rs12439738

Homo sapiens
C>T
SLCO3A1 : Intron Variant
LOC107984747 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0294 (8812/29910,GnomAD)
T=0311 (9062/29118,TOPMED)
T=0324 (1624/5008,1000G)
T=0215 (829/3854,ALSPAC)
T=0217 (805/3708,TWINSUK)
chr15:91992321 (GRCh38.p7) (15q26.1)
ND
GWASdb2
2   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.91992321C>T
GRCh37.p13 chr 15NC_000015.9:g.92535551C>T

Gene: SLCO3A1, solute carrier organic anion transporter family member 3A1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLCO3A1 transcript variant 2NM_001145044.1:c.N/AIntron Variant
SLCO3A1 transcript variant 1NM_013272.3:c.N/AIntron Variant
SLCO3A1 transcript variant 3NR_135775.1:n.N/AIntron Variant
SLCO3A1 transcript variant X1XM_005254889.1:c.N/AIntron Variant
SLCO3A1 transcript variant X3XM_005254891.2:c.N/AIntron Variant
SLCO3A1 transcript variant X2XM_011521456.2:c.N/AIntron Variant
SLCO3A1 transcript variant X4XR_931795.1:n.N/AIntron Variant
SLCO3A1 transcript variant X5XR_931796.2:n.N/AIntron Variant

Gene: LOC107984747, uncharacterized LOC107984747(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107984747 transcriptXR_001751660.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.639T=0.361
1000GenomesAmericanSub694C=0.610T=0.390
1000GenomesEast AsianSub1008C=0.658T=0.342
1000GenomesEuropeSub1006C=0.753T=0.247
1000GenomesGlobalStudy-wide5008C=0.676T=0.324
1000GenomesSouth AsianSub978C=0.710T=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.785T=0.215
The Genome Aggregation DatabaseAfricanSub8700C=0.632T=0.368
The Genome Aggregation DatabaseAmericanSub834C=0.550T=0.450
The Genome Aggregation DatabaseEast AsianSub1614C=0.677T=0.323
The Genome Aggregation DatabaseEuropeSub18460C=0.748T=0.251
The Genome Aggregation DatabaseGlobalStudy-wide29910C=0.705T=0.294
The Genome Aggregation DatabaseOtherSub302C=0.750T=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.688T=0.311
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.783T=0.217
PMID Title Author Journal
18227835Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking.Berrettini WMol Psychiatry
20460270Genome-wide association study identifies a susceptibility locus for biliary atresia on 10q24.2.Garcia-Barcelo MMHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs124397380.000531nicotine dependence18227835

eQTL of rs12439738 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 rs12439738 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 )
chr159248556792486785E067-48766
chr159248686792487170E067-48381
chr159248734692487404E067-48147
chr159248742692487529E067-48022
chr159248753692487630E067-47921
chr159248768592487821E067-47730
chr159248787792487917E067-47634
chr159248791892488077E067-47474
chr159248917492489224E067-46327
chr159248928992489426E067-46125
chr159248946492489565E067-45986
chr159248957592489665E067-45886
chr159248967692489732E067-45819
chr159248974892489854E067-45697
chr159249014692492222E067-43329
chr159249229392492455E067-43096
chr159249559192495831E067-39720
chr159249588892496110E067-39441
chr159249614392496383E067-39168
chr159249647192497199E067-38352
chr159249733092497520E067-38031
chr159249753992497883E067-37668
chr159250594792505997E067-29554
chr159250819092508290E067-27261
chr159250858392509865E067-25686
chr159250993392510212E067-25339
chr159251029192510335E067-25216
chr159251058092510630E067-24921
chr159251097792511406E067-24145
chr159251149792511724E067-23827
chr159251185392512133E067-23418
chr159251215892512232E067-23319
chr159251230992512359E067-23192
chr159251291792512962E067-22589
chr159251303492513086E067-22465
chr159251317992514068E067-21483
chr159251652292516604E067-18947
chr159251684592516976E067-18575
chr159251703692517118E067-18433
chr159251731992517392E067-18159
chr159251743092517474E067-18077
chr159251762792517872E067-17679
chr159251799792518050E067-17501
chr159251856692518776E067-16775
chr159251879192519179E067-16372
chr159252901192529068E067-6483
chr159252912192529223E067-6328
chr159253222892532278E067-3273
chr159253229892532439E067-3112
chr159253406192534276E067-1275
chr159253468592534762E067-789
chr159253568292535749E067131
chr159253580792535875E067256
chr159253595292536078E067401
chr159254390092543957E0678349
chr159254400792544394E0678456
chr159254448192544556E0678930
chr159254466892544883E0679117
chr159254493092545052E0679379
chr159254510492545336E0679553
chr159254681692546970E06711265
chr159254710192547229E06711550
chr159254728492547359E06711733
chr159254746392547572E06711912
chr159254767092547720E06712119
chr159254939592549456E06713844
chr159254951992549859E06713968
chr159255004392550103E06714492
chr159255026792550307E06714716
chr159255184292552026E06716291
chr159255205392552142E06716502
chr159255235692552456E06716805
chr159255248792552640E06716936
chr159255266592552753E06717114
chr159255281892552868E06717267
chr159255294292552992E06717391
chr159255318492553298E06717633
chr159255419692554264E06718645
chr159255430792554357E06718756
chr159255454692554639E06718995
chr159255476092555808E06719209
chr159255585692555936E06720305
chr159255613092556193E06720579
chr159255624692556290E06720695
chr159255636192556449E06720810
chr159255647392556523E06720922
chr159255653892556609E06720987
chr159255661492556720E06721063
chr159255698392557033E06721432
chr159255735092557400E06721799
chr159255744392557568E06721892
chr159255762392557828E06722072
chr159255787192557921E06722320
chr159255799192558157E06722440
chr159255888292558941E06723331
chr159255897592559025E06723424
chr159256066092561866E06725109
chr159256502692565076E06729475
chr159256512292565223E06729571
chr159256523692565297E06729685
chr159256543292565485E06729881
chr159256553492565584E06729983
chr159256578692565846E06730235
chr159256591592565971E06730364
chr159257070492570847E06735153
chr159257087392570961E06735322
chr159257112692571253E06735575
chr159257129292571342E06735741
chr159257137492572807E06735823
chr159257297992573495E06737428
chr159257357592573700E06738024
chr159257402292574503E06738471
chr159257456892574700E06739017
chr159257478292574851E06739231
chr159257594792576010E06740396
chr159257649092577126E06740939
chr159257715992577234E06741608
chr159257728392577333E06741732
chr159257894992579035E06743398
chr159257914392579337E06743592
chr159257935792579569E06743806
chr159258442592584475E06748874
chr159258530192585518E06749750
chr159248556792486785E068-48766
chr159248686792487170E068-48381
chr159248734692487404E068-48147
chr159248742692487529E068-48022
chr159248753692487630E068-47921
chr159248768592487821E068-47730
chr159248787792487917E068-47634
chr159248791892488077E068-47474
chr159248883692488950E068-46601
chr159248917492489224E068-46327
chr159248928992489426E068-46125
chr159248946492489565E068-45986
chr159248957592489665E068-45886
chr159248967692489732E068-45819
chr159248974892489854E068-45697
chr159248987392490079E068-45472
chr159249014692492222E068-43329
chr159249922492500003E068-35548
chr159250819092508290E068-27261
chr159250858392509865E068-25686
chr159250993392510212E068-25339
chr159251029192510335E068-25216
chr159251058092510630E068-24921
chr159251097792511406E068-24145
chr159251149792511724E068-23827
chr159251185392512133E068-23418
chr159251215892512232E068-23319
chr159251230992512359E068-23192
chr159251291792512962E068-22589
chr159251303492513086E068-22465
chr159251317992514068E068-21483
chr159251410192514163E068-21388
chr159251417392514307E068-21244
chr159251452992514579E068-20972
chr159251473292514800E068-20751
chr159251480392514853E068-20698
chr159251500392515096E068-20455
chr159251684592516976E068-18575
chr159251703692517118E068-18433
chr159251731992517392E068-18159
chr159251743092517474E068-18077
chr159251762792517872E068-17679
chr159251799792518050E068-17501
chr159251856692518776E068-16775
chr159251879192519179E068-16372
chr159252251492522653E068-12898
chr159252269492522744E068-12807
chr159252278892522902E068-12649
chr159252295292523125E068-12426
chr159252317692523590E068-11961
chr159252834392528454E068-7097
chr159252880292528852E068-6699
chr159252887592528982E068-6569
chr159253352992533688E068-1863
chr159253373492533860E068-1691
chr159253406192534276E068-1275
chr159254666592546778E06811114
chr159254681692546970E06811265
chr159254710192547229E06811550
chr159254728492547359E06811733
chr159254746392547572E06811912
chr159254767092547720E06812119
chr159254782392547871E06812272
chr159254847292548851E06812921
chr159254897492549028E06813423
chr159254908392549253E06813532
chr159254939592549456E06813844
chr159254951992549859E06813968
chr159255004392550103E06814492
chr159255026792550307E06814716
chr159255062992550716E06815078
chr159255235692552456E06816805
chr159255248792552640E06816936
chr159255266592552753E06817114
chr159255281892552868E06817267
chr159255294292552992E06817391
chr159255318492553298E06817633
chr159255357092553645E06818019
chr159255419692554264E06818645
chr159255430792554357E06818756
chr159255454692554639E06818995
chr159255476092555808E06819209
chr159255585692555936E06820305
chr159255613092556193E06820579
chr159255624692556290E06820695
chr159255636192556449E06820810
chr159255647392556523E06820922
chr159255653892556609E06820987
chr159255661492556720E06821063
chr159255698392557033E06821432
chr159255735092557400E06821799
chr159255744392557568E06821892
chr159255762392557828E06822072
chr159255787192557921E06822320
chr159255799192558157E06822440
chr159256212292562524E06826571
chr159256502692565076E06829475
chr159256512292565223E06829571
chr159256523692565297E06829685
chr159256722792567435E06831676
chr159256743892567521E06831887
chr159256766492567708E06832113
chr159256860592568880E06833054
chr159256899292569271E06833441
chr159256946492569514E06833913
chr159256954692569586E06833995
chr159257649092577126E06840939
chr159257715992577234E06841608
chr159257728392577333E06841732
chr159258442592584475E06848874
chr159258514892585198E06849597
chr159258530192585518E06849750
chr159248556792486785E069-48766
chr159248686792487170E069-48381
chr159248734692487404E069-48147
chr159248742692487529E069-48022
chr159248753692487630E069-47921
chr159248768592487821E069-47730
chr159248787792487917E069-47634
chr159248791892488077E069-47474
chr159248917492489224E069-46327
chr159248928992489426E069-46125
chr159248946492489565E069-45986
chr159248957592489665E069-45886
chr159248967692489732E069-45819
chr159248974892489854E069-45697
chr159248987392490079E069-45472
chr159249014692492222E069-43329
chr159249229392492455E069-43096
chr159249330292493713E069-41838
chr159249647192497199E069-38352
chr159249794192498026E069-37525
chr159249814592498252E069-37299
chr159249834492498394E069-37157
chr159249841792498508E069-37043
chr159249909192499223E069-36328
chr159250574692505822E069-29729
chr159250594792505997E069-29554
chr159250603692506123E069-29428
chr159250819092508290E069-27261
chr159250858392509865E069-25686
chr159250993392510212E069-25339
chr159251029192510335E069-25216
chr159251058092510630E069-24921
chr159251097792511406E069-24145
chr159251149792511724E069-23827
chr159251185392512133E069-23418
chr159251215892512232E069-23319
chr159251230992512359E069-23192
chr159251291792512962E069-22589
chr159251303492513086E069-22465
chr159251317992514068E069-21483
chr159251410192514163E069-21388
chr159251417392514307E069-21244
chr159251452992514579E069-20972
chr159251473292514800E069-20751
chr159251480392514853E069-20698
chr159251641392516486E069-19065
chr159251652292516604E069-18947
chr159251684592516976E069-18575
chr159251703692517118E069-18433
chr159251731992517392E069-18159
chr159251743092517474E069-18077
chr159251762792517872E069-17679
chr159251799792518050E069-17501
chr159251856692518776E069-16775
chr159251879192519179E069-16372
chr159252317692523590E069-11961
chr159252422292524371E069-11180
chr159252834392528454E069-7097
chr159252851092528560E069-6991
chr159252880292528852E069-6699
chr159252887592528982E069-6569
chr159253332192533401E069-2150
chr159253352992533688E069-1863
chr159253373492533860E069-1691
chr159253406192534276E069-1275
chr159253540092535450E069-101
chr159253568292535749E069131
chr159253580792535875E069256
chr159253595292536078E069401
chr159253609092536208E069539
chr159253625592536543E069704
chr159253662592536706E0691074
chr159253802792538106E0692476
chr159253866492538704E0693113
chr159254390092543957E0698349
chr159254400792544394E0698456
chr159254466892544883E0699117
chr159254641892546483E06910867
chr159254652692546596E06910975
chr159254666592546778E06911114
chr159254681692546970E06911265
chr159254710192547229E06911550
chr159254728492547359E06911733
chr159254746392547572E06911912
chr159254767092547720E06912119
chr159254782392547871E06912272
chr159254908392549253E06913532
chr159254939592549456E06913844
chr159254951992549859E06913968
chr159255004392550103E06914492
chr159255026792550307E06914716
chr159255062992550716E06915078
chr159255281892552868E06917267
chr159255294292552992E06917391
chr159255318492553298E06917633
chr159255357092553645E06918019
chr159255419692554264E06918645
chr159255430792554357E06918756
chr159255454692554639E06918995
chr159255476092555808E06919209
chr159255585692555936E06920305
chr159255613092556193E06920579
chr159255624692556290E06920695
chr159255636192556449E06920810
chr159255647392556523E06920922
chr159255653892556609E06920987
chr159255661492556720E06921063
chr159255698392557033E06921432
chr159255735092557400E06921799
chr159255744392557568E06921892
chr159255762392557828E06922072
chr159255787192557921E06922320
chr159255799192558157E06922440
chr159255888292558941E06923331
chr159255897592559025E06923424
chr159255968892559766E06924137
chr159255990392559953E06924352
chr159256033292560400E06924781
chr159256066092561866E06925109
chr159256212292562524E06926571
chr159256282392562888E06927272
chr159256293292562996E06927381
chr159256311392563165E06927562
chr159256317292563257E06927621
chr159256722792567435E06931676
chr159256743892567521E06931887
chr159256766492567708E06932113
chr159256812792568224E06932576
chr159256840492568452E06932853
chr159256860592568880E06933054
chr159256899292569271E06933441
chr159256946492569514E06933913
chr159256954692569586E06933995
chr159257297992573495E06937428
chr159257357592573700E06938024
chr159257402292574503E06938471
chr159257456892574700E06939017
chr159257478292574851E06939231
chr159257511392575157E06939562
chr159257524292575284E06939691
chr159257552592575575E06939974
chr159257594792576010E06940396
chr159257649092577126E06940939
chr159257715992577234E06941608
chr159257728392577333E06941732
chr159257761392577718E06942062
chr159257894992579035E06943398
chr159257914392579337E06943592
chr159257935792579569E06943806
chr159258471392584962E06949162
chr159258514892585198E06949597
chr159258530192585518E06949750
chr159254400792544394E0708456
chr159254448192544556E0708930
chr159254466892544883E0709117
chr159254493092545052E0709379
chr159248556792486785E071-48766
chr159248686792487170E071-48381
chr159248734692487404E071-48147
chr159248742692487529E071-48022
chr159248753692487630E071-47921
chr159248768592487821E071-47730
chr159248787792487917E071-47634
chr159248791892488077E071-47474
chr159248917492489224E071-46327
chr159248928992489426E071-46125
chr159248946492489565E071-45986
chr159248957592489665E071-45886
chr159248967692489732E071-45819
chr159248974892489854E071-45697
chr159248987392490079E071-45472
chr159249014692492222E071-43329
chr159249229392492455E071-43096
chr159249272892492809E071-42742
chr159249287292492922E071-42629
chr159249295092492990E071-42561
chr159249330292493713E071-41838
chr159249380892494561E071-40990
chr159249457492494728E071-40823
chr159249513492495203E071-40348
chr159249559192495831E071-39720
chr159249588892496110E071-39441
chr159249614392496383E071-39168
chr159249647192497199E071-38352
chr159249733092497520E071-38031
chr159249753992497883E071-37668
chr159249794192498026E071-37525
chr159249814592498252E071-37299
chr159249834492498394E071-37157
chr159249841792498508E071-37043
chr159249896992499036E071-36515
chr159249909192499223E071-36328
chr159250453092504879E071-30672
chr159250492892504982E071-30569
chr159250501292505088E071-30463
chr159250574692505822E071-29729
chr159250594792505997E071-29554
chr159250603692506123E071-29428
chr159250742492507474E071-28077
chr159250751192507585E071-27966
chr159250763492507689E071-27862
chr159250819092508290E071-27261
chr159250858392509865E071-25686
chr159250993392510212E071-25339
chr159251029192510335E071-25216
chr159251058092510630E071-24921
chr159251097792511406E071-24145
chr159251149792511724E071-23827
chr159251185392512133E071-23418
chr159251215892512232E071-23319
chr159251230992512359E071-23192
chr159251291792512962E071-22589
chr159251303492513086E071-22465
chr159251317992514068E071-21483
chr159251410192514163E071-21388
chr159251417392514307E071-21244
chr159251452992514579E071-20972
chr159251473292514800E071-20751
chr159251480392514853E071-20698
chr159251500392515096E071-20455
chr159251553092515610E071-19941
chr159251568692515730E071-19821
chr159251641392516486E071-19065
chr159251652292516604E071-18947
chr159251684592516976E071-18575
chr159251703692517118E071-18433
chr159251731992517392E071-18159
chr159251743092517474E071-18077
chr159251762792517872E071-17679
chr159251799792518050E071-17501
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chr159251856692518776E081-16775
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chr159254354892543609E0817997
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chr159257137492572807E08135823
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chr159257728392577333E08141732
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chr159248556792486785E082-48766
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chr159254466892544883E0829117
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chr159255476092555808E08219209