SNP Detail Info-rs4894243

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC105373760 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0441 (13201/29878,GnomAD)
C==0492 (14340/29118,TOPMED)
C==0383 (1920/5008,1000G)
C==0367 (1415/3854,ALSPAC)
C==0384 (1424/3708,TWINSUK)

Position: chr2:177097413 (GRCh38.p7) (2q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.177097413C>T
GRCh37.p13 chr 2	NC_000002.11:g.177962141C>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373760 transcript variant X1	XR_001739795.1:n.	N/A	Intron Variant
LOC105373760 transcript variant X3	XR_001739796.1:n.	N/A	Intron Variant
LOC105373760 transcript variant X2	XR_923622.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.669	T=0.331
1000Genomes	American	Sub	694	C=0.290	T=0.710
1000Genomes	East Asian	Sub	1008	C=0.201	T=0.799
1000Genomes	Europe	Sub	1006	C=0.420	T=0.580
1000Genomes	Global	Study-wide	5008	C=0.383	T=0.617
1000Genomes	South Asian	Sub	978	C=0.210	T=0.790
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.367	T=0.633
The Genome Aggregation Database	African	Sub	8682	C=0.635	T=0.365
The Genome Aggregation Database	American	Sub	834	C=0.270	T=0.730
The Genome Aggregation Database	East Asian	Sub	1612	C=0.203	T=0.797
The Genome Aggregation Database	Europe	Sub	18450	C=0.379	T=0.620
The Genome Aggregation Database	Global	Study-wide	29878	C=0.441	T=0.558
The Genome Aggregation Database	Other	Sub	300	C=0.430	T=0.570
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.492	T=0.507
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.384	T=0.616

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

SNP ID	p-value	Traits	Study
rs4894243	7.46E-05	alcohol dependence	19581569

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 )
chr2	177916653	177916740	E070	-45401
chr2	177916901	177916955	E070	-45186
chr2	177917070	177917313	E070	-44828
chr2	177917736	177917840	E070	-44301
chr2	177916901	177916955	E081	-45186
chr2	177917070	177917313	E081	-44828
chr2	177936905	177937174	E081	-24967
chr2	178011652	178011747	E082	49511

rs4894243