rs422729

Homo sapiens
A>G
TOX : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0484 (14512/29952,GnomAD)
G=0423 (12340/29118,TOPMED)
G=0462 (2313/5008,1000G)
A==0363 (1400/3854,ALSPAC)
A==0373 (1383/3708,TWINSUK)
chr8:58995470 (GRCh38.p7) (8q12.1)
ND
GWASdb2
1   publication(s)
See rs on genome
109 Enhancers around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.58995470A>G
GRCh37.p13 chr 8NC_000008.10:g.59908029A>G
TOX RefSeqGeneNG_011993.1:g.128739T>C

Gene: TOX, thymocyte selection associated high mobility group box(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TOX transcriptNM_014729.2:c.N/AIntron Variant
TOX transcript variant X1XM_017014085.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.810G=0.190
1000GenomesAmericanSub694A=0.530G=0.470
1000GenomesEast AsianSub1008A=0.452G=0.548
1000GenomesEuropeSub1006A=0.376G=0.624
1000GenomesGlobalStudy-wide5008A=0.538G=0.462
1000GenomesSouth AsianSub978A=0.430G=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.363G=0.637
The Genome Aggregation DatabaseAfricanSub8724A=0.750G=0.250
The Genome Aggregation DatabaseAmericanSub838A=0.520G=0.480
The Genome Aggregation DatabaseEast AsianSub1618A=0.433G=0.567
The Genome Aggregation DatabaseEuropeSub18470A=0.361G=0.638
The Genome Aggregation DatabaseGlobalStudy-wide29952A=0.484G=0.515
The Genome Aggregation DatabaseOtherSub302A=0.510G=0.490
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.576G=0.423
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.373G=0.627
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs4227290.000977nicotine dependence17158188

eQTL of rs422729 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 rs422729 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 )
chr85990368059904009E067-4020
chr85990333259903456E068-4573
chr85991887959919002E06810850
chr85991944159919501E06811412
chr85991956259919612E06811533
chr85992759359927766E06819564
chr85992779259927999E06819763
chr85995624759956771E06848218
chr85995677559957000E06848746
chr85987059859870689E070-37340
chr85987083359871046E070-36983
chr85987116759871473E070-36556
chr85987183259872072E070-35957
chr85987211759873051E070-34978
chr85987336059873448E070-34581
chr85987346159873511E070-34518
chr85987373659873925E070-34104
chr85989077459890824E070-17205
chr85989086159890901E070-17128
chr85989131959891416E070-16613
chr85991944159919501E07011412
chr85992096159921034E07012932
chr85992109459921251E07013065
chr85992344459923494E07015415
chr85992359059923640E07015561
chr85992639959926470E07018370
chr85992659659926733E07018567
chr85992693959927233E07018910
chr85992726459927450E07019235
chr85992759359927766E07019564
chr85992779259927999E07019763
chr85992832759928432E07020298
chr85992897159929021E07020942
chr85992926159929322E07021232
chr85992942659929543E07021397
chr85992955759929756E07021528
chr85993133459931417E07023305
chr85993194859932035E07023919
chr85993495159935001E07026922
chr85993532759935400E07027298
chr85994175659942202E07033727
chr85994223859942334E07034209
chr85994239059942750E07034361
chr85994286459943399E07034835
chr85994347059943576E07035441
chr85994363859943716E07035609
chr85994388759943937E07035858
chr85994395759944007E07035928
chr85995136459951672E07043335
chr85995169059951900E07043661
chr85995191459952340E07043885
chr85995246659952516E07044437
chr85995611659956166E07048087
chr85995624759956771E07048218
chr85995677559957000E07048746
chr85995726059957316E07049231
chr85995740659957570E07049377
chr85995624759956771E07148218
chr85995677559957000E07148746
chr85992483659925081E07216807
chr85990368059904009E074-4020
chr85986510359865310E081-42719
chr85986537059865420E081-42609
chr85986542359865512E081-42517
chr85986577159865880E081-42149
chr85986593059866362E081-41667
chr85986955859869777E081-38252
chr85987002759870388E081-37641
chr85987059859870689E081-37340
chr85987083359871046E081-36983
chr85987116759871473E081-36556
chr85987183259872072E081-35957
chr85987211759873051E081-34978
chr85987336059873448E081-34581
chr85987346159873511E081-34518
chr85987373659873925E081-34104
chr85987399559874066E081-33963
chr85987410859874158E081-33871
chr85987434059874427E081-33602
chr85987449659874865E081-33164
chr85990368059904009E081-4020
chr85991659059916805E0818561
chr85991826159918612E08110232
chr85992726459927450E08119235
chr85992759359927766E08119564
chr85992779259927999E08119763
chr85994175659942202E08133727
chr85994286459943399E08134835
chr85995191459952340E08143885
chr85995301459953713E08144985
chr85995611659956166E08148087
chr85995624759956771E08148218
chr85995677559957000E08148746
chr85995726059957316E08149231
chr85995740659957570E08149377
chr85986593059866362E082-41667
chr85986664259866763E082-41266
chr85987059859870689E082-37340
chr85987083359871046E082-36983
chr85987183259872072E082-35957
chr85987211759873051E082-34978
chr85987336059873448E082-34581
chr85987346159873511E082-34518
chr85987373659873925E082-34104
chr85992693959927233E08218910
chr85992726459927450E08219235
chr85992759359927766E08219564
chr85992779259927999E08219763
chr85995624759956771E08248218








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr85990408659904871E067-3158
chr85990408659904871E068-3158
chr85990492059905023E068-3006
chr85990408659904871E069-3158
chr85990408659904871E071-3158
chr85990492059905023E071-3006
chr85990408659904871E072-3158
chr85990492059905023E072-3006
chr85990408659904871E073-3158
chr85990492059905023E073-3006
chr85990408659904871E074-3158