rs17791001

Homo sapiens
A>C
PCDH9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0158 (4752/29926,GnomAD)
C=0168 (4905/29116,TOPMED)
C=0134 (671/5008,1000G)
C=0191 (737/3854,ALSPAC)
C=0189 (700/3708,TWINSUK)
chr13:66946882 (GRCh38.p7) (13q21.32)
AD
GWASdb2
1   publication(s)
See rs on genome
248 Enhancers around
21 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.66946882A>C
GRCh37.p13 chr 13NC_000013.10:g.67521014A>C
PCDH9 RefSeqGeneNG_011876.1:g.288455T>G

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 X2XM_017020620.1: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 X5XM_017020621.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.837C=0.163
1000GenomesAmericanSub694A=0.880C=0.120
1000GenomesEast AsianSub1008A=0.966C=0.034
1000GenomesEuropeSub1006A=0.827C=0.173
1000GenomesGlobalStudy-wide5008A=0.866C=0.134
1000GenomesSouth AsianSub978A=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.809C=0.191
The Genome Aggregation DatabaseAfricanSub8716A=0.840C=0.160
The Genome Aggregation DatabaseAmericanSub834A=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1608A=0.975C=0.025
The Genome Aggregation DatabaseEuropeSub18466A=0.826C=0.173
The Genome Aggregation DatabaseGlobalStudy-wide29926A=0.841C=0.158
The Genome Aggregation DatabaseOtherSub302A=0.910C=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.831C=0.168
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.811C=0.189
PMID Title Author Journal
20202923A genome-wide association study of alcohol dependence.Bierut LJProc Natl Acad Sci U S A

P-Value

SNP ID p-value Traits Study
rs177910015.4E-06alcohol dependence20202923

eQTL of rs17791001 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 rs17791001 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 )
chr136747366867473794E067-47220
chr136747429867474370E067-46644
chr136750042167500529E067-20485
chr136750062167500880E067-20134
chr136750092167501266E067-19748
chr136752320067523467E0672186
chr136752363467523730E0672620
chr136752482467524889E0673810
chr136752489767525061E0673883
chr136752519567525249E0674181
chr136752553867525618E0674524
chr136753289267532984E06711878
chr136753820167538251E06717187
chr136754040467540454E06719390
chr136754047967540552E06719465
chr136754058667540644E06719572
chr136754102767541302E06720013
chr136754236567542415E06721351
chr136754244967542570E06721435
chr136754260467542660E06721590
chr136754504367545174E06724029
chr136755134667551603E06730332
chr136755169467551744E06730680
chr136755176267551826E06730748
chr136756640967566629E06745395
chr136756670967566851E06745695
chr136756689267567262E06745878
chr136756905367569240E06748039
chr136756931867569854E06748304
chr136747429867474370E068-46644
chr136748962667490132E068-30882
chr136749036267490412E068-30602
chr136749042967490553E068-30461
chr136750042167500529E068-20485
chr136750062167500880E068-20134
chr136750092167501266E068-19748
chr136750130067501545E068-19469
chr136752320067523467E0682186
chr136752363467523730E0682620
chr136752407967524129E0683065
chr136752443767524506E0683423
chr136752482467524889E0683810
chr136752489767525061E0683883
chr136752519567525249E0684181
chr136752553867525618E0684524
chr136752570867525817E0684694
chr136752585067526032E0684836
chr136752623167526324E0685217
chr136754194267542316E06820928
chr136754236567542415E06821351
chr136754244967542570E06821435
chr136754489067544940E06823876
chr136754504367545174E06824029
chr136754689767547055E06825883
chr136756640967566629E06845395
chr136756931867569854E06848304
chr136756995067570035E06848936
chr136757009867570227E06849084
chr136757024067570339E06849226
chr136757035867570408E06849344
chr136757076567570901E06849751
chr136748812567488353E069-32661
chr136748962667490132E069-30882
chr136750042167500529E069-20485
chr136750062167500880E069-20134
chr136750092167501266E069-19748
chr136750130067501545E069-19469
chr136752320067523467E0692186
chr136752363467523730E0692620
chr136752407967524129E0693065
chr136752443767524506E0693423
chr136753127567531325E06910261
chr136753163167531681E06910617
chr136753181967531869E06910805
chr136753289267532984E06911878
chr136754194267542316E06920928
chr136754236567542415E06921351
chr136754244967542570E06921435
chr136754260467542660E06921590
chr136754306567543244E06922051
chr136754489067544940E06923876
chr136754504367545174E06924029
chr136755134667551603E06930332
chr136755169467551744E06930680
chr136755176267551826E06930748
chr136756670967566851E06945695
chr136756689267567262E06945878
chr136756886767569007E06947853
chr136756905367569240E06948039
chr136756931867569854E06948304
chr136756995067570035E06948936
chr136757009867570227E06949084
chr136757024067570339E06949226
chr136757035867570408E06949344
chr136757076567570901E06949751
chr136752443767524506E0703423
chr136754489067544940E07023876
chr136754504367545174E07024029
chr136747366867473794E071-47220
chr136747429867474370E071-46644
chr136749036267490412E071-30602
chr136749042967490553E071-30461
chr136752320067523467E0712186
chr136752363467523730E0712620
chr136752407967524129E0713065
chr136752443767524506E0713423
chr136752482467524889E0713810
chr136752489767525061E0713883
chr136752519567525249E0714181
chr136752553867525618E0714524
chr136752570867525817E0714694
chr136752585067526032E0714836
chr136752623167526324E0715217
chr136752640167526441E0715387
chr136754102767541302E07120013
chr136754194267542316E07120928
chr136754236567542415E07121351
chr136754244967542570E07121435
chr136754260467542660E07121590
chr136754306567543244E07122051
chr136754489067544940E07123876
chr136754504367545174E07124029
chr136755134667551603E07130332
chr136755169467551744E07130680
chr136755176267551826E07130748
chr136756640967566629E07145395
chr136756670967566851E07145695
chr136756689267567262E07145878
chr136756905367569240E07148039
chr136756931867569854E07148304
chr136756995067570035E07148936
chr136748962667490132E072-30882
chr136750042167500529E072-20485
chr136750062167500880E072-20134
chr136750092167501266E072-19748
chr136752363467523730E0722620
chr136752407967524129E0723065
chr136752443767524506E0723423
chr136752482467524889E0723810
chr136752489767525061E0723883
chr136752519567525249E0724181
chr136752585067526032E0724836
chr136752623167526324E0725217
chr136754236567542415E07221351
chr136754244967542570E07221435
chr136754260467542660E07221590
chr136754504367545174E07224029
chr136755134667551603E07230332
chr136755169467551744E07230680
chr136755176267551826E07230748
chr136756640967566629E07245395
chr136756670967566851E07245695
chr136756689267567262E07245878
chr136756905367569240E07248039
chr136756931867569854E07248304
chr136748764467487698E073-33316
chr136750042167500529E073-20485
chr136750062167500880E073-20134
chr136750092167501266E073-19748
chr136752443767524506E0733423
chr136752482467524889E0733810
chr136752489767525061E0733883
chr136752519567525249E0734181
chr136752553867525618E0734524
chr136752570867525817E0734694
chr136752585067526032E0734836
chr136752623167526324E0735217
chr136754489067544940E07323876
chr136754504367545174E07324029
chr136755134667551603E07330332
chr136755169467551744E07330680
chr136755176267551826E07330748
chr136756886767569007E07347853
chr136756905367569240E07348039
chr136756931867569854E07348304
chr136747429867474370E074-46644
chr136748764467487698E074-33316
chr136748812567488353E074-32661
chr136748835667488537E074-32477
chr136749036267490412E074-30602
chr136749042967490553E074-30461
chr136750062167500880E074-20134
chr136750092167501266E074-19748
chr136752407967524129E0743065
chr136752443767524506E0743423
chr136752482467524889E0743810
chr136752489767525061E0743883
chr136752519567525249E0744181
chr136752553867525618E0744524
chr136752570867525817E0744694
chr136752585067526032E0744836
chr136752623167526324E0745217
chr136752640167526441E0745387
chr136753127567531325E07410261
chr136753163167531681E07410617
chr136753181967531869E07410805
chr136753289267532984E07411878
chr136754023867540361E07419224
chr136754040467540454E07419390
chr136754047967540552E07419465
chr136754058667540644E07419572
chr136754194267542316E07420928
chr136754236567542415E07421351
chr136754244967542570E07421435
chr136754260467542660E07421590
chr136754306567543244E07422051
chr136754489067544940E07423876
chr136754504367545174E07424029
chr136755134667551603E07430332
chr136755169467551744E07430680
chr136755176267551826E07430748
chr136755850567558689E07437491
chr136756640967566629E07445395
chr136756670967566851E07445695
chr136756689267567262E07445878
chr136756886767569007E07447853
chr136756905367569240E07448039
chr136756931867569854E07448304
chr136756995067570035E07448936
chr136757009867570227E07449084
chr136757024067570339E07449226
chr136757035867570408E07449344
chr136757076567570901E07449751
chr136752320067523467E0812186
chr136752363467523730E0812620
chr136753933267539422E08118318
chr136753943367539629E08118419
chr136754002367540073E08119009
chr136754023867540361E08119224
chr136754040467540454E08119390
chr136754047967540552E08119465
chr136754058667540644E08119572
chr136754194267542316E08120928
chr136754236567542415E08121351
chr136754244967542570E08121435
chr136754260467542660E08121590
chr136756886767569007E08147853
chr136754023867540361E08219224
chr136754040467540454E08219390
chr136754047967540552E08219465
chr136754058667540644E08219572
chr136754194267542316E08220928
chr136754236567542415E08221351
chr136754244967542570E08221435
chr136754260467542660E08221590
chr136754306567543244E08222051
chr136756886767569007E08247853
chr136756905367569240E08248039










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr136756801667568096E06747002
chr136756821067568838E06747196
chr136756791767567967E06846903
chr136756801667568096E06847002
chr136756821067568838E06847196
chr136756791767567967E06946903
chr136756801667568096E06947002
chr136756821067568838E06947196
chr136756791767567967E07146903
chr136756801667568096E07147002
chr136756821067568838E07147196
chr136756791767567967E07246903
chr136756801667568096E07247002
chr136756821067568838E07247196
chr136756791767567967E07346903
chr136756801667568096E07347002
chr136756821067568838E07347196
chr136756791767567967E07446903
chr136756801667568096E07447002
chr136756821067568838E07447196
chr136756821067568838E08247196