rs12559898

Homo sapiens
G>A
GRIA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0280 (5813/20732,GnomAD)
A=0240 (905/3775,1000G)
A=0380 (1408/3708,TWINSUK)
A=0384 (1108/2889,ALSPAC)
chrX:123197971 (GRCh38.p7) (Xq25)
ND
GWASdb2
1   publication(s)
See rs on genome
90 Enhancers around
131 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr XNC_000023.11:g.123197971G>A
GRCh37.p13 chr XNC_000023.10:g.122331823G>A
GRIA3 RefSeqGeneNG_009377.2:g.18729G>A

Gene: GRIA3, glutamate ionotropic receptor AMPA type subunit 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GRIA3 transcript variant 2NM_000828.4:c.N/AIntron Variant
GRIA3 transcript variant 3NM_001256743.1:c.N/AIntron Variant
GRIA3 transcript variant 1NM_007325.4:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1003G=0.906A=0.094
1000GenomesAmericanSub524G=0.590A=0.410
1000GenomesEast AsianSub764G=0.800A=0.200
1000GenomesEuropeSub766G=0.650A=0.350
1000GenomesGlobalStudy-wide3775G=0.760A=0.240
1000GenomesSouth AsianSub718G=0.750A=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide2889G=0.616A=0.384
The Genome Aggregation DatabaseAfricanSub5846G=0.882A=0.118
The Genome Aggregation DatabaseAmericanSub619G=0.570A=0.430
The Genome Aggregation DatabaseEast AsianSub1003G=0.816A=0.184
The Genome Aggregation DatabaseEuropeSub13081G=0.646A=0.353
The Genome Aggregation DatabaseGlobalStudy-wide20732G=0.719A=0.280
The Genome Aggregation DatabaseOtherSub183G=0.700A=0.300
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.620A=0.380
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
rs125598980.000778nicotine dependence17158188

eQTL of rs12559898 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 rs12559898 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 )
chrX122323358122323445E067-8378
chrX122324071122324249E067-7574
chrX122349321122349469E06717498
chrX122349650122349925E06717827
chrX122349990122350052E06718167
chrX122350316122350360E06718493
chrX122350532122350586E06718709
chrX122350751122350813E06718928
chrX122350856122350900E06719033
chrX122350924122351214E06719101
chrX122351263122351313E06719440
chrX122353525122354204E06721702
chrX122354976122355040E06723153
chrX122356884122357112E06725061
chrX122357164122357374E06725341
chrX122357752122357796E06725929
chrX122322032122322179E068-9644
chrX122322767122322817E068-9006
chrX122350316122350360E06818493
chrX122353525122354204E06821702
chrX122335717122335811E0693894
chrX122336271122336378E0694448
chrX122336505122336609E0694682
chrX122349990122350052E06918167
chrX122352634122352827E06920811
chrX122352872122352961E06921049
chrX122353525122354204E06921702
chrX122356884122357112E06925061
chrX122357164122357374E06925341
chrX122324071122324249E070-7574
chrX122324335122324466E070-7357
chrX122322032122322179E071-9644
chrX122349321122349469E07117498
chrX122349650122349925E07117827
chrX122349990122350052E07118167
chrX122350316122350360E07118493
chrX122350532122350586E07118709
chrX122350751122350813E07118928
chrX122350856122350900E07119033
chrX122350924122351214E07119101
chrX122351263122351313E07119440
chrX122353525122354204E07121702
chrX122356884122357112E07125061
chrX122357164122357374E07125341
chrX122364608122364990E07132785
chrX122365585122365644E07133762
chrX122381219122381269E07149396
chrX122381275122381343E07149452
chrX122322767122322817E072-9006
chrX122323358122323445E072-8378
chrX122349650122349925E07217827
chrX122349990122350052E07218167
chrX122350316122350360E07218493
chrX122350532122350586E07218709
chrX122350751122350813E07218928
chrX122350856122350900E07219033
chrX122353525122354204E07221702
chrX122356661122356725E07224838
chrX122356884122357112E07225061
chrX122357164122357374E07225341
chrX122349321122349469E07317498
chrX122349650122349925E07317827
chrX122350856122350900E07319033
chrX122350924122351214E07319101
chrX122351263122351313E07319440
chrX122353525122354204E07321702
chrX122349321122349469E07417498
chrX122349650122349925E07417827
chrX122349990122350052E07418167
chrX122350316122350360E07418493
chrX122350532122350586E07418709
chrX122350751122350813E07418928
chrX122350856122350900E07419033
chrX122350924122351214E07419101
chrX122352634122352827E07420811
chrX122352872122352961E07421049
chrX122353525122354204E07421702
chrX122356661122356725E07424838
chrX122356884122357112E07425061
chrX122364608122364990E07432785
chrX122315069122315123E081-16700
chrX122315163122315350E081-16473
chrX122324071122324249E081-7574
chrX122324335122324466E081-7357
chrX122339527122339577E0817704
chrX122339794122340465E0817971
chrX122340559122340863E0818736
chrX122340907122340990E0819084
chrX122339527122339577E0827704
chrX122339794122340465E0827971










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chrX122317212122317807E067-14016
chrX122317895122318495E067-13328
chrX122318532122318612E067-13211
chrX122318644122318694E067-13129
chrX122318736122319168E067-12655
chrX122319180122319246E067-12577
chrX122319425122319475E067-12348
chrX122319486122319553E067-12270
chrX122319643122319877E067-11946
chrX122319978122320035E067-11788
chrX122320160122320404E067-11419
chrX122317212122317807E068-14016
chrX122317895122318495E068-13328
chrX122318532122318612E068-13211
chrX122318644122318694E068-13129
chrX122318736122319168E068-12655
chrX122319180122319246E068-12577
chrX122319425122319475E068-12348
chrX122319486122319553E068-12270
chrX122319643122319877E068-11946
chrX122319978122320035E068-11788
chrX122320160122320404E068-11419
chrX122320723122320868E068-10955
chrX122321117122321260E068-10563
chrX122317070122317193E069-14630
chrX122317212122317807E069-14016
chrX122317895122318495E069-13328
chrX122318532122318612E069-13211
chrX122318644122318694E069-13129
chrX122318736122319168E069-12655
chrX122319180122319246E069-12577
chrX122319425122319475E069-12348
chrX122319486122319553E069-12270
chrX122319643122319877E069-11946
chrX122319978122320035E069-11788
chrX122320160122320404E069-11419
chrX122320723122320868E069-10955
chrX122321117122321260E069-10563
chrX122321272122321366E069-10457
chrX122321578122321710E069-10113
chrX122317070122317193E070-14630
chrX122317212122317807E070-14016
chrX122317895122318495E070-13328
chrX122318532122318612E070-13211
chrX122318644122318694E070-13129
chrX122318736122319168E070-12655
chrX122319180122319246E070-12577
chrX122319425122319475E070-12348
chrX122319486122319553E070-12270
chrX122319643122319877E070-11946
chrX122319978122320035E070-11788
chrX122320160122320404E070-11419
chrX122317212122317807E071-14016
chrX122317895122318495E071-13328
chrX122318532122318612E071-13211
chrX122318644122318694E071-13129
chrX122318736122319168E071-12655
chrX122319180122319246E071-12577
chrX122319425122319475E071-12348
chrX122319486122319553E071-12270
chrX122319643122319877E071-11946
chrX122319978122320035E071-11788
chrX122320160122320404E071-11419
chrX122320723122320868E071-10955
chrX122317070122317193E072-14630
chrX122317212122317807E072-14016
chrX122317895122318495E072-13328
chrX122318532122318612E072-13211
chrX122318644122318694E072-13129
chrX122318736122319168E072-12655
chrX122319180122319246E072-12577
chrX122319425122319475E072-12348
chrX122319486122319553E072-12270
chrX122319643122319877E072-11946
chrX122319978122320035E072-11788
chrX122320160122320404E072-11419
chrX122320723122320868E072-10955
chrX122321117122321260E072-10563
chrX122321272122321366E072-10457
chrX122321578122321710E072-10113
chrX122317212122317807E073-14016
chrX122317895122318495E073-13328
chrX122318532122318612E073-13211
chrX122318644122318694E073-13129
chrX122318736122319168E073-12655
chrX122319180122319246E073-12577
chrX122319425122319475E073-12348
chrX122319486122319553E073-12270
chrX122319643122319877E073-11946
chrX122319978122320035E073-11788
chrX122320160122320404E073-11419
chrX122320723122320868E073-10955
chrX122321117122321260E073-10563
chrX122321272122321366E073-10457
chrX122321578122321710E073-10113
chrX122317212122317807E074-14016
chrX122317895122318495E074-13328
chrX122318532122318612E074-13211
chrX122318644122318694E074-13129
chrX122318736122319168E074-12655
chrX122319180122319246E074-12577
chrX122319425122319475E074-12348
chrX122319486122319553E074-12270
chrX122319643122319877E074-11946
chrX122319978122320035E074-11788
chrX122317895122318495E081-13328
chrX122318532122318612E081-13211
chrX122318644122318694E081-13129
chrX122318736122319168E081-12655
chrX122319180122319246E081-12577
chrX122319425122319475E081-12348
chrX122319486122319553E081-12270
chrX122319643122319877E081-11946
chrX122319978122320035E081-11788
chrX122320160122320404E081-11419
chrX122317070122317193E082-14630
chrX122317212122317807E082-14016
chrX122317895122318495E082-13328
chrX122318532122318612E082-13211
chrX122318644122318694E082-13129
chrX122318736122319168E082-12655
chrX122319180122319246E082-12577
chrX122319425122319475E082-12348
chrX122319486122319553E082-12270
chrX122319643122319877E082-11946
chrX122319978122320035E082-11788
chrX122320160122320404E082-11419
chrX122320723122320868E082-10955
chrX122321117122321260E082-10563
chrX122321272122321366E082-10457
chrX122321578122321710E082-10113