rs10402506

Homo sapiens
A>G
LOC107985347 : Intron Variant
LOC105372461 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0242 (7261/29924,GnomAD)
G=0285 (8298/29118,TOPMED)
G=0294 (1472/5008,1000G)
G=0133 (513/3854,ALSPAC)
G=0124 (459/3708,TWINSUK)
chr19:54563023 (GRCh38.p7) (19q13.42)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 19NC_000019.10:g.54563023A>G
GRCh37.p13 chr 19 fix patch HG1079_PATCHNW_004166865.1:g.537390A>G
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1NT_187693.1:g.545584A>G
GRCh37.p13 chr 19NC_000019.9:g.55074470A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1NW_003571060.1:g.467899A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1NW_003571054.1:g.469417A>G

Gene: LOC107985347, uncharacterized LOC107985347(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107985347 transcript variant X1XR_001754007.1:n.N/AIntron Variant
LOC107985347 transcript variant X3XR_001754009.1:n.N/AIntron Variant
LOC107985347 transcript variant X4XR_001754010.1:n.N/AIntron Variant
LOC107985347 transcript variant X2XR_001754008.1:n.N/AGenic Downstream Transcript Variant

Gene: LOC105372461, uncharacterized LOC105372461(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105372461 transcriptXR_936073.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.499G=0.501
1000GenomesAmericanSub694A=0.720G=0.280
1000GenomesEast AsianSub1008A=0.725G=0.275
1000GenomesEuropeSub1006A=0.873G=0.127
1000GenomesGlobalStudy-wide5008A=0.706G=0.294
1000GenomesSouth AsianSub978A=0.780G=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.867G=0.133
The Genome Aggregation DatabaseAfricanSub8690A=0.535G=0.465
The Genome Aggregation DatabaseAmericanSub838A=0.750G=0.250
The Genome Aggregation DatabaseEast AsianSub1614A=0.690G=0.310
The Genome Aggregation DatabaseEuropeSub18482A=0.866G=0.133
The Genome Aggregation DatabaseGlobalStudy-wide29924A=0.757G=0.242
The Genome Aggregation DatabaseOtherSub300A=0.860G=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.715G=0.285
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.876G=0.124
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
rs104025060.000989alcohol dependence21314694

eQTL of rs10402506 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 rs10402506 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 )
chr19534509534565E067-2825
chr19534777534827E067-2563
chr19534901535052E067-2338
chr19535090535426E067-1964
chr19535533535846E067-1544
chr19551174551336E06713784
chr19551366551552E06713976
chr19574107574278E06736717
chr19576737576824E06739347
chr19576862577212E06739472
chr19577228577350E06739838
chr19577399577504E06740009
chr19577519577623E06740129
chr19577665577879E06740275
chr19577905577955E06740515
chr19578009578184E06740619
chr19579826579966E06742436
chr19580036580097E06742646
chr19580161580257E06742771
chr19487867487927E068-49463
chr19490223490284E068-47106
chr19490308490408E068-46982
chr19534509534565E068-2825
chr19551174551336E06813784
chr19551366551552E06813976
chr19576737576824E06839347
chr19576862577212E06839472
chr19577228577350E06839838
chr19577399577504E06840009
chr19583747585118E06846357
chr19487867487927E069-49463
chr19490466490531E069-46859
chr19490543490656E069-46734
chr19534509534565E069-2825
chr19534777534827E069-2563
chr19534901535052E069-2338
chr19535090535426E069-1964
chr19535533535846E069-1544
chr19537974538060E069584
chr19538186538356E069796
chr19538422538476E0691032
chr19558802559122E06921412
chr19559207559257E06921817
chr19559311559411E06921921
chr19576737576824E06939347
chr19577399577504E06940009
chr19577519577623E06940129
chr19579478579638E06942088
chr19579705579785E06942315
chr19579826579966E06942436
chr19580036580097E06942646
chr19580161580257E06942771
chr19580365580598E06942975
chr19583747585118E06946357
chr19534901535052E070-2338
chr19535090535426E070-1964
chr19535533535846E070-1544
chr19535898535948E070-1442
chr19576737576824E07039347
chr19490466490531E071-46859
chr19491138491205E071-46185
chr19534509534565E071-2825
chr19534777534827E071-2563
chr19534901535052E071-2338
chr19535090535426E071-1964
chr19535533535846E071-1544
chr19574107574278E07136717
chr19576737576824E07139347
chr19576862577212E07139472
chr19577228577350E07139838
chr19577399577504E07140009
chr19577519577623E07140129
chr19577665577879E07140275
chr19577905577955E07140515
chr19578009578184E07140619
chr19578233578277E07140843
chr19578341578393E07140951
chr19579208579268E07141818
chr19579478579638E07142088
chr19579705579785E07142315
chr19579826579966E07142436
chr19580036580097E07142646
chr19580161580257E07142771
chr19580365580598E07142975
chr19583747585118E07146357
chr19487867487927E072-49463
chr19490466490531E072-46859
chr19490543490656E072-46734
chr19534509534565E072-2825
chr19534777534827E072-2563
chr19534901535052E072-2338
chr19535090535426E072-1964
chr19537974538060E072584
chr19538186538356E072796
chr19551366551552E07213976
chr19574107574278E07236717
chr19577228577350E07239838
chr19577399577504E07240009
chr19577519577623E07240129
chr19577665577879E07240275
chr19577905577955E07240515
chr19578009578184E07240619
chr19578233578277E07240843
chr19578341578393E07240951
chr19578520578601E07241130
chr19578612578687E07241222
chr19578938578988E07241548
chr19579208579268E07241818
chr19579478579638E07242088
chr19579705579785E07242315
chr19579826579966E07242436
chr19580036580097E07242646
chr19580161580257E07242771
chr19580365580598E07242975
chr19487867487927E073-49463
chr19494969495135E073-42255
chr19495165495275E073-42115
chr19534509534565E073-2825
chr19534777534827E073-2563
chr19534901535052E073-2338
chr19535090535426E073-1964
chr19535533535846E073-1544
chr19538958539008E0731568
chr19539021539078E0731631
chr19539157539275E0731767
chr19539377539483E0731987
chr19556697556915E07319307
chr19556944556988E07319554
chr19559207559257E07321817
chr19559311559411E07321921
chr19578009578184E07340619
chr19578233578277E07340843
chr19578341578393E07340951
chr19578520578601E07341130
chr19578612578687E07341222
chr19578938578988E07341548
chr19579208579268E07341818
chr19579478579638E07342088
chr19579705579785E07342315
chr19579826579966E07342436
chr19580036580097E07342646
chr19580161580257E07342771
chr19580365580598E07342975
chr19580624580806E07343234
chr19581834581994E07344444
chr19582070582185E07344680
chr19583747585118E07346357
chr19487867487927E074-49463
chr19534901535052E074-2338
chr19535090535426E074-1964
chr19574107574278E07436717
chr19575910576488E07438520
chr19576737576824E07439347
chr19576862577212E07439472
chr19579826579966E07442436
chr19580036580097E07442646
chr19580161580257E07442771
chr19583747585118E07446357
chr19490223490284E081-47106
chr19490308490408E081-46982
chr19490466490531E081-46859
chr19534509534565E081-2825
chr19534777534827E081-2563
chr19534901535052E081-2338
chr19535090535426E081-1964
chr19551174551336E08113784
chr19551366551552E08113976
chr19574107574278E08136717
chr19575910576488E08138520
chr19576737576824E08139347
chr19576862577212E08139472
chr19534901535052E082-2338
chr19535090535426E082-1964
chr19535533535846E082-1544
chr19535898535948E082-1442










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr19488101488299E067-49091
chr19488487490098E067-47292
chr19506372509364E067-28026
chr19530689534451E067-2939
chr19570959573974E06733569
chr19488101488299E068-49091
chr19488487490098E068-47292
chr19506372509364E068-28026
chr19530689534451E068-2939
chr19570799570868E06833409
chr19570959573974E06833569
chr19488101488299E069-49091
chr19488487490098E069-47292
chr19506372509364E069-28026
chr19530689534451E069-2939
chr19570959573974E06933569
chr19488487490098E070-47292
chr19497445497597E070-39793
chr19506372509364E070-28026
chr19530689534451E070-2939
chr19570959573974E07033569
chr19488101488299E071-49091
chr19488487490098E071-47292
chr19506372509364E071-28026
chr19530689534451E071-2939
chr19570959573974E07133569
chr19488101488299E072-49091
chr19488487490098E072-47292
chr19506372509364E072-28026
chr19530689534451E072-2939
chr19570959573974E07233569
chr19488101488299E073-49091
chr19488487490098E073-47292
chr19506372509364E073-28026
chr19530689534451E073-2939
chr19570959573974E07333569
chr19488101488299E074-49091
chr19488487490098E074-47292
chr19506372509364E074-28026
chr19530689534451E074-2939
chr19570959573974E07433569
chr19570959573974E08133569
chr19488101488299E082-49091
chr19488487490098E082-47292
chr19497053497183E082-40207
chr19497445497597E082-39793
chr19506372509364E082-28026
chr19530689534451E082-2939
chr19570959573974E08233569