rs6932538

Homo sapiens
C>T
PHF3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0466 (13805/29612,GnomAD)
C==0391 (11392/29118,TOPMED)
C==0416 (2083/5008,1000G)
T=0462 (1780/3854,ALSPAC)
T=0474 (1759/3708,TWINSUK)
chr6:63673079 (GRCh38.p7) (6q12)
AD
GWASdb2
1   publication(s)
See rs on genome
169 Enhancers around
40 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.63673079C>T
GRCh37.p13 chr 6NC_000006.11:g.64382980C>T
PHF3 RefSeqGeneNG_034034.1:g.42278C>T

Gene: PHF3, PHD finger protein 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PHF3 transcript variant 2NM_001290259.1:c.N/AIntron Variant
PHF3 transcript variant 3NM_001290260.1:c.N/AIntron Variant
PHF3 transcript variant 1NM_015153.3:c.N/AIntron Variant
PHF3 transcript variant X2XM_005248701.3:c.N/AIntron Variant
PHF3 transcript variant X4XM_005248702.3:c.N/AIntron Variant
PHF3 transcript variant X6XM_005248703.3:c.N/AIntron Variant
PHF3 transcript variant X3XM_006715426.3:c.N/AIntron Variant
PHF3 transcript variant X1XM_011535648.2:c.N/AIntron Variant
PHF3 transcript variant X5XM_017010626.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.213T=0.787
1000GenomesAmericanSub694C=0.380T=0.620
1000GenomesEast AsianSub1008C=0.547T=0.453
1000GenomesEuropeSub1006C=0.559T=0.441
1000GenomesGlobalStudy-wide5008C=0.416T=0.584
1000GenomesSouth AsianSub978C=0.430T=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.538T=0.462
The Genome Aggregation DatabaseAfricanSub8638C=0.235T=0.765
The Genome Aggregation DatabaseAmericanSub826C=0.400T=0.600
The Genome Aggregation DatabaseEast AsianSub1604C=0.548T=0.452
The Genome Aggregation DatabaseEuropeSub18244C=0.571T=0.429
The Genome Aggregation DatabaseGlobalStudy-wide29612C=0.466T=0.533
The Genome Aggregation DatabaseOtherSub300C=0.500T=0.500
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.391T=0.608
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.526T=0.474
PMID Title Author Journal
22096494A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.Zuo LPLoS One

P-Value

SNP ID p-value Traits Study
rs69325380.00094alcohol dependence22096494

eQTL of rs6932538 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64382980LGSNENSG00000146166.12C>T1.9599e-12353098Brain_Spinal_cord_cervical

meQTL of rs6932538 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 )
chr66435003264350267E067-32713
chr66435031064350429E067-32551
chr66435152264351562E067-31418
chr66435166464351729E067-31251
chr66435326564353367E067-29613
chr66435340364353453E067-29527
chr66435355064353597E067-29383
chr66435379964354122E067-28858
chr66435416464354298E067-28682
chr66435476664354995E067-27985
chr66435648464356589E067-26391
chr66435939164359514E067-23466
chr66435987964359966E067-23014
chr66436979364369833E067-13147
chr66436995664370043E067-12937
chr66437046564370839E067-12141
chr66437340864373737E067-9243
chr66438461664384840E0671636
chr66438674564387006E0673765
chr66438706764387235E0674087
chr66438727564387534E0674295
chr66440013864400208E06717158
chr66440027264400351E06717292
chr66441189064411952E06728910
chr66434815264348219E068-34761
chr66434830464348374E068-34606
chr66434916664349250E068-33730
chr66435003264350267E068-32713
chr66435031064350429E068-32551
chr66435340364353453E068-29527
chr66435355064353597E068-29383
chr66435379964354122E068-28858
chr66435416464354298E068-28682
chr66435476664354995E068-27985
chr66435500564355161E068-27819
chr66435939164359514E068-23466
chr66435987964359966E068-23014
chr66436003464360162E068-22818
chr66436979364369833E068-13147
chr66436995664370043E068-12937
chr66437046564370839E068-12141
chr66437319564373307E068-9673
chr66437407864374118E068-8862
chr66438549764385541E0682517
chr66438646464386529E0683484
chr66438674564387006E0683765
chr66438706764387235E0684087
chr66438727564387534E0684295
chr66434815264348219E069-34761
chr66434830464348374E069-34606
chr66435003264350267E069-32713
chr66435031064350429E069-32551
chr66435326564353367E069-29613
chr66435340364353453E069-29527
chr66435355064353597E069-29383
chr66435379964354122E069-28858
chr66435416464354298E069-28682
chr66435476664354995E069-27985
chr66435500564355161E069-27819
chr66435939164359514E069-23466
chr66435987964359966E069-23014
chr66436598564366056E069-16924
chr66436979364369833E069-13147
chr66436995664370043E069-12937
chr66437046564370839E069-12141
chr66437383464373908E069-9072
chr66438461664384840E0691636
chr66438508664385323E0692106
chr66438534064385412E0692360
chr66438549764385541E0692517
chr66438646464386529E0693484
chr66438674564387006E0693765
chr66438706764387235E0694087
chr66438727564387534E0694295
chr66434815264348219E070-34761
chr66434815264348219E071-34761
chr66434830464348374E071-34606
chr66434916664349250E071-33730
chr66435003264350267E071-32713
chr66435031064350429E071-32551
chr66435326564353367E071-29613
chr66435340364353453E071-29527
chr66435355064353597E071-29383
chr66435379964354122E071-28858
chr66435416464354298E071-28682
chr66435476664354995E071-27985
chr66435500564355161E071-27819
chr66435939164359514E071-23466
chr66435987964359966E071-23014
chr66436003464360162E071-22818
chr66436979364369833E071-13147
chr66436995664370043E071-12937
chr66437046564370839E071-12141
chr66437319564373307E071-9673
chr66437340864373737E071-9243
chr66437383464373908E071-9072
chr66437407864374118E071-8862
chr66438461664384840E0711636
chr66438508664385323E0712106
chr66438534064385412E0712360
chr66438549764385541E0712517
chr66438646464386529E0713484
chr66438674564387006E0713765
chr66438706764387235E0714087
chr66438727564387534E0714295
chr66435003264350267E072-32713
chr66435031064350429E072-32551
chr66435152264351562E072-31418
chr66435166464351729E072-31251
chr66435326564353367E072-29613
chr66435340364353453E072-29527
chr66435355064353597E072-29383
chr66435379964354122E072-28858
chr66435416464354298E072-28682
chr66435476664354995E072-27985
chr66435500564355161E072-27819
chr66435939164359514E072-23466
chr66435987964359966E072-23014
chr66436794864368043E072-14937
chr66436812864368168E072-14812
chr66437046564370839E072-12141
chr66438646464386529E0723484
chr66438674564387006E0723765
chr66438706764387235E0724087
chr66438727564387534E0724295
chr66439308664393166E07210106
chr66435003264350267E073-32713
chr66435031064350429E073-32551
chr66435416464354298E073-28682
chr66435476664354995E073-27985
chr66435939164359514E073-23466
chr66434453564344923E074-38057
chr66434916664349250E074-33730
chr66435003264350267E074-32713
chr66435031064350429E074-32551
chr66435152264351562E074-31418
chr66435166464351729E074-31251
chr66435326564353367E074-29613
chr66435340364353453E074-29527
chr66435355064353597E074-29383
chr66435379964354122E074-28858
chr66435416464354298E074-28682
chr66435476664354995E074-27985
chr66435500564355161E074-27819
chr66435939164359514E074-23466
chr66435987964359966E074-23014
chr66436003464360162E074-22818
chr66436979364369833E074-13147
chr66436995664370043E074-12937
chr66437046564370839E074-12141
chr66438375864383814E074778
chr66438461664384840E0741636
chr66438508664385323E0742106
chr66438534064385412E0742360
chr66438549764385541E0742517
chr66438646464386529E0743484
chr66438674564387006E0743765
chr66438706764387235E0744087
chr66438727564387534E0744295
chr66434916664349250E081-33730
chr66435003264350267E081-32713
chr66435031064350429E081-32551
chr66438706764387235E0814087
chr66438727564387534E0814295
chr66434815264348219E082-34761
chr66434830464348374E082-34606
chr66434916664349250E082-33730
chr66435379964354122E082-28858
chr66435416464354298E082-28682










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr66434507264347052E067-35928
chr66434707764347265E067-35715
chr66434730764347377E067-35603
chr66434738864347481E067-35499
chr66434507264347052E068-35928
chr66434707764347265E068-35715
chr66434730764347377E068-35603
chr66434738864347481E068-35499
chr66434507264347052E069-35928
chr66434707764347265E069-35715
chr66434730764347377E069-35603
chr66434738864347481E069-35499
chr66434507264347052E070-35928
chr66434707764347265E070-35715
chr66434730764347377E070-35603
chr66434738864347481E070-35499
chr66434507264347052E071-35928
chr66434707764347265E071-35715
chr66434730764347377E071-35603
chr66434738864347481E071-35499
chr66434507264347052E072-35928
chr66434707764347265E072-35715
chr66434730764347377E072-35603
chr66434738864347481E072-35499
chr66434507264347052E073-35928
chr66434707764347265E073-35715
chr66434730764347377E073-35603
chr66434738864347481E073-35499
chr66434507264347052E074-35928
chr66434707764347265E074-35715
chr66434730764347377E074-35603
chr66434738864347481E074-35499
chr66434507264347052E081-35928
chr66434707764347265E081-35715
chr66434730764347377E081-35603
chr66434738864347481E081-35499
chr66434507264347052E082-35928
chr66434707764347265E082-35715
chr66434730764347377E082-35603
chr66434738864347481E082-35499