SNP Detail Info-rs12094153

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

TNN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0367 (10968/29866,GnomAD)
A=0319 (9315/29118,TOPMED)
A=0256 (1282/5008,1000G)
A=0418 (1612/3854,ALSPAC)
A=0452 (1676/3708,TWINSUK)

Position: chr1:175124889 (GRCh38.p7) (1q25.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 21 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.175124889G>A
GRCh37.p13 chr 1	NC_000001.10:g.175094025G>A

Molecule type	Change	Amino acid[Codon]	SO Term
TNN transcript	NM_022093.1:c.	N/A	Intron Variant
TNN transcript variant X1	XM_017002048.1:c.	N/A	Intron Variant
TNN transcript variant X2	XM_017002049.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.724	A=0.276
1000Genomes	American	Sub	694	G=0.730	A=0.270
1000Genomes	East Asian	Sub	1008	G=0.903	A=0.097
1000Genomes	Europe	Sub	1006	G=0.562	A=0.438
1000Genomes	Global	Study-wide	5008	G=0.744	A=0.256
1000Genomes	South Asian	Sub	978	G=0.810	A=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.582	A=0.418
The Genome Aggregation Database	African	Sub	8678	G=0.724	A=0.276
The Genome Aggregation Database	American	Sub	836	G=0.760	A=0.240
The Genome Aggregation Database	East Asian	Sub	1610	G=0.912	A=0.088
The Genome Aggregation Database	Europe	Sub	18442	G=0.558	A=0.441
The Genome Aggregation Database	Global	Study-wide	29866	G=0.632	A=0.367
The Genome Aggregation Database	Other	Sub	300	G=0.700	A=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.680	A=0.319
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.548	A=0.452

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology

SNP ID	p-value	Traits	Study
rs12094153	5.49E-05	alcohol dependence	21703634

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 )
chr1	175127262	175127638	E067	33237
chr1	175127726	175127793	E067	33701
chr1	175121212	175121706	E069	27187
chr1	175138495	175138718	E069	44470
chr1	175117508	175117593	E070	23483
chr1	175131566	175131616	E070	37541
chr1	175131702	175131793	E070	37677
chr1	175131845	175132044	E070	37820
chr1	175132208	175132358	E070	38183
chr1	175121212	175121706	E072	27187
chr1	175115170	175115364	E081	21145
chr1	175115429	175115500	E081	21404
chr1	175115737	175116333	E081	21712
chr1	175116438	175116534	E081	22413
chr1	175116763	175117071	E081	22738
chr1	175117325	175117401	E081	23300
chr1	175117508	175117593	E081	23483
chr1	175120951	175121040	E081	26926
chr1	175121212	175121706	E081	27187
chr1	175127262	175127638	E082	33237
chr1	175127726	175127793	E082	33701

rs12094153