rs12798524

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0200 (6009/29952,GnomAD)
G=0216 (6295/29118,TOPMED)
G=0220 (1102/5008,1000G)
G=0179 (688/3854,ALSPAC)
G=0178 (659/3708,TWINSUK)

Position: chr11:58671182 (GRCh38.p7) (11q12.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 75 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.58671182A>G
GRCh37.p13 chr 11	NC_000011.9:g.58438655A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.789	G=0.211
1000Genomes	American	Sub	694	A=0.730	G=0.270
1000Genomes	East Asian	Sub	1008	A=0.793	G=0.207
1000Genomes	Europe	Sub	1006	A=0.814	G=0.186
1000Genomes	Global	Study-wide	5008	A=0.780	G=0.220
1000Genomes	South Asian	Sub	978	A=0.760	G=0.240
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.821	G=0.179
The Genome Aggregation Database	African	Sub	8722	A=0.791	G=0.209
The Genome Aggregation Database	American	Sub	838	A=0.740	G=0.260
The Genome Aggregation Database	East Asian	Sub	1620	A=0.820	G=0.180
The Genome Aggregation Database	Europe	Sub	18470	A=0.805	G=0.194
The Genome Aggregation Database	Global	Study-wide	29952	A=0.799	G=0.200
The Genome Aggregation Database	Other	Sub	302	A=0.720	G=0.280
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.783	G=0.216
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.822	G=0.178

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs12798524	0.0006	alcohol dependence	20201924

eQTL of rs12798524 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr11:58438655	LPXN	ENSG00000110031.8	A>G	1.6545e-3	92962	Frontal_Cortex_BA9

meQTL of rs12798524 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 )
chr11	58389499	58389539	E067	-49116
chr11	58389632	58389717	E067	-48938
chr11	58389864	58390141	E067	-48514
chr11	58390257	58390307	E067	-48348
chr11	58395047	58395837	E067	-42818
chr11	58407040	58407090	E067	-31565
chr11	58407226	58407272	E067	-31383
chr11	58407412	58407532	E067	-31123
chr11	58407620	58407707	E067	-30948
chr11	58407775	58407851	E067	-30804
chr11	58407864	58408367	E067	-30288
chr11	58408436	58408671	E067	-29984
chr11	58442769	58442819	E067	4114
chr11	58389864	58390141	E068	-48514
chr11	58395047	58395837	E068	-42818
chr11	58396039	58396197	E068	-42458
chr11	58397018	58397178	E068	-41477
chr11	58407040	58407090	E068	-31565
chr11	58407226	58407272	E068	-31383
chr11	58407412	58407532	E068	-31123
chr11	58407620	58407707	E068	-30948
chr11	58407775	58407851	E068	-30804
chr11	58407864	58408367	E068	-30288
chr11	58389632	58389717	E069	-48938
chr11	58389864	58390141	E069	-48514
chr11	58390257	58390307	E069	-48348
chr11	58395047	58395837	E069	-42818
chr11	58396039	58396197	E069	-42458
chr11	58407412	58407532	E069	-31123
chr11	58407620	58407707	E069	-30948
chr11	58407775	58407851	E069	-30804
chr11	58407864	58408367	E069	-30288
chr11	58408436	58408671	E069	-29984
chr11	58407864	58408367	E070	-30288
chr11	58389864	58390141	E071	-48514
chr11	58390257	58390307	E071	-48348
chr11	58394509	58394647	E071	-44008
chr11	58394648	58394770	E071	-43885
chr11	58395047	58395837	E071	-42818
chr11	58396039	58396197	E071	-42458
chr11	58406723	58406796	E071	-31859
chr11	58406816	58406933	E071	-31722
chr11	58407040	58407090	E071	-31565
chr11	58407226	58407272	E071	-31383
chr11	58407412	58407532	E071	-31123
chr11	58407620	58407707	E071	-30948
chr11	58407775	58407851	E071	-30804
chr11	58407864	58408367	E071	-30288
chr11	58408436	58408671	E071	-29984
chr11	58408748	58409269	E071	-29386
chr11	58442969	58443517	E071	4314
chr11	58394509	58394647	E072	-44008
chr11	58394648	58394770	E072	-43885
chr11	58395047	58395837	E072	-42818
chr11	58396039	58396197	E072	-42458
chr11	58407620	58407707	E072	-30948
chr11	58407775	58407851	E072	-30804
chr11	58407864	58408367	E072	-30288
chr11	58395047	58395837	E073	-42818
chr11	58407040	58407090	E073	-31565
chr11	58407226	58407272	E073	-31383
chr11	58407412	58407532	E073	-31123
chr11	58407620	58407707	E073	-30948
chr11	58407775	58407851	E073	-30804
chr11	58407864	58408367	E073	-30288
chr11	58408436	58408671	E073	-29984
chr11	58408748	58409269	E073	-29386
chr11	58394648	58394770	E074	-43885
chr11	58395047	58395837	E074	-42818
chr11	58396039	58396197	E074	-42458
chr11	58407412	58407532	E074	-31123
chr11	58407620	58407707	E074	-30948
chr11	58407775	58407851	E074	-30804
chr11	58407864	58408367	E074	-30288
chr11	58408436	58408671	E074	-29984