rs10120010

Homo sapiens
C>T
RAPGEF1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0095 (2846/29968,GnomAD)
T=0080 (2344/29118,TOPMED)
T=0124 (622/5008,1000G)
T=0061 (237/3854,ALSPAC)
T=0059 (217/3708,TWINSUK)
chr9:131685810 (GRCh38.p7) (9q34.13)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.131685810C>T
GRCh37.p13 chr 9NC_000009.11:g.134561197C>T

Gene: RAPGEF1, Rap guanine nucleotide exchange factor 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
RAPGEF1 transcript variant 3NM_001304275.1:c.N/AIntron Variant
RAPGEF1 transcript variant 1NM_005312.3:c.N/AIntron Variant
RAPGEF1 transcript variant 2NM_198679.1:c.N/AIntron Variant
RAPGEF1 transcript variant X6XM_005272186.4:c.N/AIntron Variant
RAPGEF1 transcript variant X15XM_005272191.3:c.N/AIntron Variant
RAPGEF1 transcript variant X3XM_011518571.2:c.N/AIntron Variant
RAPGEF1 transcript variant X4XM_011518572.2:c.N/AIntron Variant
RAPGEF1 transcript variant X7XM_011518573.2:c.N/AIntron Variant
RAPGEF1 transcript variant X8XM_017014633.1:c.N/AIntron Variant
RAPGEF1 transcript variant X5XM_006717067.3:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X14XM_006717072.3:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X23XM_006717074.3:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X1XM_011518569.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X2XM_011518570.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X9XM_011518574.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X10XM_011518575.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X19XM_011518576.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X20XM_011518577.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X21XM_011518578.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X22XM_011518579.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X27XM_011518580.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X28XM_011518581.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X29XM_011518582.2:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X11XM_017014634.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X12XM_017014635.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X13XM_017014636.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X16XM_017014637.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X17XM_017014638.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X18XM_017014639.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X24XM_017014640.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X26XM_017014641.1:c.N/AGenic Upstream Transcript Variant
RAPGEF1 transcript variant X25XR_001746282.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.937T=0.063
1000GenomesAmericanSub694C=0.900T=0.100
1000GenomesEast AsianSub1008C=0.761T=0.239
1000GenomesEuropeSub1006C=0.877T=0.123
1000GenomesGlobalStudy-wide5008C=0.876T=0.124
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.939T=0.061
The Genome Aggregation DatabaseAfricanSub8722C=0.926T=0.074
The Genome Aggregation DatabaseAmericanSub834C=0.920T=0.080
The Genome Aggregation DatabaseEast AsianSub1616C=0.731T=0.269
The Genome Aggregation DatabaseEuropeSub18494C=0.909T=0.090
The Genome Aggregation DatabaseGlobalStudy-wide29968C=0.905T=0.095
The Genome Aggregation DatabaseOtherSub302C=0.940T=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.919T=0.080
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.941T=0.059
PMID Title Author Journal
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs101200104.34E-05alcohol consumption23953852

eQTL of rs10120010 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 rs10120010 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 )
chr9134515905134516073E067-45124
chr9134525111134525261E067-35936
chr9134525350134525552E067-35645
chr9134525557134526306E067-34891
chr9134530254134531007E067-30190
chr9134531436134531510E067-29687
chr9134531546134534558E067-26639
chr9134535843134536685E067-24512
chr9134543467134547093E067-14104
chr9134547121134547248E067-13949
chr9134547261134547417E067-13780
chr9134550081134551377E067-9820
chr9134551412134555068E067-6129
chr9134555075134555371E067-5826
chr9134555372134555412E067-5785
chr9134561840134562029E067643
chr9134562083134562148E067886
chr9134570643134570940E0679446
chr9134570993134571081E0679796
chr9134571208134571318E06710011
chr9134571340134571414E06710143
chr9134571429134571547E06710232
chr9134571573134571703E06710376
chr9134572371134573124E06711174
chr9134573222134574436E06712025
chr9134579536134580126E06718339
chr9134580194134580351E06718997
chr9134580378134580446E06719181
chr9134580464134580585E06719267
chr9134580621134580719E06719424
chr9134580824134581877E06719627
chr9134582052134582223E06720855
chr9134582537134582602E06721340
chr9134582806134582886E06721609
chr9134582889134582953E06721692
chr9134583114134584077E06721917
chr9134602669134605270E06741472
chr9134606114134608087E06744917
chr9134608088134610126E06746891
chr9134515246134515866E068-45331
chr9134515905134516073E068-45124
chr9134516232134516423E068-44774
chr9134520377134521298E068-39899
chr9134525557134526306E068-34891
chr9134530140134530183E068-31014
chr9134530254134531007E068-30190
chr9134531436134531510E068-29687
chr9134531546134534558E068-26639
chr9134535506134535761E068-25436
chr9134535843134536685E068-24512
chr9134536801134536915E068-24282
chr9134536939134536979E068-24218
chr9134542690134543455E068-17742
chr9134543467134547093E068-14104
chr9134547775134548431E068-12766
chr9134549712134549798E068-11399
chr9134549842134550023E068-11174
chr9134550081134551377E068-9820
chr9134551412134555068E068-6129
chr9134555075134555371E068-5826
chr9134555372134555412E068-5785
chr9134555453134555508E068-5689
chr9134555606134555699E068-5498
chr9134556276134556389E068-4808
chr9134556403134556482E068-4715
chr9134561840134562029E068643
chr9134562083134562148E068886
chr9134562200134562293E0681003
chr9134567529134567579E0686332
chr9134567729134567942E0686532
chr9134567946134568335E0686749
chr9134568477134568531E0687280
chr9134568902134568969E0687705
chr9134568985134569845E0687788
chr9134570643134570940E0689446
chr9134570993134571081E0689796
chr9134571208134571318E06810011
chr9134571340134571414E06810143
chr9134571429134571547E06810232
chr9134571573134571703E06810376
chr9134572371134573124E06811174
chr9134573222134574436E06812025
chr9134574541134574610E06813344
chr9134574968134575076E06813771
chr9134575101134575155E06813904
chr9134575410134575460E06814213
chr9134575492134575542E06814295
chr9134576084134576149E06814887
chr9134576169134576219E06814972
chr9134579087134579336E06817890
chr9134579358134579472E06818161
chr9134579536134580126E06818339
chr9134580194134580351E06818997
chr9134580378134580446E06819181
chr9134580464134580585E06819267
chr9134580621134580719E06819424
chr9134580824134581877E06819627
chr9134582052134582223E06820855
chr9134582537134582602E06821340
chr9134582806134582886E06821609
chr9134582889134582953E06821692
chr9134583114134584077E06821917
chr9134584178134584241E06822981
chr9134584817134586127E06823620
chr9134588542134588739E06827345
chr9134588820134589089E06827623
chr9134590148134590238E06828951
chr9134590386134590495E06829189
chr9134590577134590627E06829380
chr9134590738134590788E06829541
chr9134591607134591853E06830410
chr9134592303134592413E06831106
chr9134592540134592690E06831343
chr9134592727134592777E06831530
chr9134593468134593863E06832271
chr9134594152134595264E06832955
chr9134595338134595411E06834141
chr9134595758134595941E06834561
chr9134602495134602622E06841298
chr9134602669134605270E06841472
chr9134606114134608087E06844917
chr9134608088134610126E06846891
chr9134610141134610425E06848944
chr9134515246134515866E069-45331
chr9134515905134516073E069-45124
chr9134516232134516423E069-44774
chr9134525111134525261E069-35936
chr9134525350134525552E069-35645
chr9134525557134526306E069-34891
chr9134530254134531007E069-30190
chr9134531546134534558E069-26639
chr9134534636134534723E069-26474
chr9134534885134535226E069-25971
chr9134535506134535761E069-25436
chr9134535843134536685E069-24512
chr9134542690134543455E069-17742
chr9134543467134547093E069-14104
chr9134547121134547248E069-13949
chr9134547261134547417E069-13780
chr9134547450134547538E069-13659
chr9134547710134547760E069-13437
chr9134547775134548431E069-12766
chr9134549842134550023E069-11174
chr9134550081134551377E069-9820
chr9134551412134555068E069-6129
chr9134555075134555371E069-5826
chr9134555372134555412E069-5785
chr9134555453134555508E069-5689
chr9134555606134555699E069-5498
chr9134556276134556389E069-4808
chr9134557735134558064E069-3133
chr9134561317134561655E069120
chr9134561673134561769E069476
chr9134567729134567942E0696532
chr9134567946134568335E0696749
chr9134568477134568531E0697280
chr9134572371134573124E06911174
chr9134573222134574436E06912025
chr9134574541134574610E06913344
chr9134574968134575076E06913771
chr9134575101134575155E06913904
chr9134575410134575460E06914213
chr9134575492134575542E06914295
chr9134579536134580126E06918339
chr9134580194134580351E06918997
chr9134580378134580446E06919181
chr9134580464134580585E06919267
chr9134580621134580719E06919424
chr9134582052134582223E06920855
chr9134582537134582602E06921340
chr9134582806134582886E06921609
chr9134582889134582953E06921692
chr9134583114134584077E06921917
chr9134595758134595941E06934561
chr9134595968134596014E06934771
chr9134602669134605270E06941472
chr9134606114134608087E06944917
chr9134608088134610126E06946891
chr9134610141134610425E06948944
chr9134515905134516073E070-45124
chr9134531436134531510E070-29687
chr9134535843134536685E070-24512
chr9134543467134547093E070-14104
chr9134557735134558064E070-3133
chr9134572371134573124E07011174
chr9134579536134580126E07018339
chr9134580194134580351E07018997
chr9134580378134580446E07019181
chr9134580464134580585E07019267
chr9134580621134580719E07019424
chr9134580824134581877E07019627
chr9134597562134598017E07036365
chr9134606114134608087E07044917
chr9134515246134515866E071-45331
chr9134515905134516073E071-45124
chr9134516232134516423E071-44774
chr9134525557134526306E071-34891
chr9134528046134528188E071-33009
chr9134528827134528867E071-32330
chr9134528870134528968E071-32229
chr9134529046134529161E071-32036
chr9134530254134531007E071-30190
chr9134531436134531510E071-29687
chr9134531546134534558E071-26639
chr9134534636134534723E071-26474
chr9134534885134535226E071-25971
chr9134535506134535761E071-25436
chr9134535843134536685E071-24512
chr9134542247134542480E071-18717
chr9134542690134543455E071-17742
chr9134543467134547093E071-14104
chr9134547121134547248E071-13949
chr9134547261134547417E071-13780
chr9134547450134547538E071-13659
chr9134547710134547760E071-13437
chr9134547775134548431E071-12766
chr9134548463134548548E071-12649
chr9134548676134548752E071-12445
chr9134548831134548871E071-12326
chr9134548988134549116E071-12081
chr9134549121134549209E071-11988
chr9134549226134549290E071-11907
chr9134549712134549798E071-11399
chr9134549842134550023E071-11174
chr9134550081134551377E071-9820
chr9134551412134555068E071-6129
chr9134555075134555371E071-5826
chr9134556693134556772E071-4425
chr9134557059134557177E071-4020
chr9134557348134557591E071-3606
chr9134557735134558064E071-3133
chr9134561673134561769E071476
chr9134561840134562029E071643
chr9134562083134562148E071886
chr9134567729134567942E0716532
chr9134567946134568335E0716749
chr9134570643134570940E0719446
chr9134570993134571081E0719796
chr9134571208134571318E07110011
chr9134571340134571414E07110143
chr9134571429134571547E07110232
chr9134571573134571703E07110376
chr9134572135134572185E07110938
chr9134572371134573124E07111174
chr9134573222134574436E07112025
chr9134574541134574610E07113344
chr9134574968134575076E07113771
chr9134575101134575155E07113904
chr9134575410134575460E07114213
chr9134575492134575542E07114295
chr9134576084134576149E07114887
chr9134576169134576219E07114972
chr9134576318134576404E07115121
chr9134578990134579047E07117793
chr9134579087134579336E07117890
chr9134579358134579472E07118161
chr9134579536134580126E07118339
chr9134580194134580351E07118997
chr9134580378134580446E07119181
chr9134580464134580585E07119267
chr9134580621134580719E07119424
chr9134580824134581877E07119627
chr9134582052134582223E07120855
chr9134582537134582602E07121340
chr9134582806134582886E07121609
chr9134582889134582953E07121692
chr9134583114134584077E07121917
chr9134587450134587646E07126253
chr9134587756134588070E07126559
chr9134593295134593421E07132098
chr9134593468134593863E07132271
chr9134594152134595264E07132955
chr9134599980134601091E07138783
chr9134602669134605270E07141472
chr9134608088134610126E07146891
chr9134610141134610425E07148944
chr9134515246134515866E072-45331
chr9134515905134516073E072-45124
chr9134516232134516423E072-44774
chr9134525557134526306E072-34891
chr9134530254134531007E072-30190
chr9134531436134531510E072-29687
chr9134531546134534558E072-26639
chr9134534636134534723E072-26474
chr9134534885134535226E072-25971
chr9134535506134535761E072-25436
chr9134535843134536685E072-24512
chr9134542690134543455E072-17742
chr9134543467134547093E072-14104
chr9134549842134550023E072-11174
chr9134550081134551377E072-9820
chr9134551412134555068E072-6129
chr9134555075134555371E072-5826
chr9134555372134555412E072-5785
chr9134555453134555508E072-5689
chr9134572371134573124E07211174
chr9134573222134574436E07212025
chr9134574541134574610E07213344
chr9134574968134575076E07213771
chr9134575101134575155E07213904
chr9134579536134580126E07218339
chr9134580194134580351E07218997
chr9134580378134580446E07219181
chr9134580464134580585E07219267
chr9134583114134584077E07221917
chr9134593468134593863E07232271
chr9134594152134595264E07232955
chr9134599980134601091E07238783
chr9134602669134605270E07241472
chr9134606114134608087E07244917
chr9134515246134515866E073-45331
chr9134515905134516073E073-45124
chr9134516232134516423E073-44774
chr9134516536134518492E073-42705
chr9134525111134525261E073-35936
chr9134525350134525552E073-35645
chr9134525557134526306E073-34891
chr9134530140134530183E073-31014
chr9134530254134531007E073-30190
chr9134531436134531510E073-29687
chr9134531546134534558E073-26639
chr9134534636134534723E073-26474
chr9134534885134535226E073-25971
chr9134535843134536685E073-24512
chr9134536801134536915E073-24282
chr9134536939134536979E073-24218
chr9134542690134543455E073-17742
chr9134543467134547093E073-14104
chr9134547121134547248E073-13949
chr9134547261134547417E073-13780
chr9134547450134547538E073-13659
chr9134547710134547760E073-13437
chr9134547775134548431E073-12766
chr9134548463134548548E073-12649
chr9134549842134550023E073-11174
chr9134550081134551377E073-9820
chr9134551412134555068E073-6129
chr9134555372134555412E073-5785
chr9134555453134555508E073-5689
chr9134557348134557591E073-3606
chr9134557735134558064E073-3133
chr9134567946134568335E0736749
chr9134570415134570602E0739218
chr9134570643134570940E0739446
chr9134570993134571081E0739796
chr9134573222134574436E07312025
chr9134574541134574610E07313344
chr9134579536134580126E07318339
chr9134580194134580351E07318997
chr9134580378134580446E07319181
chr9134580464134580585E07319267
chr9134580621134580719E07319424
chr9134583114134584077E07321917
chr9134588542134588739E07327345
chr9134588820134589089E07327623
chr9134590148134590238E07328951
chr9134590386134590495E07329189
chr9134590577134590627E07329380
chr9134590738134590788E07329541
chr9134593468134593863E07332271
chr9134602669134605270E07341472
chr9134606114134608087E07344917
chr9134608088134610126E07346891
chr9134610141134610425E07348944
chr9134515246134515866E074-45331
chr9134515905134516073E074-45124
chr9134516232134516423E074-44774
chr9134516536134518492E074-42705
chr9134518614134518706E074-42491
chr9134530254134531007E074-30190
chr9134531546134534558E074-26639
chr9134534636134534723E074-26474
chr9134534885134535226E074-25971
chr9134535506134535761E074-25436
chr9134535843134536685E074-24512
chr9134536801134536915E074-24282
chr9134536939134536979E074-24218
chr9134543467134547093E074-14104
chr9134547121134547248E074-13949
chr9134547261134547417E074-13780
chr9134547450134547538E074-13659
chr9134547710134547760E074-13437
chr9134547775134548431E074-12766
chr9134548463134548548E074-12649
chr9134549712134549798E074-11399
chr9134549842134550023E074-11174
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