rs3801187

Homo sapiens
G>A
GLI3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0213 (6382/29890,GnomAD)
A=0277 (8077/29118,TOPMED)
A=0198 (994/5008,1000G)
A=0140 (539/3854,ALSPAC)
A=0142 (527/3708,TWINSUK)
chr7:42116764 (GRCh38.p7) (7p14.1)
ND
GWASdb2
1   publication(s)
See rs on genome
143 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.42116764G>A
GRCh37.p13 chr 7NC_000007.13:g.42156363G>A
GLI3 RefSeqGeneNG_008434.1:g.125256C>T

Gene: GLI3, GLI family zinc finger 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GLI3 transcriptNM_000168.5:c.N/AIntron Variant
GLI3 transcript variant X2XM_011515274.2:c.N/AIntron Variant
GLI3 transcript variant X1XM_017011997.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.485A=0.515
1000GenomesAmericanSub694G=0.870A=0.130
1000GenomesEast AsianSub1008G=0.991A=0.009
1000GenomesEuropeSub1006G=0.874A=0.126
1000GenomesGlobalStudy-wide5008G=0.802A=0.198
1000GenomesSouth AsianSub978G=0.910A=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.860A=0.140
The Genome Aggregation DatabaseAfricanSub8676G=0.533A=0.467
The Genome Aggregation DatabaseAmericanSub838G=0.890A=0.110
The Genome Aggregation DatabaseEast AsianSub1618G=0.992A=0.008
The Genome Aggregation DatabaseEuropeSub18458G=0.881A=0.118
The Genome Aggregation DatabaseGlobalStudy-wide29890G=0.786A=0.213
The Genome Aggregation DatabaseOtherSub300G=0.910A=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.722A=0.277
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.858A=0.142
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs38011870.000652nicotine smoking19268276

eQTL of rs3801187 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 rs3801187 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 )
chr74210776842107818E068-48545
chr74210787142107951E068-48412
chr74210801242108981E068-47382
chr74211111042111244E068-45119
chr74211135242111837E068-44526
chr74215014742150264E068-6099
chr74215075042151122E068-5241
chr74215117642151278E068-5085
chr74216493442165292E0688571
chr74216529842165472E0688935
chr74217762142177846E06821258
chr74213080842132197E069-24166
chr74213598342137839E069-18524
chr74214628742146436E069-9927
chr74214645242146548E069-9815
chr74214682042146940E069-9423
chr74216469742164850E0698334
chr74216493442165292E0698571
chr74218144542181495E06925082
chr74218176142181815E06925398
chr74219370842194080E06937345
chr74219410142194283E06937738
chr74219434542194661E06937982
chr74210801242108981E070-47382
chr74210914942109189E070-47174
chr74211135242111837E070-44526
chr74211205242112383E070-43980
chr74211243642113091E070-43272
chr74211321842113383E070-42980
chr74211349242113571E070-42792
chr74211364642113798E070-42565
chr74211493642115676E070-40687
chr74213080842132197E070-24166
chr74213598342137839E070-18524
chr74213785142137942E070-18421
chr74213797842138114E070-18249
chr74214628742146436E070-9927
chr74214645242146548E070-9815
chr74214682042146940E070-9423
chr74214790542149105E070-7258
chr74214919442149590E070-6773
chr74214967142149721E070-6642
chr74214980842149853E070-6510
chr74214998642150058E070-6305
chr74215014742150264E070-6099
chr74215928142159630E0702918
chr74216007142160163E0703708
chr74216030142160351E0703938
chr74216060842160992E0704245
chr74216114542161200E0704782
chr74216155542161609E0705192
chr74217532442175416E07018961
chr74217550342175563E07019140
chr74217583042175880E07019467
chr74217606742176117E07019704
chr74217762142177846E07021258
chr74217800242178053E07021639
chr74217819642178761E07021833
chr74219009942190322E07033736
chr74219042742190535E07034064
chr74219324942193430E07036886
chr74219343842193600E07037075
chr74219370842194080E07037345
chr74219410142194283E07037738
chr74219434542194661E07037982
chr74216493442165292E0718571
chr74212639342126526E073-29837
chr74216469742164850E0748334
chr74216493442165292E0748571
chr74217267942172754E07416316
chr74217280342172895E07416440
chr74210668842106778E081-49585
chr74210687542107100E081-49263
chr74210721242107319E081-49044
chr74210735242107535E081-48828
chr74210757442107628E081-48735
chr74210776842107818E081-48545
chr74211092142110980E081-45383
chr74211111042111244E081-45119
chr74211135242111837E081-44526
chr74211205242112383E081-43980
chr74211382542113925E081-42438
chr74211401342114241E081-42122
chr74212037542122208E081-34155
chr74213080842132197E081-24166
chr74213598342137839E081-18524
chr74215928142159630E0812918
chr74216007142160163E0813708
chr74216030142160351E0813938
chr74216060842160992E0814245
chr74216439842164625E0818035
chr74216469742164850E0818334
chr74216493442165292E0818571
chr74216529842165472E0818935
chr74216580842166099E0819445
chr74216615942166245E0819796
chr74216642742166505E08110064
chr74216652042166560E08110157
chr74216660542166841E08110242
chr74216694042167108E08110577
chr74217280342172895E08116440
chr74217290842173210E08116545
chr74217327342173325E08116910
chr74217381342173874E08117450
chr74217452242174577E08118159
chr74217800242178053E08121639
chr74217819642178761E08121833
chr74218032942180637E08123966
chr74218069942181007E08124336
chr74218723142187285E08130868
chr74218732142187448E08130958
chr74218747442187629E08131111
chr74219069742193191E08134334
chr74219324942193430E08136886
chr74219343842193600E08137075
chr74219370842194080E08137345
chr74219410142194283E08137738
chr74219434542194661E08137982
chr74219516142196552E08138798
chr74219838242199382E08142019
chr74210668842106778E082-49585
chr74210687542107100E082-49263
chr74210721242107319E082-49044
chr74210735242107535E082-48828
chr74211205242112383E082-43980
chr74211364642113798E082-42565
chr74211615542116280E082-40083
chr74213080842132197E082-24166
chr74217679742176851E08220434
chr74217697242177012E08220609
chr74217709742177221E08220734
chr74217762142177846E08221258
chr74217800242178053E08221639
chr74217819642178761E08221833
chr74217879442178844E08222431
chr74218013642180267E08223773
chr74218032942180637E08223966
chr74218069942181007E08224336
chr74218113042181170E08224767
chr74219324942193430E08236886
chr74219343842193600E08237075
chr74219410142194283E08237738
chr74219434542194661E08237982








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr74218621042186316E08229847