rs6913109

Homo sapiens
T>C
GCNT2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0119 (3579/29920,GnomAD)
C=0145 (4235/29118,TOPMED)
C=0126 (631/5008,1000G)
C=0060 (231/3854,ALSPAC)
C=0055 (204/3708,TWINSUK)
chr6:10607699 (GRCh38.p7) (6p24.2)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
45 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.10607699T>C
GRCh37.p13 chr 6NC_000006.11:g.10607932T>C
GCNT2 RefSeqGeneNG_007469.3:g.120477T>C

Gene: GCNT2, glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GCNT2 transcript variant 2NM_001491.2:c.N/AIntron Variant
GCNT2 transcript variant 1NM_145649.4:c.N/AIntron Variant
GCNT2 transcript variant 3NM_145655.3:c.N/AIntron Variant
GCNT2 transcript variant X4XM_005248999.2:c.N/AIntron Variant
GCNT2 transcript variant X1XM_006715052.3:c.N/AIntron Variant
GCNT2 transcript variant X4XM_011514466.2:c.N/AIntron Variant
GCNT2 transcript variant X2XM_005248997.3:c.N/AGenic Downstream Transcript Variant
GCNT2 transcript variant X6XM_011514468.2:c.N/AGenic Downstream Transcript Variant
GCNT2 transcript variant X7XM_017010732.1:c.N/AGenic Downstream Transcript Variant
GCNT2 transcript variant X3XR_926136.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.688C=0.312
1000GenomesAmericanSub694T=0.870C=0.130
1000GenomesEast AsianSub1008T=0.996C=0.004
1000GenomesEuropeSub1006T=0.941C=0.059
1000GenomesGlobalStudy-wide5008T=0.874C=0.126
1000GenomesSouth AsianSub978T=0.930C=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.940C=0.060
The Genome Aggregation DatabaseAfricanSub8712T=0.737C=0.263
The Genome Aggregation DatabaseAmericanSub834T=0.880C=0.120
The Genome Aggregation DatabaseEast AsianSub1618T=0.990C=0.010
The Genome Aggregation DatabaseEuropeSub18454T=0.937C=0.062
The Genome Aggregation DatabaseGlobalStudy-wide29920T=0.880C=0.119
The Genome Aggregation DatabaseOtherSub302T=0.960C=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.854C=0.145
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.945C=0.055
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
rs69131090.000924alcohol dependence20201924

eQTL of rs6913109 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 rs6913109 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 )
chr61056307710563127E070-44805
chr61056471210564796E070-43136
chr61058092610580992E070-26940
chr61058111310581177E070-26755
chr61059895410599026E070-8906
chr61059933510599488E070-8444
chr61059977910599841E070-8091
chr61056177010562594E073-45338
chr61056177010562594E081-45338
chr61058501410585291E081-22641
chr61058904410589094E081-18838
chr61058940410589914E081-18018
chr61058485010584933E082-22999
chr61058501410585291E082-22641




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr61055883110559153E067-48779
chr61058531910586254E067-21678
chr61055823110558339E068-49593
chr61055836710558493E068-49439
chr61055854610558596E068-49336
chr61055883110559153E068-48779
chr61055883110559153E069-48779
chr61058531910586254E069-21678
chr61055823110558339E070-49593
chr61055836710558493E070-49439
chr61055854610558596E070-49336
chr61055883110559153E070-48779
chr61056016710560299E070-47633
chr61056043510560587E070-47345
chr61056071210560930E070-47002
chr61056095010561064E070-46868
chr61058531910586254E070-21678
chr61055823110558339E071-49593
chr61055836710558493E071-49439
chr61055854610558596E071-49336
chr61055883110559153E071-48779
chr61058531910586254E071-21678
chr61058643710586933E071-20999
chr61055883110559153E072-48779
chr61058531910586254E072-21678
chr61056016710560299E073-47633
chr61058531910586254E073-21678
chr61055883110559153E074-48779
chr61058531910586254E074-21678
chr61058643710586933E074-20999
chr61058698110587110E074-20822
chr61055823110558339E081-49593
chr61055836710558493E081-49439
chr61055854610558596E081-49336
chr61055883110559153E081-48779
chr61056016710560299E081-47633
chr61055823110558339E082-49593
chr61055836710558493E082-49439
chr61055854610558596E082-49336
chr61055883110559153E082-48779
chr61056016710560299E082-47633
chr61056043510560587E082-47345
chr61056071210560930E082-47002
chr61056095010561064E082-46868
chr61058531910586254E082-21678