SNP Detail Info-rs6540681

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0148 (4450/29886,GnomAD)
A==0174 (5082/29116,TOPMED)
A==0155 (774/5008,1000G)
A==0169 (652/3854,ALSPAC)
A==0183 (680/3708,TWINSUK)

Position: chr1:211320231 (GRCh38.p7) (1q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 38 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.211320231A>G
GRCh37.p13 chr 1	NC_000001.10:g.211493573A>G

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.185	G=0.815
1000Genomes	American	Sub	694	A=0.100	G=0.900
1000Genomes	East Asian	Sub	1008	A=0.046	G=0.954
1000Genomes	Europe	Sub	1006	A=0.189	G=0.811
1000Genomes	Global	Study-wide	5008	A=0.155	G=0.845
1000Genomes	South Asian	Sub	978	A=0.230	G=0.770
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.169	G=0.831
The Genome Aggregation Database	African	Sub	8702	A=0.175	G=0.825
The Genome Aggregation Database	American	Sub	834	A=0.080	G=0.920
The Genome Aggregation Database	East Asian	Sub	1620	A=0.028	G=0.972
The Genome Aggregation Database	Europe	Sub	18428	A=0.150	G=0.849
The Genome Aggregation Database	Global	Study-wide	29886	A=0.148	G=0.851
The Genome Aggregation Database	Other	Sub	302	A=0.150	G=0.850
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.174	G=0.825
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.183	G=0.817

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

SNP ID	p-value	Traits	Study
rs6540681	0.00068	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:211493573	SNX25P1	ENSG00000236809.2	A>G	3.0509e-4	-96794	Caudate_basal_ganglia

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	211460582	211460892	E067	-32681
chr1	211485839	211485893	E067	-7680
chr1	211505339	211505411	E067	11766
chr1	211505532	211505639	E067	11959
chr1	211505785	211505836	E067	12212
chr1	211454758	211454944	E068	-38629
chr1	211486350	211486512	E068	-7061
chr1	211505532	211505639	E068	11959
chr1	211505785	211505836	E068	12212
chr1	211506322	211506421	E068	12749
chr1	211478423	211478642	E069	-14931
chr1	211486350	211486512	E069	-7061
chr1	211505339	211505411	E069	11766
chr1	211505532	211505639	E069	11959
chr1	211505785	211505836	E069	12212
chr1	211499216	211499266	E070	5643
chr1	211445505	211445568	E071	-48005
chr1	211485839	211485893	E071	-7680
chr1	211486350	211486512	E071	-7061
chr1	211505339	211505411	E071	11766
chr1	211505532	211505639	E071	11959
chr1	211505785	211505836	E071	12212
chr1	211454383	211454577	E072	-38996
chr1	211454758	211454944	E072	-38629
chr1	211505339	211505411	E073	11766
chr1	211505532	211505639	E073	11959
chr1	211505785	211505836	E073	12212
chr1	211519015	211519392	E073	25442
chr1	211445505	211445568	E074	-48005
chr1	211486350	211486512	E074	-7061
chr1	211502291	211502413	E081	8718
chr1	211502483	211502690	E081	8910
chr1	211505339	211505411	E081	11766
chr1	211505532	211505639	E081	11959
chr1	211505785	211505836	E081	12212
chr1	211530454	211530649	E081	36881
chr1	211502291	211502413	E082	8718
chr1	211502483	211502690	E082	8910

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	211499514	211501335	E067	5941
chr1	211499514	211501335	E068	5941
chr1	211499514	211501335	E069	5941
chr1	211499514	211501335	E070	5941
chr1	211499514	211501335	E071	5941
chr1	211499514	211501335	E072	5941
chr1	211499514	211501335	E073	5941
chr1	211499514	211501335	E074	5941
chr1	211499514	211501335	E081	5941
chr1	211499514	211501335	E082	5941

rs6540681