rs9540953

Homo sapiens
T>C
PCDH9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0158 (4731/29902,GnomAD)
C=0167 (4890/29116,TOPMED)
C=0133 (668/5008,1000G)
C=0191 (735/3854,ALSPAC)
C=0188 (697/3708,TWINSUK)
chr13:66949126 (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.66949126T>C
GRCh37.p13 chr 13NC_000013.10:g.67523258T>C
PCDH9 RefSeqGeneNG_011876.1:g.286211A>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
1000GenomesAfricanSub1322T=0.837C=0.163
1000GenomesAmericanSub694T=0.880C=0.120
1000GenomesEast AsianSub1008T=0.966C=0.034
1000GenomesEuropeSub1006T=0.829C=0.171
1000GenomesGlobalStudy-wide5008T=0.867C=0.133
1000GenomesSouth AsianSub978T=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.809C=0.191
The Genome Aggregation DatabaseAfricanSub8718T=0.840C=0.160
The Genome Aggregation DatabaseAmericanSub830T=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1612T=0.975C=0.025
The Genome Aggregation DatabaseEuropeSub18440T=0.827C=0.172
The Genome Aggregation DatabaseGlobalStudy-wide29902T=0.841C=0.158
The Genome Aggregation DatabaseOtherSub302T=0.910C=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.832C=0.167
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.812C=0.188
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
rs95409533.42E-06alcohol dependence20202923

eQTL of rs9540953 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 rs9540953 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 )
chr136747366867473794E067-49464
chr136747429867474370E067-48888
chr136750042167500529E067-22729
chr136750062167500880E067-22378
chr136750092167501266E067-21992
chr136752320067523467E0670
chr136752363467523730E067376
chr136752482467524889E0671566
chr136752489767525061E0671639
chr136752519567525249E0671937
chr136752553867525618E0672280
chr136753289267532984E0679634
chr136753820167538251E06714943
chr136754040467540454E06717146
chr136754047967540552E06717221
chr136754058667540644E06717328
chr136754102767541302E06717769
chr136754236567542415E06719107
chr136754244967542570E06719191
chr136754260467542660E06719346
chr136754504367545174E06721785
chr136755134667551603E06728088
chr136755169467551744E06728436
chr136755176267551826E06728504
chr136756640967566629E06743151
chr136756670967566851E06743451
chr136756689267567262E06743634
chr136756905367569240E06745795
chr136756931867569854E06746060
chr136747429867474370E068-48888
chr136748962667490132E068-33126
chr136749036267490412E068-32846
chr136749042967490553E068-32705
chr136750042167500529E068-22729
chr136750062167500880E068-22378
chr136750092167501266E068-21992
chr136750130067501545E068-21713
chr136752320067523467E0680
chr136752363467523730E068376
chr136752407967524129E068821
chr136752443767524506E0681179
chr136752482467524889E0681566
chr136752489767525061E0681639
chr136752519567525249E0681937
chr136752553867525618E0682280
chr136752570867525817E0682450
chr136752585067526032E0682592
chr136752623167526324E0682973
chr136754194267542316E06818684
chr136754236567542415E06819107
chr136754244967542570E06819191
chr136754489067544940E06821632
chr136754504367545174E06821785
chr136754689767547055E06823639
chr136756640967566629E06843151
chr136756931867569854E06846060
chr136756995067570035E06846692
chr136757009867570227E06846840
chr136757024067570339E06846982
chr136757035867570408E06847100
chr136757076567570901E06847507
chr136748812567488353E069-34905
chr136748962667490132E069-33126
chr136750042167500529E069-22729
chr136750062167500880E069-22378
chr136750092167501266E069-21992
chr136750130067501545E069-21713
chr136752320067523467E0690
chr136752363467523730E069376
chr136752407967524129E069821
chr136752443767524506E0691179
chr136753127567531325E0698017
chr136753163167531681E0698373
chr136753181967531869E0698561
chr136753289267532984E0699634
chr136754194267542316E06918684
chr136754236567542415E06919107
chr136754244967542570E06919191
chr136754260467542660E06919346
chr136754306567543244E06919807
chr136754489067544940E06921632
chr136754504367545174E06921785
chr136755134667551603E06928088
chr136755169467551744E06928436
chr136755176267551826E06928504
chr136756670967566851E06943451
chr136756689267567262E06943634
chr136756886767569007E06945609
chr136756905367569240E06945795
chr136756931867569854E06946060
chr136756995067570035E06946692
chr136757009867570227E06946840
chr136757024067570339E06946982
chr136757035867570408E06947100
chr136757076567570901E06947507
chr136752443767524506E0701179
chr136754489067544940E07021632
chr136754504367545174E07021785
chr136747366867473794E071-49464
chr136747429867474370E071-48888
chr136749036267490412E071-32846
chr136749042967490553E071-32705
chr136752320067523467E0710
chr136752363467523730E071376
chr136752407967524129E071821
chr136752443767524506E0711179
chr136752482467524889E0711566
chr136752489767525061E0711639
chr136752519567525249E0711937
chr136752553867525618E0712280
chr136752570867525817E0712450
chr136752585067526032E0712592
chr136752623167526324E0712973
chr136752640167526441E0713143
chr136754102767541302E07117769
chr136754194267542316E07118684
chr136754236567542415E07119107
chr136754244967542570E07119191
chr136754260467542660E07119346
chr136754306567543244E07119807
chr136754489067544940E07121632
chr136754504367545174E07121785
chr136755134667551603E07128088
chr136755169467551744E07128436
chr136755176267551826E07128504
chr136756640967566629E07143151
chr136756670967566851E07143451
chr136756689267567262E07143634
chr136756905367569240E07145795
chr136756931867569854E07146060
chr136756995067570035E07146692
chr136748962667490132E072-33126
chr136750042167500529E072-22729
chr136750062167500880E072-22378
chr136750092167501266E072-21992
chr136752363467523730E072376
chr136752407967524129E072821
chr136752443767524506E0721179
chr136752482467524889E0721566
chr136752489767525061E0721639
chr136752519567525249E0721937
chr136752585067526032E0722592
chr136752623167526324E0722973
chr136754236567542415E07219107
chr136754244967542570E07219191
chr136754260467542660E07219346
chr136754504367545174E07221785
chr136755134667551603E07228088
chr136755169467551744E07228436
chr136755176267551826E07228504
chr136756640967566629E07243151
chr136756670967566851E07243451
chr136756689267567262E07243634
chr136756905367569240E07245795
chr136756931867569854E07246060
chr136748764467487698E073-35560
chr136750042167500529E073-22729
chr136750062167500880E073-22378
chr136750092167501266E073-21992
chr136752443767524506E0731179
chr136752482467524889E0731566
chr136752489767525061E0731639
chr136752519567525249E0731937
chr136752553867525618E0732280
chr136752570867525817E0732450
chr136752585067526032E0732592
chr136752623167526324E0732973
chr136754489067544940E07321632
chr136754504367545174E07321785
chr136755134667551603E07328088
chr136755169467551744E07328436
chr136755176267551826E07328504
chr136756886767569007E07345609
chr136756905367569240E07345795
chr136756931867569854E07346060
chr136747429867474370E074-48888
chr136748764467487698E074-35560
chr136748812567488353E074-34905
chr136748835667488537E074-34721
chr136749036267490412E074-32846
chr136749042967490553E074-32705
chr136750062167500880E074-22378
chr136750092167501266E074-21992
chr136752407967524129E074821
chr136752443767524506E0741179
chr136752482467524889E0741566
chr136752489767525061E0741639
chr136752519567525249E0741937
chr136752553867525618E0742280
chr136752570867525817E0742450
chr136752585067526032E0742592
chr136752623167526324E0742973
chr136752640167526441E0743143
chr136753127567531325E0748017
chr136753163167531681E0748373
chr136753181967531869E0748561
chr136753289267532984E0749634
chr136754023867540361E07416980
chr136754040467540454E07417146
chr136754047967540552E07417221
chr136754058667540644E07417328
chr136754194267542316E07418684
chr136754236567542415E07419107
chr136754244967542570E07419191
chr136754260467542660E07419346
chr136754306567543244E07419807
chr136754489067544940E07421632
chr136754504367545174E07421785
chr136755134667551603E07428088
chr136755169467551744E07428436
chr136755176267551826E07428504
chr136755850567558689E07435247
chr136756640967566629E07443151
chr136756670967566851E07443451
chr136756689267567262E07443634
chr136756886767569007E07445609
chr136756905367569240E07445795
chr136756931867569854E07446060
chr136756995067570035E07446692
chr136757009867570227E07446840
chr136757024067570339E07446982
chr136757035867570408E07447100
chr136757076567570901E07447507
chr136752320067523467E0810
chr136752363467523730E081376
chr136753933267539422E08116074
chr136753943367539629E08116175
chr136754002367540073E08116765
chr136754023867540361E08116980
chr136754040467540454E08117146
chr136754047967540552E08117221
chr136754058667540644E08117328
chr136754194267542316E08118684
chr136754236567542415E08119107
chr136754244967542570E08119191
chr136754260467542660E08119346
chr136756886767569007E08145609
chr136754023867540361E08216980
chr136754040467540454E08217146
chr136754047967540552E08217221
chr136754058667540644E08217328
chr136754194267542316E08218684
chr136754236567542415E08219107
chr136754244967542570E08219191
chr136754260467542660E08219346
chr136754306567543244E08219807
chr136756886767569007E08245609
chr136756905367569240E08245795










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr136756801667568096E06744758
chr136756821067568838E06744952
chr136756791767567967E06844659
chr136756801667568096E06844758
chr136756821067568838E06844952
chr136756791767567967E06944659
chr136756801667568096E06944758
chr136756821067568838E06944952
chr136756791767567967E07144659
chr136756801667568096E07144758
chr136756821067568838E07144952
chr136756791767567967E07244659
chr136756801667568096E07244758
chr136756821067568838E07244952
chr136756791767567967E07344659
chr136756801667568096E07344758
chr136756821067568838E07344952
chr136756791767567967E07444659
chr136756801667568096E07444758
chr136756821067568838E07444952
chr136756821067568838E08244952