rs10412340

Homo sapiens
G>A
PRKD2 : 2KB Upstream Variant
LOC107987269 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0098 (2946/29910,GnomAD)
A=0108 (3157/29118,TOPMED)
A=0100 (500/5008,1000G)
A=0087 (337/3854,ALSPAC)
A=0078 (291/3708,TWINSUK)
chr19:46718501 (GRCh38.p7) (19q13.32)
AD
GWASdb2
1   publication(s)
See rs on genome
268 Enhancers around
50 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 19NC_000019.10:g.46718501G>A
GRCh37.p13 chr 19NC_000019.9:g.47221758G>A

Gene: PRKD2, protein kinase D2(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
PRKD2 transcript variant 2NM_001079880.1:c.N/AUpstream Transcript Variant
PRKD2 transcript variant 3NM_001079881.1:c.N/AUpstream Transcript Variant
PRKD2 transcript variant 1NM_016457.4:c.N/AUpstream Transcript Variant
PRKD2 transcript variant 4NM_001079882.1:c.N/AN/A
PRKD2 transcript variant X1XM_005258716.2:c.N/AN/A

Gene: LOC107987269, uncharacterized LOC107987269(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107987269 transcriptXM_017027568.1:c....XM_017027568.1:c.420C>TA [GCC]> A [GCT]Coding Sequence Variant
uncharacterized protein LOC107987269XP_016883057.1:p....XP_016883057.1:p.Ala140=A [Ala]> A [Ala]Synonymous Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.846A=0.154
1000GenomesAmericanSub694G=0.900A=0.100
1000GenomesEast AsianSub1008G=0.900A=0.100
1000GenomesEuropeSub1006G=0.914A=0.086
1000GenomesGlobalStudy-wide5008G=0.900A=0.100
1000GenomesSouth AsianSub978G=0.960A=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.913A=0.087
The Genome Aggregation DatabaseAfricanSub8686G=0.858A=0.142
The Genome Aggregation DatabaseAmericanSub838G=0.910A=0.090
The Genome Aggregation DatabaseEast AsianSub1620G=0.920A=0.080
The Genome Aggregation DatabaseEuropeSub18464G=0.919A=0.080
The Genome Aggregation DatabaseGlobalStudy-wide29910G=0.901A=0.098
The Genome Aggregation DatabaseOtherSub302G=0.940A=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.891A=0.108
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.922A=0.078
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs104123400.00041alcohol dependence20201924

eQTL of rs10412340 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr19:47221758PRKD2ENSG00000105287.8G>A4.9845e-51374Cerebellum
Chr19:47221758PRKD2ENSG00000105287.8G>A1.5163e-31374Nucleus_accumbens_basal_ganglia

meQTL of rs10412340 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 )
chr194720009547200214E067-21544
chr194722976147229896E0678003
chr194722995147230030E0678193
chr194723013947230566E0678381
chr194723061747230825E0678859
chr194723108347231432E0679325
chr194723145047232720E0679692
chr194723279447232885E06711036
chr194723525547235468E06713497
chr194723548647235571E06713728
chr194723560247235694E06713844
chr194723583447235897E06714076
chr194723601247236062E06714254
chr194723617847236268E06714420
chr194723973647240210E06717978
chr194724023947240383E06718481
chr194724045347240955E06718695
chr194724107147241212E06719313
chr194724131847241415E06719560
chr194724155647241627E06719798
chr194724177847241832E06720020
chr194724187347241977E06720115
chr194724399747244061E06722239
chr194724408347244183E06722325
chr194724426347244317E06722505
chr194724436347244448E06722605
chr194724473647244790E06722978
chr194724488847245298E06723130
chr194724533447245621E06723576
chr194724617947246630E06724421
chr194724665647246764E06724898
chr194725068747250773E06728929
chr194722995147230030E0688193
chr194723013947230566E0688381
chr194723061747230825E0688859
chr194723108347231432E0689325
chr194723145047232720E0689692
chr194723399547235246E06812237
chr194723525547235468E06813497
chr194723548647235571E06813728
chr194723560247235694E06813844
chr194723583447235897E06814076
chr194723601247236062E06814254
chr194723617847236268E06814420
chr194723652147237152E06814763
chr194723973647240210E06817978
chr194724023947240383E06818481
chr194724045347240955E06818695
chr194724107147241212E06819313
chr194724131847241415E06819560
chr194724155647241627E06819798
chr194724164747241771E06819889
chr194724177847241832E06820020
chr194724187347241977E06820115
chr194724225047242411E06820492
chr194724245247243143E06820694
chr194724317947243261E06821421
chr194724368847243955E06821930
chr194724399747244061E06822239
chr194724408347244183E06822325
chr194724426347244317E06822505
chr194724436347244448E06822605
chr194724473647244790E06822978
chr194724488847245298E06823130
chr194724533447245621E06823576
chr194724562647245689E06823868
chr194724601747246082E06824259
chr194724610047246154E06824342
chr194724617947246630E06824421
chr194724665647246764E06824898
chr194724737447247514E06825616
chr194724757447247639E06825816
chr194725068747250773E06828929
chr194726287647262937E06841118
chr194726297447263655E06841216
chr194722976147229896E0698003
chr194722995147230030E0698193
chr194723013947230566E0698381
chr194723061747230825E0698859
chr194723108347231432E0699325
chr194723145047232720E0699692
chr194723525547235468E06913497
chr194723548647235571E06913728
chr194723560247235694E06913844
chr194723583447235897E06914076
chr194723973647240210E06917978
chr194724023947240383E06918481
chr194724045347240955E06918695
chr194724107147241212E06919313
chr194724131847241415E06919560
chr194724155647241627E06919798
chr194724164747241771E06919889
chr194724177847241832E06920020
chr194724187347241977E06920115
chr194724225047242411E06920492
chr194724245247243143E06920694
chr194724317947243261E06921421
chr194724368847243955E06921930
chr194724399747244061E06922239
chr194724408347244183E06922325
chr194724426347244317E06922505
chr194724436347244448E06922605
chr194724473647244790E06922978
chr194724488847245298E06923130
chr194724533447245621E06923576
chr194724665647246764E06924898
chr194724737447247514E06925616
chr194724757447247639E06925816
chr194721598047216057E070-5701
chr194724737447247514E07025616
chr194725068747250773E07028929
chr194725093347251419E07029175
chr194725685247257471E07035094
chr194726287647262937E07041118
chr194726297447263655E07041216
chr194722976147229896E0718003
chr194722995147230030E0718193
chr194723013947230566E0718381
chr194723061747230825E0718859
chr194723108347231432E0719325
chr194723145047232720E0719692
chr194723279447232885E07111036
chr194723291947233045E07111161
chr194723311547233298E07111357
chr194723333947233598E07111581
chr194723372747233991E07111969
chr194723399547235246E07112237
chr194723525547235468E07113497
chr194723548647235571E07113728
chr194723560247235694E07113844
chr194723583447235897E07114076
chr194723601247236062E07114254
chr194723617847236268E07114420
chr194723652147237152E07114763
chr194723718147237588E07115423
chr194723973647240210E07117978
chr194724023947240383E07118481
chr194724225047242411E07120492
chr194724245247243143E07120694
chr194724317947243261E07121421
chr194724399747244061E07122239
chr194724408347244183E07122325
chr194724426347244317E07122505
chr194724436347244448E07122605
chr194724473647244790E07122978
chr194724488847245298E07123130
chr194724533447245621E07123576
chr194724562647245689E07123868
chr194724601747246082E07124259
chr194724610047246154E07124342
chr194724617947246630E07124421
chr194724665647246764E07124898
chr194724737447247514E07125616
chr194724757447247639E07125816
chr194725068747250773E07128929
chr194725685247257471E07135094
chr194726297447263655E07141216
chr194726472247265050E07142964
chr194717980147179852E072-41906
chr194717992247179962E072-41796
chr194722976147229896E0728003
chr194722995147230030E0728193
chr194723013947230566E0728381
chr194723061747230825E0728859
chr194723108347231432E0729325
chr194723145047232720E0729692
chr194723279447232885E07211036
chr194723291947233045E07211161
chr194723311547233298E07211357
chr194723333947233598E07211581
chr194723372747233991E07211969
chr194723399547235246E07212237
chr194723525547235468E07213497
chr194723548647235571E07213728
chr194723560247235694E07213844
chr194723583447235897E07214076
chr194723601247236062E07214254
chr194723617847236268E07214420
chr194723973647240210E07217978
chr194724023947240383E07218481
chr194724225047242411E07220492
chr194724245247243143E07220694
chr194724317947243261E07221421
chr194724368847243955E07221930
chr194724399747244061E07222239
chr194724408347244183E07222325
chr194724426347244317E07222505
chr194724436347244448E07222605
chr194724488847245298E07223130
chr194724533447245621E07223576
chr194724601747246082E07224259
chr194724610047246154E07224342
chr194724617947246630E07224421
chr194724665647246764E07224898
chr194722976147229896E0738003
chr194722995147230030E0738193
chr194723013947230566E0738381
chr194723061747230825E0738859
chr194723108347231432E0739325
chr194723145047232720E0739692
chr194723279447232885E07311036
chr194723291947233045E07311161
chr194723311547233298E07311357
chr194723372747233991E07311969
chr194723399547235246E07312237
chr194723525547235468E07313497
chr194723548647235571E07313728
chr194723560247235694E07313844
chr194723583447235897E07314076
chr194723601247236062E07314254
chr194723617847236268E07314420
chr194723652147237152E07314763
chr194723973647240210E07317978
chr194724023947240383E07318481
chr194724045347240955E07318695
chr194724107147241212E07319313
chr194724131847241415E07319560
chr194724155647241627E07319798
chr194724164747241771E07319889
chr194724177847241832E07320020
chr194724187347241977E07320115
chr194724225047242411E07320492
chr194724245247243143E07320694
chr194724317947243261E07321421
chr194724368847243955E07321930
chr194724399747244061E07322239
chr194724408347244183E07322325
chr194724426347244317E07322505
chr194724436347244448E07322605
chr194724473647244790E07322978
chr194724488847245298E07323130
chr194724533447245621E07323576
chr194724562647245689E07323868
chr194724601747246082E07324259
chr194724610047246154E07324342
chr194724617947246630E07324421
chr194724665647246764E07324898
chr194726116747261379E07339409
chr194722995147230030E0748193
chr194723013947230566E0748381
chr194723145047232720E0749692
chr194723372747233991E07411969
chr194723399547235246E07412237
chr194723525547235468E07413497
chr194723548647235571E07413728
chr194723560247235694E07413844
chr194723583447235897E07414076
chr194723973647240210E07417978
chr194724023947240383E07418481
chr194724665647246764E07424898
chr194724737447247514E07425616
chr194724757447247639E07425816
chr194720009547200214E081-21544
chr194724617947246630E08124421
chr194724665647246764E08124898
chr194724737447247514E08125616
chr194724757447247639E08125816
chr194725068747250773E08128929
chr194725093347251419E08129175
chr194725685247257471E08135094
chr194724426347244317E08222505
chr194724436347244448E08222605
chr194724473647244790E08222978
chr194724488847245298E08223130
chr194724665647246764E08224898
chr194724737447247514E08225616
chr194725093347251419E08229175
chr194725685247257471E08235094










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr194720027747201280E067-20478
chr194721668547218339E067-3419
chr194724837247248713E06726614
chr194724871947249596E06726961
chr194724960347250628E06727845
chr194721668547218339E068-3419
chr194721871447222446E0680
chr194724837247248713E06826614
chr194724871947249596E06826961
chr194724960347250628E06827845
chr194720027747201280E069-20478
chr194721668547218339E069-3419
chr194721871447222446E0690
chr194724837247248713E06926614
chr194724871947249596E06926961
chr194724960347250628E06927845
chr194721668547218339E070-3419
chr194721871447222446E0700
chr194724837247248713E07026614
chr194724871947249596E07026961
chr194724960347250628E07027845
chr194720027747201280E071-20478
chr194721668547218339E071-3419
chr194724837247248713E07126614
chr194724871947249596E07126961
chr194724960347250628E07127845
chr194721668547218339E072-3419
chr194721871447222446E0720
chr194724837247248713E07226614
chr194724871947249596E07226961
chr194724960347250628E07227845
chr194720027747201280E073-20478
chr194721668547218339E073-3419
chr194721871447222446E0730
chr194724837247248713E07326614
chr194724871947249596E07326961
chr194724960347250628E07327845
chr194720027747201280E074-20478
chr194721668547218339E074-3419
chr194721871447222446E0740
chr194724837247248713E07426614
chr194724871947249596E07426961
chr194724837247248713E08126614
chr194724871947249596E08126961
chr194720027747201280E082-20478
chr194721668547218339E082-3419
chr194721871447222446E0820
chr194724837247248713E08226614
chr194724871947249596E08226961
chr194724960347250628E08227845