rs12586198

Homo sapiens
T>C
NPAS3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0148 (4440/29966,GnomAD)
C=0155 (4537/29118,TOPMED)
C=0156 (779/5008,1000G)
C=0124 (478/3854,ALSPAC)
C=0120 (446/3708,TWINSUK)
chr14:32972410 (GRCh38.p7) (14q13.1)
ND
GWASdb2
1   publication(s)
See rs on genome
259 Enhancers around
77 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.32972410T>C
GRCh37.p13 chr 14NC_000014.8:g.33441616T>C
NPAS3 RefSeqGeneNG_013036.1:g.38158T>C

Gene: NPAS3, neuronal PAS domain protein 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NPAS3 transcript variant 1NM_001164749.1:c.N/AIntron Variant
NPAS3 transcript variant 4NM_001165893.1:c.N/AIntron Variant
NPAS3 transcript variant 2NM_022123.2:c.N/AIntron Variant
NPAS3 transcript variant 3NM_173159.2:c.N/AIntron Variant
NPAS3 transcript variant X3XM_005267991.3:c.N/AIntron Variant
NPAS3 transcript variant X4XM_005267992.3:c.N/AIntron Variant
NPAS3 transcript variant X7XM_011537067.2:c.N/AIntron Variant
NPAS3 transcript variant X5XM_011537069.2:c.N/AIntron Variant
NPAS3 transcript variant X10XM_011537070.2:c.N/AIntron Variant
NPAS3 transcript variant X9XM_011537071.2:c.N/AIntron Variant
NPAS3 transcript variant X11XM_011537072.2:c.N/AIntron Variant
NPAS3 transcript variant X1XM_017021582.1:c.N/AIntron Variant
NPAS3 transcript variant X2XM_017021583.1:c.N/AIntron Variant
NPAS3 transcript variant X6XM_017021584.1:c.N/AIntron Variant
NPAS3 transcript variant X8XM_017021585.1:c.N/AIntron Variant
NPAS3 transcript variant X12XM_017021586.1:c.N/AGenic Upstream Transcript Variant
NPAS3 transcript variant X13XM_017021587.1:c.N/AGenic Upstream Transcript Variant
NPAS3 transcript variant X14XM_017021588.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.793C=0.207
1000GenomesAmericanSub694T=0.870C=0.130
1000GenomesEast AsianSub1008T=0.863C=0.137
1000GenomesEuropeSub1006T=0.884C=0.116
1000GenomesGlobalStudy-wide5008T=0.844C=0.156
1000GenomesSouth AsianSub978T=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.876C=0.124
The Genome Aggregation DatabaseAfricanSub8722T=0.790C=0.210
The Genome Aggregation DatabaseAmericanSub836T=0.820C=0.180
The Genome Aggregation DatabaseEast AsianSub1620T=0.898C=0.102
The Genome Aggregation DatabaseEuropeSub18486T=0.877C=0.122
The Genome Aggregation DatabaseGlobalStudy-wide29966T=0.851C=0.148
The Genome Aggregation DatabaseOtherSub302T=0.900C=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.844C=0.155
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.880C=0.120
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
rs125861980.000541nicotine smoking19268276

eQTL of rs12586198 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 rs12586198 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 )
chr143341008933410139E067-31477
chr143341015533410306E067-31310
chr143341040833410493E067-31123
chr143341095433411118E067-30498
chr143341194333412034E067-29582
chr143341207733412150E067-29466
chr143341229633412420E067-29196
chr143341469533414745E067-26871
chr143341492933415178E067-26438
chr143341706233417251E067-24365
chr143341807333418126E067-23490
chr143341831633418374E067-23242
chr143341988733420232E067-21384
chr143342026133420301E067-21315
chr143343836133438415E067-3201
chr143344226433442330E067648
chr143344236733442558E067751
chr143345347233453785E06711856
chr143345395033454442E06712334
chr143345558533455804E06713969
chr143345590333456463E06714287
chr143345760533457695E06715989
chr143345777433457852E06716158
chr143345811033458211E06716494
chr143345827133458362E06716655
chr143345899833459048E06717382
chr143346098833461250E06719372
chr143346167033461721E06720054
chr143348055533480595E06738939
chr143348864333488693E06747027
chr143348884733488897E06747231
chr143348896633489040E06747350
chr143341008933410139E068-31477
chr143341015533410306E068-31310
chr143341040833410493E068-31123
chr143341061933410693E068-30923
chr143341070633410830E068-30786
chr143341121933411269E068-30347
chr143341194333412034E068-29582
chr143341207733412150E068-29466
chr143341229633412420E068-29196
chr143341469533414745E068-26871
chr143341492933415178E068-26438
chr143341531833415388E068-26228
chr143341550633415550E068-26066
chr143341558833415655E068-25961
chr143341645033416604E068-25012
chr143341988733420232E068-21384
chr143342026133420301E068-21315
chr143343836133438415E068-3201
chr143344521633445259E0683600
chr143344530133445376E0683685
chr143345101833451112E0689402
chr143345204633452096E06810430
chr143345347233453785E06811856
chr143345395033454442E06812334
chr143345558533455804E06813969
chr143345590333456463E06814287
chr143345646433456644E06814848
chr143345681133456866E06815195
chr143345691133456965E06815295
chr143345760533457695E06815989
chr143345777433457852E06816158
chr143345811033458211E06816494
chr143345827133458362E06816655
chr143346098833461250E06819372
chr143346449933464539E06822883
chr143348055533480595E06838939
chr143348632033486471E06844704
chr143348748433487524E06845868
chr143348845933488513E06846843
chr143348864333488693E06847027
chr143348884733488897E06847231
chr143348896633489040E06847350
chr143341008933410139E069-31477
chr143341015533410306E069-31310
chr143341040833410493E069-31123
chr143341061933410693E069-30923
chr143341070633410830E069-30786
chr143341095433411118E069-30498
chr143341121933411269E069-30347
chr143341194333412034E069-29582
chr143341207733412150E069-29466
chr143341229633412420E069-29196
chr143341492933415178E069-26438
chr143341531833415388E069-26228
chr143341550633415550E069-26066
chr143341558833415655E069-25961
chr143341645033416604E069-25012
chr143341706233417251E069-24365
chr143341807333418126E069-23490
chr143341988733420232E069-21384
chr143342026133420301E069-21315
chr143343836133438415E069-3201
chr143344181233441886E069196
chr143344226433442330E069648
chr143344236733442558E069751
chr143345347233453785E06911856
chr143345395033454442E06912334
chr143345502633455513E06913410
chr143345558533455804E06913969
chr143345590333456463E06914287
chr143345646433456644E06914848
chr143345777433457852E06916158
chr143345811033458211E06916494
chr143345827133458362E06916655
chr143346098833461250E06919372
chr143346167033461721E06920054
chr143348055533480595E06938939
chr143348845933488513E06946843
chr143348864333488693E06947027
chr143348884733488897E06947231
chr143348896633489040E06947350
chr143340132333401416E070-40200
chr143341040833410493E070-31123
chr143341061933410693E070-30923
chr143341070633410830E070-30786
chr143341095433411118E070-30498
chr143341121933411269E070-30347
chr143341831633418374E070-23242
chr143345395033454442E07012334
chr143345590333456463E07014287
chr143345646433456644E07014848
chr143346098833461250E07019372
chr143347490033474950E07033284
chr143347513433475184E07033518
chr143347537433475424E07033758
chr143347548933475556E07033873
chr143347566433475745E07034048
chr143348845933488513E07046843
chr143348864333488693E07047027
chr143348884733488897E07047231
chr143348896633489040E07047350
chr143341070633410830E071-30786
chr143341095433411118E071-30498
chr143341121933411269E071-30347
chr143341194333412034E071-29582
chr143341207733412150E071-29466
chr143341229633412420E071-29196
chr143341469533414745E071-26871
chr143341492933415178E071-26438
chr143341531833415388E071-26228
chr143341550633415550E071-26066
chr143341558833415655E071-25961
chr143341572033415800E071-25816
chr143341590933415978E071-25638
chr143341645033416604E071-25012
chr143341706233417251E071-24365
chr143341807333418126E071-23490
chr143341988733420232E071-21384
chr143342026133420301E071-21315
chr143343836133438415E071-3201
chr143344457433444637E0712958
chr143344521633445259E0713600
chr143344530133445376E0713685
chr143345347233453785E07111856
chr143345395033454442E07112334
chr143345502633455513E07113410
chr143345558533455804E07113969
chr143345590333456463E07114287
chr143345646433456644E07114848
chr143345777433457852E07116158
chr143345811033458211E07116494
chr143345827133458362E07116655
chr143346037633460426E07118760
chr143346098833461250E07119372
chr143341040833410493E072-31123
chr143341061933410693E072-30923
chr143341070633410830E072-30786
chr143341469533414745E072-26871
chr143341492933415178E072-26438
chr143341706233417251E072-24365
chr143341807333418126E072-23490
chr143341831633418374E072-23242
chr143343786733437909E072-3707
chr143343836133438415E072-3201
chr143344521633445259E0723600
chr143344530133445376E0723685
chr143345395033454442E07212334
chr143345502633455513E07213410
chr143345558533455804E07213969
chr143345646433456644E07214848
chr143346098833461250E07219372
chr143348864333488693E07247027
chr143348884733488897E07247231
chr143348896633489040E07247350
chr143340132333401416E073-40200
chr143341988733420232E073-21384
chr143342026133420301E073-21315
chr143344521633445259E0733600
chr143344530133445376E0733685
chr143345502633455513E07313410
chr143345558533455804E07313969
chr143340121533401292E074-40324
chr143340132333401416E074-40200
chr143340643133406517E074-35099
chr143340652033406926E074-34690
chr143341015533410306E074-31310
chr143341040833410493E074-31123
chr143341061933410693E074-30923
chr143341121933411269E074-30347
chr143341194333412034E074-29582
chr143341207733412150E074-29466
chr143341229633412420E074-29196
chr143341469533414745E074-26871
chr143341492933415178E074-26438
chr143341531833415388E074-26228
chr143341550633415550E074-26066
chr143341558833415655E074-25961
chr143341572033415800E074-25816
chr143341590933415978E074-25638
chr143341645033416604E074-25012
chr143341706233417251E074-24365
chr143341988733420232E074-21384
chr143342026133420301E074-21315
chr143343786733437909E074-3707
chr143343836133438415E074-3201
chr143344181233441886E074196
chr143344521633445259E0743600
chr143344530133445376E0743685
chr143345101833451112E0749402
chr143345347233453785E07411856
chr143345395033454442E07412334
chr143345502633455513E07413410
chr143345558533455804E07413969
chr143345590333456463E07414287
chr143345646433456644E07414848
chr143345681133456866E07415195
chr143345691133456965E07415295
chr143345811033458211E07416494
chr143345827133458362E07416655
chr143346098833461250E07419372
chr143346167033461721E07420054
chr143346773433467973E07426118
chr143346924733469297E07427631
chr143347093733470977E07429321
chr143347537433475424E07433758
chr143347548933475556E07433873
chr143347974833479990E07438132
chr143348055533480595E07438939
chr143348120733481301E07439591
chr143348748433487524E07445868
chr143348845933488513E07446843
chr143348864333488693E07447027
chr143348884733488897E07447231
chr143348896633489040E07447350
chr143341550633415550E081-26066
chr143341558833415655E081-25961
chr143341572033415800E081-25816
chr143344992733450078E0818311
chr143345018633450866E0818570
chr143345558533455804E08113969
chr143345590333456463E08114287
chr143345502633455513E08213410
chr143345558533455804E08213969
chr143348845933488513E08246843
chr143348864333488693E08247027
chr143348884733488897E08247231
chr143348896633489040E08247350










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr143340142333404088E067-37528
chr143340413133405103E067-36513
chr143340518933405279E067-36337
chr143340573033405816E067-35800
chr143340693433408362E067-33254
chr143340836333409852E067-31764
chr143340142333404088E068-37528
chr143340413133405103E068-36513
chr143340518933405279E068-36337
chr143340573033405816E068-35800
chr143340581833405968E068-35648
chr143340598133406089E068-35527
chr143340627233406340E068-35276
chr143340693433408362E068-33254
chr143340836333409852E068-31764
chr143340142333404088E069-37528
chr143340413133405103E069-36513
chr143340518933405279E069-36337
chr143340573033405816E069-35800
chr143340581833405968E069-35648
chr143340598133406089E069-35527
chr143340627233406340E069-35276
chr143340693433408362E069-33254
chr143340836333409852E069-31764
chr143340142333404088E070-37528
chr143340413133405103E070-36513
chr143340518933405279E070-36337
chr143340573033405816E070-35800
chr143340581833405968E070-35648
chr143340598133406089E070-35527
chr143340627233406340E070-35276
chr143340693433408362E070-33254
chr143340836333409852E070-31764
chr143340142333404088E071-37528
chr143340413133405103E071-36513
chr143340518933405279E071-36337
chr143340573033405816E071-35800
chr143340581833405968E071-35648
chr143340598133406089E071-35527
chr143340627233406340E071-35276
chr143340693433408362E071-33254
chr143340836333409852E071-31764
chr143340142333404088E072-37528
chr143340413133405103E072-36513
chr143340518933405279E072-36337
chr143340573033405816E072-35800
chr143340581833405968E072-35648
chr143340598133406089E072-35527
chr143340627233406340E072-35276
chr143340693433408362E072-33254
chr143340836333409852E072-31764
chr143340142333404088E073-37528
chr143340413133405103E073-36513
chr143340518933405279E073-36337
chr143340573033405816E073-35800
chr143340581833405968E073-35648
chr143340598133406089E073-35527
chr143340627233406340E073-35276
chr143340693433408362E073-33254
chr143340836333409852E073-31764
chr143340142333404088E074-37528
chr143340413133405103E074-36513
chr143340573033405816E074-35800
chr143340581833405968E074-35648
chr143340598133406089E074-35527
chr143340627233406340E074-35276
chr143340693433408362E074-33254
chr143340836333409852E074-31764
chr143340518933405279E081-36337
chr143340142333404088E082-37528
chr143340518933405279E082-36337
chr143340573033405816E082-35800
chr143340581833405968E082-35648
chr143340598133406089E082-35527
chr143340627233406340E082-35276
chr143340693433408362E082-33254
chr143340836333409852E082-31764