SNP Detail Info-rs3740169

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

CUBN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0281 (8414/29946,GnomAD)
A=0335 (9754/29118,TOPMED)
A=0326 (1633/5008,1000G)
A=0201 (776/3854,ALSPAC)
A=0215 (799/3708,TWINSUK)

Position: chr10:16831548 (GRCh38.p7) (10p13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 17 Enhancers around

Promoter: 4 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
CUBN transcript	NM_001081.3:c.	N/A	Intron Variant
CUBN transcript variant X2	XM_011519709.2:c.	N/A	Intron Variant
CUBN transcript variant X3	XM_011519710.2:c.	N/A	Intron Variant
CUBN transcript variant X4	XM_011519711.2:c.	N/A	Intron Variant
CUBN transcript variant X1	XM_011519708.2:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.500	A=0.500
1000Genomes	American	Sub	694	G=0.770	A=0.230
1000Genomes	East Asian	Sub	1008	G=0.628	A=0.372
1000Genomes	Europe	Sub	1006	G=0.805	A=0.195
1000Genomes	Global	Study-wide	5008	G=0.674	A=0.326
1000Genomes	South Asian	Sub	978	G=0.760	A=0.240
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.799	A=0.201
The Genome Aggregation Database	African	Sub	8702	G=0.549	A=0.451
The Genome Aggregation Database	American	Sub	838	G=0.770	A=0.23,
The Genome Aggregation Database	East Asian	Sub	1612	G=0.639	A=0.361
The Genome Aggregation Database	Europe	Sub	18492	G=0.803	A=0.197
The Genome Aggregation Database	Global	Study-wide	29946	G=0.719	A=0.281
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.24,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.665	A=0.335
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.785	A=0.215

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs3740169	0.000513	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr10	23581784	23581895	E067	2044
chr10	23581784	23581895	E068	2044
chr10	23570320	23570596	E070	-9144
chr10	23581784	23581895	E071	2044
chr10	23582633	23582697	E071	2893
chr10	23582760	23582830	E071	3020
chr10	23582633	23582697	E072	2893
chr10	23582760	23582830	E072	3020
chr10	23580626	23580888	E073	886
chr10	23580172	23580264	E074	432
chr10	23580626	23580888	E074	886
chr10	23580626	23580888	E081	886
chr10	23582633	23582697	E081	2893
chr10	23582633	23582697	E082	2893
chr10	23582760	23582830	E082	3020
chr10	23582838	23582899	E082	3098
chr10	23583043	23583227	E082	3303

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr10	23580477	23580624	E067	737
chr10	23580477	23580624	E069	737
chr10	23580477	23580624	E071	737
chr10	23580477	23580624	E072	737

rs3740169