rs1982305

Homo sapiens
G>A
PCDH9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0263 (7878/29890,GnomAD)
G==0284 (8285/29116,TOPMED)
G==0303 (1515/5008,1000G)
G==0212 (817/3854,ALSPAC)
G==0219 (813/3708,TWINSUK)
chr13:66334267 (GRCh38.p7) (13q21.32)
AD
GWASdb2
1   publication(s)
See rs on genome
221 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.66334267G>A
GRCh37.p13 chr 13NC_000013.10:g.66908399G>A
PCDH9 RefSeqGeneNG_011876.1:g.901070C>T

Gene: PCDH9, protocadherin 9(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PCDH9 transcript variant 3NM_001318372.1:c.N/AIntron Variant
PCDH9 transcript variant 4NM_001318373.1:c.N/AIntron Variant
PCDH9 transcript variant 2NM_020403.4:c.N/AIntron Variant
PCDH9 transcript variant 1NM_203487.2:c.N/AIntron Variant
PCDH9 transcript variant 5NM_001318374.1:c.N/AGenic Downstream Transcript Variant
PCDH9 transcript variant X1XM_017020619.1:c.N/AIntron Variant
PCDH9 transcript variant X4XM_005266408.3:c.N/AGenic Downstream Transcript Variant
PCDH9 transcript variant X3XM_011535099.2:c.N/AGenic Downstream Transcript Variant
PCDH9 transcript variant X2XM_017020620.1:c.N/AGenic Downstream Transcript Variant
PCDH9 transcript variant X5XM_017020621.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.334A=0.666
1000GenomesAmericanSub694G=0.270A=0.730
1000GenomesEast AsianSub1008G=0.387A=0.613
1000GenomesEuropeSub1006G=0.236A=0.764
1000GenomesGlobalStudy-wide5008G=0.303A=0.697
1000GenomesSouth AsianSub978G=0.270A=0.730
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.212A=0.788
The Genome Aggregation DatabaseAfricanSub8696G=0.287A=0.713
The Genome Aggregation DatabaseAmericanSub830G=0.300A=0.700
The Genome Aggregation DatabaseEast AsianSub1600G=0.444A=0.556
The Genome Aggregation DatabaseEuropeSub18464G=0.233A=0.766
The Genome Aggregation DatabaseGlobalStudy-wide29890G=0.263A=0.736
The Genome Aggregation DatabaseOtherSub300G=0.370A=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.284A=0.715
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.219A=0.781
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs19823050.000591alcohol dependence21314694

eQTL of rs1982305 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 rs1982305 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 )
chr136690414166904740E067-3659
chr136690485766905038E067-3361
chr136690519366905285E067-3114
chr136691531666915409E0676917
chr136691543066915684E0677031
chr136691572766915778E0677328
chr136691890866920093E06710509
chr136692069266920922E06712293
chr136692092466920982E06712525
chr136692101266921139E06712613
chr136692292566923847E06714526
chr136692419066924234E06715791
chr136692431066924447E06715911
chr136692449666924641E06716097
chr136692653566926722E06718136
chr136692686266926912E06718463
chr136692695566927048E06718556
chr136692713366927183E06718734
chr136692730766927357E06718908
chr136692752866927606E06719129
chr136692790766928096E06719508
chr136692811566928270E06719716
chr136692899866929132E06720599
chr136692914166929219E06720742
chr136692923566929485E06720836
chr136694637766946522E06737978
chr136694665666946732E06738257
chr136695091166950961E06742512
chr136695299766953069E06744598
chr136695310866953266E06744709
chr136695328966953339E06744890
chr136688911666889201E068-19198
chr136688922666889386E068-19013
chr136688951166889561E068-18838
chr136688957766889817E068-18582
chr136690367866903728E068-4671
chr136690376566903853E068-4546
chr136690391866903995E068-4404
chr136690414166904740E068-3659
chr136692069266920922E06812293
chr136692292566923847E06814526
chr136692419066924234E06815791
chr136692431066924447E06815911
chr136687520666875534E069-32865
chr136688269166882851E069-25548
chr136688287366882923E069-25476
chr136688901566889065E069-19334
chr136688911666889201E069-19198
chr136688922666889386E069-19013
chr136690367866903728E069-4671
chr136690376566903853E069-4546
chr136690391866903995E069-4404
chr136690414166904740E069-3659
chr136690485766905038E069-3361
chr136690519366905285E069-3114
chr136691890866920093E06910509
chr136692092466920982E06912525
chr136692292566923847E06914526
chr136692653566926722E06918136
chr136692686266926912E06918463
chr136692695566927048E06918556
chr136692713366927183E06918734
chr136692730766927357E06918908
chr136692752866927606E06919129
chr136692790766928096E06919508
chr136692811566928270E06919716
chr136693513666935190E06926737
chr136693526066935321E06926861
chr136694597766946333E06937578
chr136694637766946522E06937978
chr136694665666946732E06938257
chr136695310866953266E06944709
chr136695328966953339E06944890
chr136691890866920093E07010509
chr136692069266920922E07012293
chr136692092466920982E07012525
chr136692292566923847E07014526
chr136692419066924234E07015791
chr136687520666875534E071-32865
chr136688269166882851E071-25548
chr136688287366882923E071-25476
chr136688764466887889E071-20510
chr136688901566889065E071-19334
chr136690367866903728E071-4671
chr136690376566903853E071-4546
chr136690391866903995E071-4404
chr136690414166904740E071-3659
chr136690485766905038E071-3361
chr136691890866920093E07110509
chr136692069266920922E07112293
chr136692092466920982E07112525
chr136692101266921139E07112613
chr136692266866922904E07114269
chr136692292566923847E07114526
chr136692419066924234E07115791
chr136692431066924447E07115911
chr136692449666924641E07116097
chr136692653566926722E07118136
chr136692686266926912E07118463
chr136692695566927048E07118556
chr136692713366927183E07118734
chr136692730766927357E07118908
chr136692752866927606E07119129
chr136692790766928096E07119508
chr136692811566928270E07119716
chr136692899866929132E07120599
chr136693166766931717E07123268
chr136693495966934999E07126560
chr136693513666935190E07126737
chr136693526066935321E07126861
chr136693647466936709E07128075
chr136693688366936933E07128484
chr136688901566889065E072-19334
chr136688911666889201E072-19198
chr136688922666889386E072-19013
chr136688951166889561E072-18838
chr136690414166904740E072-3659
chr136691531666915409E0726917
chr136691543066915684E0727031
chr136691572766915778E0727328
chr136691590766916073E0727508
chr136691608766916144E0727688
chr136691890866920093E07210509
chr136692292566923847E07214526
chr136692419066924234E07215791
chr136692431066924447E07215911
chr136692653566926722E07218136
chr136692686266926912E07218463
chr136692695566927048E07218556
chr136692713366927183E07218734
chr136692730766927357E07218908
chr136692752866927606E07219129
chr136692790766928096E07219508
chr136692923566929485E07220836
chr136692967566929744E07221276
chr136693364566933822E07225246
chr136693384366933895E07225444
chr136693495966934999E07226560
chr136693513666935190E07226737
chr136693526066935321E07226861
chr136694597766946333E07237578
chr136694637766946522E07237978
chr136694665666946732E07238257
chr136695299766953069E07244598
chr136695310866953266E07244709
chr136695328966953339E07244890
chr136690376566903853E073-4546
chr136690391866903995E073-4404
chr136690414166904740E073-3659
chr136691572766915778E0737328
chr136691890866920093E07310509
chr136692069266920922E07312293
chr136692092466920982E07312525
chr136692292566923847E07314526
chr136692419066924234E07315791
chr136692431066924447E07315911
chr136687520666875534E074-32865
chr136688911666889201E074-19198
chr136688922666889386E074-19013
chr136690336966903409E074-4990
chr136690414166904740E074-3659
chr136690485766905038E074-3361
chr136690519366905285E074-3114
chr136690679566906877E074-1522
chr136691459166914696E0746192
chr136691531666915409E0746917
chr136691543066915684E0747031
chr136691572766915778E0747328
chr136691590766916073E0747508
chr136692069266920922E07412293
chr136692092466920982E07412525
chr136692101266921139E07412613
chr136692131266921397E07412913
chr136692162666921713E07413227
chr136692176366921932E07413364
chr136692196366922147E07413564
chr136692224966922320E07413850
chr136692292566923847E07414526
chr136692419066924234E07415791
chr136692431066924447E07415911
chr136692449666924641E07416097
chr136692695566927048E07418556
chr136692713366927183E07418734
chr136692730766927357E07418908
chr136692752866927606E07419129
chr136692790766928096E07419508
chr136692811566928270E07419716
chr136692894466928994E07420545
chr136692899866929132E07420599
chr136692914166929219E07420742
chr136692923566929485E07420836
chr136692967566929744E07421276
chr136693364566933822E07425246
chr136693384366933895E07425444
chr136693495966934999E07426560
chr136693513666935190E07426737
chr136693889066939599E07430491
chr136690367866903728E081-4671
chr136690376566903853E081-4546
chr136690391866903995E081-4404
chr136690414166904740E081-3659
chr136690485766905038E081-3361
chr136690519366905285E081-3114
chr136691890866920093E08110509
chr136692069266920922E08112293
chr136692092466920982E08112525
chr136692162666921713E08113227
chr136692176366921932E08113364
chr136692196366922147E08113564
chr136692292566923847E08114526
chr136692419066924234E08115791
chr136694637766946522E08137978
chr136694665666946732E08138257
chr136690414166904740E082-3659
chr136691890866920093E08210509
chr136692092466920982E08212525
chr136692101266921139E08212613
chr136692292566923847E08214526
chr136692713366927183E08218734
chr136692790766928096E08219508
chr136693889066939599E08230491