rs896543

Homo sapiens
G>A
LOC107986001 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0317 (9519/29960,GnomAD)
A=0405 (11812/29118,TOPMED)
A=0352 (1761/5008,1000G)
chr2:236600564 (GRCh38.p7) (2q37.3)
AD
GWASdb2 | GWASCatalog
2   publication(s)
See rs on genome
125 Enhancers around
45 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.236600564G>A
GRCh37.p13 chr 2NC_000002.11:g.237509207G>A

Gene: LOC107986001, uncharacterized LOC107986001(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107986001 transcript variant X1XR_001739950.1:n.N/AIntron Variant
LOC107986001 transcript variant X2XR_001739951.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.238A=0.762
1000GenomesAmericanSub694G=0.840A=0.160
1000GenomesEast AsianSub1008G=0.805A=0.195
1000GenomesEuropeSub1006G=0.804A=0.196
1000GenomesGlobalStudy-wide5008G=0.648A=0.352
1000GenomesSouth AsianSub978G=0.750A=0.250
The Genome Aggregation DatabaseAfricanSub8722G=0.317A=0.683
The Genome Aggregation DatabaseAmericanSub838G=0.860A=0.140
The Genome Aggregation DatabaseEast AsianSub1616G=0.782A=0.218
The Genome Aggregation DatabaseEuropeSub18482G=0.835A=0.164
The Genome Aggregation DatabaseGlobalStudy-wide29960G=0.682A=0.317
The Genome Aggregation DatabaseOtherSub302G=0.820A=0.180
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.594A=0.405
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend
23089632A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.Wang JCMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs8965430.000000475alcohol dependence23089632
rs8965430.000001alcohol dependence (age at onset)24962325
rs8965430.00000435alcohol dependence23089632

eQTL of rs896543 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 rs896543 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 )
chr2237481042237481559E067-27648
chr2237481570237482025E067-27182
chr2237487622237487975E067-21232
chr2237488021237488075E067-21132
chr2237488238237488418E067-20789
chr2237488500237488907E067-20300
chr2237538984237539374E06729777
chr2237468059237468109E068-41098
chr2237484754237485097E068-24110
chr2237485162237485354E068-23853
chr2237485667237485904E068-23303
chr2237486488237487091E068-22116
chr2237522085237522176E06812878
chr2237534685237534740E06825478
chr2237538984237539374E06829777
chr2237539431237539520E06830224
chr2237539626237539827E06830419
chr2237487622237487975E069-21232
chr2237488021237488075E069-21132
chr2237488238237488418E069-20789
chr2237488500237488907E069-20300
chr2237538984237539374E06929777
chr2237539431237539520E06930224
chr2237539626237539827E06930419
chr2237539863237540345E06930656
chr2237540358237540459E06931151
chr2237485162237485354E070-23853
chr2237485667237485904E070-23303
chr2237524722237525153E07015515
chr2237525341237525551E07016134
chr2237525752237526482E07016545
chr2237526554237526634E07017347
chr2237534685237534740E07025478
chr2237534920237535000E07025713
chr2237539626237539827E07030419
chr2237539863237540345E07030656
chr2237466643237466811E071-42396
chr2237466934237467036E071-42171
chr2237482579237482754E071-26453
chr2237482791237482927E071-26280
chr2237484754237485097E071-24110
chr2237485162237485354E071-23853
chr2237485667237485904E071-23303
chr2237487273237487328E071-21879
chr2237487622237487975E071-21232
chr2237488021237488075E071-21132
chr2237488238237488418E071-20789
chr2237488500237488907E071-20300
chr2237521857237521932E07112650
chr2237522085237522176E07112878
chr2237522433237522641E07113226
chr2237534373237534518E07125166
chr2237538984237539374E07129777
chr2237539431237539520E07130224
chr2237481570237482025E072-27182
chr2237482137237482275E072-26932
chr2237482332237482520E072-26687
chr2237482579237482754E072-26453
chr2237487273237487328E072-21879
chr2237487622237487975E072-21232
chr2237488021237488075E072-21132
chr2237488238237488418E072-20789
chr2237488500237488907E072-20300
chr2237490341237490483E072-18724
chr2237521857237521932E07212650
chr2237522085237522176E07212878
chr2237522433237522641E07213226
chr2237534373237534518E07225166
chr2237538984237539374E07229777
chr2237539431237539520E07230224
chr2237539626237539827E07230419
chr2237539863237540345E07230656
chr2237540358237540459E07231151
chr2237481570237482025E073-27182
chr2237482137237482275E073-26932
chr2237482332237482520E073-26687
chr2237487273237487328E073-21879
chr2237466643237466811E074-42396
chr2237488021237488075E074-21132
chr2237488238237488418E074-20789
chr2237488500237488907E074-20300
chr2237521857237521932E07412650
chr2237522085237522176E07412878
chr2237522433237522641E07413226
chr2237534373237534518E07425166
chr2237538984237539374E07429777
chr2237539431237539520E07430224
chr2237539626237539827E07430419
chr2237539863237540345E07430656
chr2237540358237540459E07431151
chr2237483169237483758E081-25449
chr2237483759237483822E081-25385
chr2237484300237484542E081-24665
chr2237484754237485097E081-24110
chr2237485162237485354E081-23853
chr2237488238237488418E081-20789
chr2237488500237488907E081-20300
chr2237497942237498290E081-10917
chr2237521497237521694E08112290
chr2237521857237521932E08112650
chr2237522085237522176E08112878
chr2237522433237522641E08113226
chr2237523023237523127E08113816
chr2237523281237523441E08114074
chr2237523633237523683E08114426
chr2237524722237525153E08115515
chr2237525341237525551E08116134
chr2237525752237526482E08116545
chr2237526554237526634E08117347
chr2237538984237539374E08129777
chr2237539431237539520E08130224
chr2237539626237539827E08130419
chr2237539863237540345E08130656
chr2237540358237540459E08131151
chr2237496250237496385E082-12822
chr2237521497237521694E08212290
chr2237521857237521932E08212650
chr2237522085237522176E08212878
chr2237522433237522641E08213226
chr2237523023237523127E08213816
chr2237523281237523441E08214074
chr2237523633237523683E08214426
chr2237525341237525551E08216134
chr2237525752237526482E08216545
chr2237540358237540459E08231151










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2237476609237479749E067-29458
chr2237479804237480012E067-29195
chr2237480080237480193E067-29014
chr2237480285237480401E067-28806
chr2237476012237476545E068-32662
chr2237476609237479749E068-29458
chr2237479804237480012E068-29195
chr2237480080237480193E068-29014
chr2237480285237480401E068-28806
chr2237480652237480707E068-28500
chr2237480715237480784E068-28423
chr2237476609237479749E069-29458
chr2237479804237480012E069-29195
chr2237480080237480193E069-29014
chr2237480285237480401E069-28806
chr2237480652237480707E069-28500
chr2237480715237480784E069-28423
chr2237480080237480193E070-29014
chr2237480285237480401E070-28806
chr2237480652237480707E070-28500
chr2237480715237480784E070-28423
chr2237476609237479749E071-29458
chr2237479804237480012E071-29195
chr2237480080237480193E071-29014
chr2237480285237480401E071-28806
chr2237480652237480707E071-28500
chr2237480715237480784E071-28423
chr2237476609237479749E072-29458
chr2237479804237480012E072-29195
chr2237480080237480193E072-29014
chr2237476012237476545E073-32662
chr2237476609237479749E073-29458
chr2237479804237480012E073-29195
chr2237480080237480193E073-29014
chr2237476609237479749E074-29458
chr2237479804237480012E074-29195
chr2237480080237480193E074-29014
chr2237480285237480401E074-28806
chr2237480652237480707E074-28500
chr2237480715237480784E074-28423
chr2237476609237479749E082-29458
chr2237479804237480012E082-29195
chr2237480285237480401E082-28806
chr2237480652237480707E082-28500
chr2237480715237480784E082-28423