOPMED)
A=0264 (1320/5008,1000G)
A=0284 (1095/3854,ALSPAC)
A=0270 (1001/3708,TWINSUK)
chr1:230127626 (GRCh38.p7) (1q42.13)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.230127626G>A
GRCh38.p7 chr 1NC_000001.11:g.230127626G>T
GRCh37.p13 chr 1NC_000001.10:g.230263373G>A
GRCh37.p13 chr 1NC_000001.10:g.230263373G>T
GALNT2 RefSeqGeneNG_011854.2:g.74838G>A
GALNT2 RefSeqGeneNG_011854.2:g.74838G>T

Gene: GALNT2, polypeptide N-acetylgalactosaminyltransferase 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GALNT2 transcript variant 2NM_001291866.1:c.N/AIntron Variant
GALNT2 transcript variant 1NM_004481.4:c.N/AIntron Variant
GALNT2 transcript variant 3NR_120373.1:n.N/AGenic Downstream Transcript Variant
GALNT2 transcript variant X1XM_017000963.1:c.N/AIntron Variant
GALNT2 transcript variant X2XM_017000964.1:c.N/AIntron Variant
GALNT2 transcript variant X3XM_017000965.1:c.N/AIntron Variant
GALNT2 transcript variant X4XM_017000966.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.659A=0.341
1000GenomesAmericanSub694G=0.790A=0.210
1000GenomesEast AsianSub1008G=0.736A=0.264
1000GenomesEuropeSub1006G=0.751A=0.249
1000GenomesGlobalStudy-wide5008G=0.736A=0.264
1000GenomesSouth AsianSub978G=0.790A=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.716A=0.284
The Genome Aggregation DatabaseAfricanSub8620G=0.682A=0.318
The Genome Aggregation DatabaseAmericanSub836G=0.790A=0.210
The Genome Aggregation DatabaseEast AsianSub1610G=0.739A=0.261
The Genome Aggregation DatabaseEuropeSub18130G=0.737A=0.262
The Genome Aggregation DatabaseGlobalStudy-wide29494G=0.723A=0.276
The Genome Aggregation DatabaseOtherSub298G=0.770A=0.230
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.698A=0.301
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.730A=0.270
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
rs120863470.000105alcohol consumption23743675

eQTL of rs12086347 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 rs12086347 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.