rs3800091

Homo sapiens
T>C
GMDS : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0483 (14456/29924,GnomAD)
C=0412 (12003/29118,TOPMED)
C=0358 (1792/5008,1000G)
T==0376 (1450/3854,ALSPAC)
T==0372 (1378/3708,TWINSUK)
chr6:1837594 (GRCh38.p7) (6p25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
112 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.1837594T>C
GRCh37.p13 chr 6NC_000006.11:g.1837828T>C

Gene: GMDS, GDP-mannose 4,6-dehydratase(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GMDS transcript variant 2NM_001253846.1:c.N/AIntron Variant
GMDS transcript variant 1NM_001500.3:c.N/AIntron Variant
GMDS transcript variant X1XM_011514500.1:c.N/AIntron Variant
GMDS transcript variant X3XM_011514502.2:c.N/AIntron Variant
GMDS transcript variant X10XM_011514507.1:c.N/AIntron Variant
GMDS transcript variant X6XM_017010752.1:c.N/AIntron Variant
GMDS transcript variant X4XM_006715066.2:c.N/AGenic Downstream Transcript Variant
GMDS transcript variant X7XM_011514503.2:c.N/AGenic Downstream Transcript Variant
GMDS transcript variant X8XM_011514505.1:c.N/AGenic Downstream Transcript Variant
GMDS transcript variant X9XM_011514506.1:c.N/AGenic Downstream Transcript Variant
GMDS transcript variant X2XR_001743349.1:n.N/AIntron Variant
GMDS transcript variant X5XR_001743350.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.892C=0.108
1000GenomesAmericanSub694T=0.400C=0.600
1000GenomesEast AsianSub1008T=0.755C=0.245
1000GenomesEuropeSub1006T=0.377C=0.623
1000GenomesGlobalStudy-wide5008T=0.642C=0.358
1000GenomesSouth AsianSub978T=0.630C=0.370
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.376C=0.624
The Genome Aggregation DatabaseAfricanSub8708T=0.829C=0.171
The Genome Aggregation DatabaseAmericanSub836T=0.350C=0.650
The Genome Aggregation DatabaseEast AsianSub1618T=0.789C=0.211
The Genome Aggregation DatabaseEuropeSub18460T=0.354C=0.645
The Genome Aggregation DatabaseGlobalStudy-wide29924T=0.516C=0.483
The Genome Aggregation DatabaseOtherSub302T=0.440C=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.587C=0.412
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.372C=0.628
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
rs38000910.000902alcohol dependence20201924

eQTL of rs3800091 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 rs3800091 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 )
chr618562371856309E06718409
chr618563531856414E06718525
chr618566691856892E06718841
chr618659301866095E06728102
chr618662641866412E06728436
chr618723181872517E06734490
chr618726921873351E06734864
chr618734971873621E06735669
chr618327741832874E068-4954
chr618329491833020E068-4808
chr618379861838073E068158
chr618382411838398E068413
chr618384861838560E068658
chr618562371856309E06818409
chr618563531856414E06818525
chr618566691856892E06818841
chr618723181872517E06834490
chr618726921873351E06834864
chr618734971873621E06835669
chr618736841873751E06835856
chr618563531856414E06918525
chr618566691856892E06918841
chr618662641866412E06928436
chr618726921873351E06934864
chr618734971873621E06935669
chr618736841873751E06935856
chr618327741832874E070-4954
chr618329491833020E070-4808
chr618330351833355E070-4473
chr618333611833702E070-4126
chr618338291833960E070-3868
chr618379861838073E070158
chr618382411838398E070413
chr618384861838560E070658
chr618389081838991E0701080
chr618390351839216E0701207
chr618392661839369E0701438
chr618394071839470E0701579
chr618399041839993E0702076
chr618400531840113E0702225
chr618501011850243E07012273
chr618503591850788E07012531
chr618548681854989E07017040
chr618556271855690E07017799
chr618562371856309E07018409
chr618563531856414E07018525
chr618566691856892E07018841
chr618571951857245E07019367
chr618718961872234E07034068
chr618723181872517E07034490
chr618726921873351E07034864
chr618566691856892E07118841
chr618659301866095E07128102
chr618662641866412E07128436
chr618718961872234E07134068
chr618726921873351E07134864
chr618734971873621E07135669
chr618736841873751E07135856
chr618218761822647E072-15181
chr618327741832874E072-4954
chr618329491833020E072-4808
chr618330351833355E072-4473
chr618333611833702E072-4126
chr618562371856309E07218409
chr618563531856414E07218525
chr618566691856892E07218841
chr618723181872517E07234490
chr618726921873351E07234864
chr618734971873621E07235669
chr618736841873751E07235856
chr618739691874316E07236141
chr618771461877229E07239318
chr618325381832610E073-5218
chr618327741832874E073-4954
chr618718961872234E07334068
chr618723181872517E07334490
chr618726921873351E07334864
chr618734971873621E07335669
chr618736841873751E07335856
chr618739691874316E07336141
chr618327741832874E074-4954
chr618329491833020E074-4808
chr618330351833355E074-4473
chr618563531856414E07418525
chr618566691856892E07418841
chr618726921873351E07434864
chr618734971873621E07435669
chr617985051798555E081-39273
chr617986921798790E081-39038
chr617988071798928E081-38900
chr617989791799434E081-38394
chr618066591806718E081-31110
chr618329491833020E081-4808
chr618330351833355E081-4473
chr618333611833702E081-4126
chr618379861838073E081158
chr618382411838398E081413
chr618384861838560E081658
chr618723181872517E08134490
chr618726921873351E08134864
chr618734971873621E08135669
chr617988071798928E082-38900
chr617989791799434E082-38394
chr618379861838073E082158
chr618382411838398E082413
chr618384861838560E082658
chr618503591850788E08212531
chr618509331851027E08213105
chr618520101852194E08214182
chr618523241852495E08214496
chr618562371856309E08218409
chr618726921873351E08234864