rs1520780

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0371 (11121/29910,GnomAD)
A=0431 (12569/29118,TOPMED)
A=0466 (2334/5008,1000G)
A=0231 (891/3854,ALSPAC)
A=0214 (795/3708,TWINSUK)

Position: chr12:118601920 (GRCh38.p7) (12q24.23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 64 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.118601920G>A
GRCh37.p13 chr 12	NC_000012.11:g.119039725G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.321	A=0.679
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.417	A=0.583
1000Genomes	Europe	Sub	1006	G=0.773	A=0.227
1000Genomes	Global	Study-wide	5008	G=0.534	A=0.466
1000Genomes	South Asian	Sub	978	G=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.769	A=0.231
The Genome Aggregation Database	African	Sub	8696	G=0.352	A=0.648
The Genome Aggregation Database	American	Sub	838	G=0.610	A=0.390
The Genome Aggregation Database	East Asian	Sub	1614	G=0.384	A=0.616
The Genome Aggregation Database	Europe	Sub	18460	G=0.780	A=0.220
The Genome Aggregation Database	Global	Study-wide	29910	G=0.628	A=0.371
The Genome Aggregation Database	Other	Sub	302	G=0.650	A=0.350
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.568	A=0.431
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.786	A=0.214

PMID	Title	Author	Journal
24277619	ALDH2 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 EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs1520780	0.000557	alcohol consumption (maxi-drinks)	24277619

eQTL of rs1520780 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 rs1520780 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 )
chr12	119019092	119019677	E067	-20048
chr12	119019709	119020258	E067	-19467
chr12	118996419	118996499	E070	-43226
chr12	118996813	118997010	E070	-42715
chr12	119019092	119019677	E070	-20048
chr12	119019709	119020258	E070	-19467
chr12	119020500	119020655	E070	-19070
chr12	119020738	119021039	E070	-18686
chr12	119048709	119048821	E070	8984
chr12	119048843	119049038	E070	9118
chr12	118994060	118994156	E071	-45569
chr12	118996813	118997010	E071	-42715
chr12	118997118	118997330	E071	-42395
chr12	118996813	118997010	E074	-42715
chr12	118997118	118997330	E074	-42395
chr12	118997798	118997880	E074	-41845
chr12	118997940	118998008	E074	-41717
chr12	118998162	118998250	E074	-41475
chr12	118993639	118993689	E081	-46036
chr12	118997940	118998008	E081	-41717
chr12	119015445	119015499	E081	-24226
chr12	119015712	119015922	E081	-23803
chr12	119016089	119016140	E081	-23585
chr12	119016263	119016502	E081	-23223
chr12	119016849	119017006	E081	-22719
chr12	119018819	119018930	E081	-20795
chr12	119019092	119019677	E081	-20048
chr12	119019709	119020258	E081	-19467
chr12	119020500	119020655	E081	-19070
chr12	119020738	119021039	E081	-18686
chr12	119026226	119026276	E081	-13449
chr12	119027366	119027496	E081	-12229
chr12	119027824	119027926	E081	-11799
chr12	119028073	119028123	E081	-11602
chr12	119028178	119028232	E081	-11493
chr12	119028326	119028481	E081	-11244
chr12	119028541	119029120	E081	-10605
chr12	119043471	119043647	E081	3746
chr12	119043701	119043779	E081	3976
chr12	119043852	119043902	E081	4127
chr12	119044091	119044158	E081	4366
chr12	119044549	119044606	E081	4824
chr12	119044624	119044818	E081	4899
chr12	119075674	119076314	E081	35949
chr12	119076363	119076444	E081	36638
chr12	118993388	118993445	E082	-46280
chr12	118993639	118993689	E082	-46036
chr12	118994060	118994156	E082	-45569
chr12	118994398	118994438	E082	-45287
chr12	118996813	118997010	E082	-42715
chr12	118997118	118997330	E082	-42395
chr12	119016263	119016502	E082	-23223
chr12	119018819	119018930	E082	-20795
chr12	119019092	119019677	E082	-20048
chr12	119019709	119020258	E082	-19467
chr12	119027366	119027496	E082	-12229
chr12	119027824	119027926	E082	-11799
chr12	119028073	119028123	E082	-11602
chr12	119028178	119028232	E082	-11493
chr12	119028326	119028481	E082	-11244
chr12	119028541	119029120	E082	-10605
chr12	119047568	119047751	E082	7843
chr12	119075674	119076314	E082	35949
chr12	119076363	119076444	E082	36638