rs12450789

Homo sapiens
C>T
RPH3AL : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0144 (4204/29006,GnomAD)
T=0150 (752/5008,1000G)
T=0105 (404/3854,ALSPAC)
T=0099 (367/3708,TWINSUK)
chr17:220063 (GRCh38.p7) (17p13.3)
AD
GWASdb2
1   publication(s)
See rs on genome
170 Enhancers around
37 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.220063C>T
GRCh37.p13 chr 17 fix patch HG417_PATCHNW_004070872.2:g.160061C>T
RPH3AL RefSeqGeneNG_023031.1:g.137780G>A
GRCh38.p7 chr 17 alt locus HSCHR17_1_CTG1NW_003315952.3:g.167433C>T
GRCh37.p13 chr 17NC_000017.10:g.69854C>T

Gene: RPH3AL, rabphilin 3A-like (without C2 domains)(minus strand)

Molecule type Change Amino acid[Codon] SO Term
RPH3AL transcript variant 2NM_001190411.1:c.N/AIntron Variant
RPH3AL transcript variant 3NM_001190412.1:c.N/AIntron Variant
RPH3AL transcript variant 4NM_001190413.1:c.N/AIntron Variant
RPH3AL transcript variant 1NM_006987.3:c.N/AIntron Variant
RPH3AL transcript variant X1XM_011535364.2:c.N/AIntron Variant
RPH3AL transcript variant X2XM_011535365.2:c.N/AIntron Variant
RPH3AL transcript variant X3XM_011535366.2:c.N/AIntron Variant
RPH3AL transcript variant X4XM_011535367.2:c.N/AIntron Variant
RPH3AL transcript variant X5XM_011535368.2:c.N/AIntron Variant
RPH3AL transcript variant X8XM_011535369.2:c.N/AIntron Variant
RPH3AL transcript variant X6XM_017025367.1:c.N/AIntron Variant
RPH3AL transcript variant X7XM_017025368.1:c.N/AIntron Variant
RPH3AL transcript variant X9XM_017025369.1:c.N/AIntron Variant
RPH3AL transcript variant X10XM_017025370.1:c.N/AIntron Variant
RPH3AL transcript variant X13XM_017025371.1:c.N/AGenic Downstream Transcript Variant
RPH3AL transcript variant X11XR_001752693.1:n.N/AIntron Variant
RPH3AL transcript variant X12XR_001752694.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.835T=0.165
1000GenomesAmericanSub694C=0.840T=0.160
1000GenomesEast AsianSub1008C=0.787T=0.213
1000GenomesEuropeSub1006C=0.896T=0.104
1000GenomesGlobalStudy-wide5008C=0.850T=0.150
1000GenomesSouth AsianSub978C=0.890T=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.895T=0.105
The Genome Aggregation DatabaseAfricanSub8664C=0.835T=0.165
The Genome Aggregation DatabaseAmericanSub828C=0.850T=0.150
The Genome Aggregation DatabaseEast AsianSub1616C=0.790T=0.210
The Genome Aggregation DatabaseEuropeSub17630C=0.870T=0.129
The Genome Aggregation DatabaseGlobalStudy-wide29006C=0.855T=0.144
The Genome Aggregation DatabaseOtherSub268C=0.870T=0.130
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.901T=0.099
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs124507890.000373alcohol consumption (maxi-drinks)24277619

eQTL of rs12450789 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 rs12450789 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 )
chr17159698160308E0670
chr17183384183538E06723323
chr17183551183753E06723490
chr17199545200096E06739484
chr17115542116033E068-44028
chr17157463158121E068-1940
chr17158129158233E068-1828
chr17183029183198E06822968
chr17198482199270E06838421
chr17199319199373E06839258
chr17199545200096E06839484
chr17200332201485E06840271
chr17115542116033E069-44028
chr17116041116095E069-43966
chr17116375116457E069-43604
chr17154074154717E069-5344
chr17159037159645E069-416
chr17159698160308E0690
chr17160355160628E069294
chr17180231180428E06920170
chr17180504180558E06920443
chr17183029183198E06922968
chr17183384183538E06923323
chr17183551183753E06923490
chr17184432184489E06924371
chr17188389188627E06928328
chr17200332201485E06940271
chr17201793203618E06941732
chr17110526110586E070-49475
chr17110611110661E070-49400
chr17110690110745E070-49316
chr17115542116033E070-44028
chr17116041116095E070-43966
chr17116375116457E070-43604
chr17116483116740E070-43321
chr17116772116886E070-43175
chr17116921117586E070-42475
chr17117588117722E070-42339
chr17154814155468E070-4593
chr17155846155935E070-4126
chr17156007156062E070-3999
chr17156114156164E070-3897
chr17156224156358E070-3703
chr17156366156602E070-3459
chr17159037159645E070-416
chr17159698160308E0700
chr17160355160628E070294
chr17160770161331E070709
chr17161375161913E0701314
chr17183551183753E07023490
chr17185438185825E07025377
chr17185871186548E07025810
chr17186583186743E07026522
chr17116483116740E071-43321
chr17116772116886E071-43175
chr17116921117586E071-42475
chr17117588117722E071-42339
chr17157463158121E071-1940
chr17158129158233E071-1828
chr17158357158413E071-1648
chr17158525158575E071-1486
chr17159037159645E071-416
chr17159698160308E0710
chr17180231180428E07120170
chr17180504180558E07120443
chr17183029183198E07122968
chr17183384183538E07123323
chr17183551183753E07123490
chr17199545200096E07139484
chr17200194200234E07140133
chr17200332201485E07140271
chr17115542116033E072-44028
chr17116041116095E072-43966
chr17116375116457E072-43604
chr17116483116740E072-43321
chr17116772116886E072-43175
chr17116921117586E072-42475
chr17117588117722E072-42339
chr17154074154717E072-5344
chr17159037159645E072-416
chr17159698160308E0720
chr17160355160628E072294
chr17160770161331E072709
chr17184432184489E07224371
chr17184770185216E07224709
chr17185438185825E07225377
chr17209801209864E07249740
chr17116041116095E073-43966
chr17116375116457E073-43604
chr17116483116740E073-43321
chr17116772116886E073-43175
chr17116921117586E073-42475
chr17119442119492E073-40569
chr17119546119596E073-40465
chr17146258146379E073-13682
chr17146566146616E073-13445
chr17158989159033E073-1028
chr17159037159645E073-416
chr17159698160308E0730
chr17184432184489E07324371
chr17184770185216E07324709
chr17199545200096E07339484
chr17116921117586E074-42475
chr17117588117722E074-42339
chr17180231180428E07420170
chr17180504180558E07420443
chr17183029183198E07422968
chr17183384183538E07423323
chr17184432184489E07424371
chr17199545200096E07439484
chr17200194200234E07440133
chr17200332201485E07440271
chr17201793203618E07441732
chr17110526110586E081-49475
chr17110611110661E081-49400
chr17110690110745E081-49316
chr17115542116033E081-44028
chr17116041116095E081-43966
chr17116375116457E081-43604
chr17116483116740E081-43321
chr17116772116886E081-43175
chr17116921117586E081-42475
chr17117588117722E081-42339
chr17119442119492E081-40569
chr17119546119596E081-40465
chr17119787120156E081-39905
chr17130836130923E081-29138
chr17131010131050E081-29011
chr17131253131303E081-28758
chr17140172140247E081-19814
chr17140266140353E081-19708
chr17140504140619E081-19442
chr17140646140697E081-19364
chr17142007142057E081-18004
chr17142462143207E081-16854
chr17157341157434E081-2627
chr17157463158121E081-1940
chr17159037159645E081-416
chr17159698160308E0810
chr17160355160628E081294
chr17160770161331E081709
chr17171258172015E08111197
chr17172107172290E08112046
chr17172761172801E08112700
chr17180231180428E08120170
chr17180504180558E08120443
chr17184770185216E08124709
chr17185240185316E08125179
chr17185340185390E08125279
chr17185438185825E08125377
chr17187268187643E08127207
chr17110526110586E082-49475
chr17115319115369E082-44692
chr17115542116033E082-44028
chr17116041116095E082-43966
chr17116375116457E082-43604
chr17116483116740E082-43321
chr17116772116886E082-43175
chr17116921117586E082-42475
chr17117588117722E082-42339
chr17119442119492E082-40569
chr17119546119596E082-40465
chr17119787120156E082-39905
chr17120357120437E082-39624
chr17142007142057E082-18004
chr17159698160308E0820
chr17160355160628E082294
chr17172107172290E08212046
chr17185438185825E08225377
chr17185871186548E08225810










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr17181153181448E06721092
chr17181626181692E06721565
chr17181757181878E06721696
chr17181923182203E06721862
chr17183766184305E06723705
chr17181153181448E06821092
chr17181626181692E06821565
chr17181757181878E06821696
chr17181923182203E06821862
chr17182231182953E06822170
chr17183766184305E06823705
chr17181153181448E06921092
chr17181626181692E06921565
chr17181757181878E06921696
chr17181923182203E06921862
chr17183766184305E06923705
chr17181153181448E07121092
chr17181626181692E07121565
chr17181757181878E07121696
chr17183766184305E07123705
chr17181153181448E07221092
chr17181626181692E07221565
chr17181757181878E07221696
chr17181923182203E07221862
chr17182231182953E07222170
chr17183766184305E07223705
chr17181153181448E07321092
chr17181626181692E07321565
chr17181757181878E07321696
chr17181923182203E07321862
chr17182231182953E07322170
chr17183766184305E07323705
chr17181153181448E07421092
chr17181626181692E07421565
chr17181757181878E07421696
chr17181923182203E07421862
chr17183766184305E07423705