rs3800043

Homo sapiens
C>T
GMDS : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0295 (8612/29118,TOPMED)
T=0337 (9668/28624,GnomAD)
T=0299 (1499/5008,1000G)
T=0389 (1498/3854,ALSPAC)
T=0396 (1467/3708,TWINSUK)
chr6:1764090 (GRCh38.p7) (6p25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
71 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.1764090C>T
GRCh37.p13 chr 6NC_000006.11:g.1764324C>T

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
1000GenomesAfricanSub1322C=0.847T=0.153
1000GenomesAmericanSub694C=0.620T=0.380
1000GenomesEast AsianSub1008C=0.674T=0.326
1000GenomesEuropeSub1006C=0.650T=0.350
1000GenomesGlobalStudy-wide5008C=0.701T=0.299
1000GenomesSouth AsianSub978C=0.640T=0.360
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.611T=0.389
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.704T=0.295
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.604T=0.396
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs38000436.93E-05alcohol dependence21703634

eQTL of rs3800043 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 rs3800043 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 )
chr617461441746434E067-17890
chr617782721778375E06713948
chr617783811778436E06714057
chr617784431778636E06714119
chr617786371778763E06714313
chr617208891721407E068-42917
chr617461441746434E068-17890
chr617464741746524E068-17800
chr617676431768200E0683319
chr617783811778436E06814057
chr617784431778636E06814119
chr617786371778763E06814313
chr617789011779036E06814577
chr617461441746434E069-17890
chr617464741746524E069-17800
chr617616371762434E069-1890
chr617293981729448E070-34876
chr617371231737238E070-27086
chr617386941738753E070-25571
chr617388121738873E070-25451
chr617389321739156E070-25168
chr617393471739459E070-24865
chr617396711739742E070-24582
chr617399831740284E070-24040
chr617611331761193E070-3131
chr617616371762434E070-1890
chr617624971762973E070-1351
chr617716791771880E0707355
chr617216981722006E071-42318
chr617220581722215E071-42109
chr617457791745829E071-18495
chr617461441746434E071-17890
chr617464741746524E071-17800
chr617611331761193E071-3131
chr617616371762434E071-1890
chr617782721778375E07113948
chr617783811778436E07114057
chr617784431778636E07114119
chr617786371778763E07114313
chr617208891721407E072-42917
chr617461441746434E072-17890
chr617616371762434E072-1890
chr617624971762973E072-1351
chr617461441746434E073-17890
chr617782721778375E07313948
chr617783811778436E07314057
chr617784431778636E07314119
chr617786371778763E07314313
chr617789011779036E07314577
chr617208891721407E074-42917
chr617616371762434E074-1890
chr617676431768200E0743319
chr617682151768300E0743891
chr617683541768460E0744030
chr617777231777801E07413399
chr617782721778375E07413948
chr617783811778436E07414057
chr617784431778636E07414119
chr617786371778763E07414313
chr617789011779036E07414577
chr617616371762434E081-1890
chr617624971762973E081-1351
chr617716791771880E0817355
chr617985051798555E08134181
chr617986921798790E08134368
chr617988071798928E08134483
chr617989791799434E08134655
chr618066591806718E08142335
chr617777231777801E08213399
chr617988071798928E08234483
chr617989791799434E08234655