SNP Detail Info-rs4356270

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105369901 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0443 (13280/29952,GnomAD)
G==0494 (14406/29118,TOPMED)
A=0436 (2183/5008,1000G)
A=0375 (1447/3854,ALSPAC)
A=0364 (1351/3708,TWINSUK)

Position: chr12:91925439 (GRCh38.p7) (12q21.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 14 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.91925439G>A
GRCh37.p13 chr 12	NC_000012.11:g.92319215G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105369901 transcript variant X2	XR_001749253.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X3	XR_001749254.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X4	XR_001749255.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X5	XR_001749256.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X1	XR_945202.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.297	A=0.703
1000Genomes	American	Sub	694	G=0.560	A=0.440
1000Genomes	East Asian	Sub	1008	G=0.905	A=0.095
1000Genomes	Europe	Sub	1006	G=0.613	A=0.387
1000Genomes	Global	Study-wide	5008	G=0.564	A=0.436
1000Genomes	South Asian	Sub	978	G=0.530	A=0.470
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.625	A=0.375
The Genome Aggregation Database	African	Sub	8722	G=0.317	A=0.683
The Genome Aggregation Database	American	Sub	834	G=0.580	A=0.420
The Genome Aggregation Database	East Asian	Sub	1622	G=0.880	A=0.120
The Genome Aggregation Database	Europe	Sub	18472	G=0.638	A=0.361
The Genome Aggregation Database	Global	Study-wide	29952	G=0.556	A=0.443
The Genome Aggregation Database	Other	Sub	302	G=0.650	A=0.350
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.494	A=0.505
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.636	A=0.364

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
23691058	Dosage transmission disequilibrium test (dTDT) for linkage and association detection.	Zhang Z	PLoS One

SNP ID	p-value	Traits	Study
rs4356270	0.00000842	alcohol dependence	23691058
rs4356270	0.000044	alcohol dependence	20201924
rs4356270	0.0000444	alcoholism	pha002892
rs4356270	0.00036	alcohol dependence(early age of onset)	20201924

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 )
chr12	92285227	92285267	E070	-33948
chr12	92285612	92285704	E070	-33511
chr12	92285769	92286134	E070	-33081
chr12	92286204	92286429	E070	-32786
chr12	92286494	92286710	E070	-32505
chr12	92290484	92291024	E070	-28191
chr12	92291102	92291152	E070	-28063
chr12	92278137	92278506	E081	-40709
chr12	92285769	92286134	E081	-33081
chr12	92286204	92286429	E081	-32786
chr12	92286494	92286710	E081	-32505
chr12	92291102	92291152	E081	-28063
chr12	92285769	92286134	E082	-33081
chr12	92286204	92286429	E082	-32786

rs4356270