rs10485358

Homo sapiens
C>T
PHF3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0459 (13731/29910,GnomAD)
C==0381 (11098/29118,TOPMED)
C==0408 (2044/5008,1000G)
T=0467 (1801/3854,ALSPAC)
T=0480 (1778/3708,TWINSUK)
chr6:63676159 (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.63676159C>T
GRCh37.p13 chr 6NC_000006.11:g.64386060C>T
PHF3 RefSeqGeneNG_034034.1:g.45358C>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=0.188T=0.812
1000GenomesAmericanSub694C=0.380T=0.620
1000GenomesEast AsianSub1008C=0.547T=0.453
1000GenomesEuropeSub1006C=0.557T=0.443
1000GenomesGlobalStudy-wide5008C=0.408T=0.592
1000GenomesSouth AsianSub978C=0.430T=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.533T=0.467
The Genome Aggregation DatabaseAfricanSub8702C=0.216T=0.784
The Genome Aggregation DatabaseAmericanSub830C=0.400T=0.600
The Genome Aggregation DatabaseEast AsianSub1612C=0.550T=0.450
The Genome Aggregation DatabaseEuropeSub18464C=0.567T=0.432
The Genome Aggregation DatabaseGlobalStudy-wide29910C=0.459T=0.540
The Genome Aggregation DatabaseOtherSub302C=0.490T=0.510
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.381T=0.618
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.520T=0.480
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
rs104853580.00032alcohol dependence22096494

eQTL of rs10485358 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:64386060LGSNENSG00000146166.12C>T1.9599e-12356178Brain_Spinal_cord_cervical

meQTL of rs10485358 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 )
chr66435003264350267E067-35793
chr66435031064350429E067-35631
chr66435152264351562E067-34498
chr66435166464351729E067-34331
chr66435326564353367E067-32693
chr66435340364353453E067-32607
chr66435355064353597E067-32463
chr66435379964354122E067-31938
chr66435416464354298E067-31762
chr66435476664354995E067-31065
chr66435648464356589E067-29471
chr66435939164359514E067-26546
chr66435987964359966E067-26094
chr66436979364369833E067-16227
chr66436995664370043E067-16017
chr66437046564370839E067-15221
chr66437340864373737E067-12323
chr66438461664384840E067-1220
chr66438674564387006E067685
chr66438706764387235E0671007
chr66438727564387534E0671215
chr66440013864400208E06714078
chr66440027264400351E06714212
chr66441189064411952E06725830
chr66434815264348219E068-37841
chr66434830464348374E068-37686
chr66434916664349250E068-36810
chr66435003264350267E068-35793
chr66435031064350429E068-35631
chr66435340364353453E068-32607
chr66435355064353597E068-32463
chr66435379964354122E068-31938
chr66435416464354298E068-31762
chr66435476664354995E068-31065
chr66435500564355161E068-30899
chr66435939164359514E068-26546
chr66435987964359966E068-26094
chr66436003464360162E068-25898
chr66436979364369833E068-16227
chr66436995664370043E068-16017
chr66437046564370839E068-15221
chr66437319564373307E068-12753
chr66437407864374118E068-11942
chr66438549764385541E068-519
chr66438646464386529E068404
chr66438674564387006E068685
chr66438706764387235E0681007
chr66438727564387534E0681215
chr66434815264348219E069-37841
chr66434830464348374E069-37686
chr66435003264350267E069-35793
chr66435031064350429E069-35631
chr66435326564353367E069-32693
chr66435340364353453E069-32607
chr66435355064353597E069-32463
chr66435379964354122E069-31938
chr66435416464354298E069-31762
chr66435476664354995E069-31065
chr66435500564355161E069-30899
chr66435939164359514E069-26546
chr66435987964359966E069-26094
chr66436598564366056E069-20004
chr66436979364369833E069-16227
chr66436995664370043E069-16017
chr66437046564370839E069-15221
chr66437383464373908E069-12152
chr66438461664384840E069-1220
chr66438508664385323E069-737
chr66438534064385412E069-648
chr66438549764385541E069-519
chr66438646464386529E069404
chr66438674564387006E069685
chr66438706764387235E0691007
chr66438727564387534E0691215
chr66434815264348219E070-37841
chr66434815264348219E071-37841
chr66434830464348374E071-37686
chr66434916664349250E071-36810
chr66435003264350267E071-35793
chr66435031064350429E071-35631
chr66435326564353367E071-32693
chr66435340364353453E071-32607
chr66435355064353597E071-32463
chr66435379964354122E071-31938
chr66435416464354298E071-31762
chr66435476664354995E071-31065
chr66435500564355161E071-30899
chr66435939164359514E071-26546
chr66435987964359966E071-26094
chr66436003464360162E071-25898
chr66436979364369833E071-16227
chr66436995664370043E071-16017
chr66437046564370839E071-15221
chr66437319564373307E071-12753
chr66437340864373737E071-12323
chr66437383464373908E071-12152
chr66437407864374118E071-11942
chr66438461664384840E071-1220
chr66438508664385323E071-737
chr66438534064385412E071-648
chr66438549764385541E071-519
chr66438646464386529E071404
chr66438674564387006E071685
chr66438706764387235E0711007
chr66438727564387534E0711215
chr66435003264350267E072-35793
chr66435031064350429E072-35631
chr66435152264351562E072-34498
chr66435166464351729E072-34331
chr66435326564353367E072-32693
chr66435340364353453E072-32607
chr66435355064353597E072-32463
chr66435379964354122E072-31938
chr66435416464354298E072-31762
chr66435476664354995E072-31065
chr66435500564355161E072-30899
chr66435939164359514E072-26546
chr66435987964359966E072-26094
chr66436794864368043E072-18017
chr66436812864368168E072-17892
chr66437046564370839E072-15221
chr66438646464386529E072404
chr66438674564387006E072685
chr66438706764387235E0721007
chr66438727564387534E0721215
chr66439308664393166E0727026
chr66435003264350267E073-35793
chr66435031064350429E073-35631
chr66435416464354298E073-31762
chr66435476664354995E073-31065
chr66435939164359514E073-26546
chr66434453564344923E074-41137
chr66434916664349250E074-36810
chr66435003264350267E074-35793
chr66435031064350429E074-35631
chr66435152264351562E074-34498
chr66435166464351729E074-34331
chr66435326564353367E074-32693
chr66435340364353453E074-32607
chr66435355064353597E074-32463
chr66435379964354122E074-31938
chr66435416464354298E074-31762
chr66435476664354995E074-31065
chr66435500564355161E074-30899
chr66435939164359514E074-26546
chr66435987964359966E074-26094
chr66436003464360162E074-25898
chr66436979364369833E074-16227
chr66436995664370043E074-16017
chr66437046564370839E074-15221
chr66438375864383814E074-2246
chr66438461664384840E074-1220
chr66438508664385323E074-737
chr66438534064385412E074-648
chr66438549764385541E074-519
chr66438646464386529E074404
chr66438674564387006E074685
chr66438706764387235E0741007
chr66438727564387534E0741215
chr66434916664349250E081-36810
chr66435003264350267E081-35793
chr66435031064350429E081-35631
chr66438706764387235E0811007
chr66438727564387534E0811215
chr66434815264348219E082-37841
chr66434830464348374E082-37686
chr66434916664349250E082-36810
chr66435379964354122E082-31938
chr66435416464354298E082-31762










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr66434507264347052E067-39008
chr66434707764347265E067-38795
chr66434730764347377E067-38683
chr66434738864347481E067-38579
chr66434507264347052E068-39008
chr66434707764347265E068-38795
chr66434730764347377E068-38683
chr66434738864347481E068-38579
chr66434507264347052E069-39008
chr66434707764347265E069-38795
chr66434730764347377E069-38683
chr66434738864347481E069-38579
chr66434507264347052E070-39008
chr66434707764347265E070-38795
chr66434730764347377E070-38683
chr66434738864347481E070-38579
chr66434507264347052E071-39008
chr66434707764347265E071-38795
chr66434730764347377E071-38683
chr66434738864347481E071-38579
chr66434507264347052E072-39008
chr66434707764347265E072-38795
chr66434730764347377E072-38683
chr66434738864347481E072-38579
chr66434507264347052E073-39008
chr66434707764347265E073-38795
chr66434730764347377E073-38683
chr66434738864347481E073-38579
chr66434507264347052E074-39008
chr66434707764347265E074-38795
chr66434730764347377E074-38683
chr66434738864347481E074-38579
chr66434507264347052E081-39008
chr66434707764347265E081-38795
chr66434730764347377E081-38683
chr66434738864347481E081-38579
chr66434507264347052E082-39008
chr66434707764347265E082-38795
chr66434730764347377E082-38683
chr66434738864347481E082-38579