SNP Detail Info-rs10489326

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

KIAA0040 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0442 (13238/29888,GnomAD)
A==0423 (12333/29118,TOPMED)
A==0333 (1668/5008,1000G)
G=0496 (1911/3854,ALSPAC)
G=0489 (1812/3708,TWINSUK)

Position: chr1:175165541 (GRCh38.p7) (1q25.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 27 Enhancers around

Promoter: 8 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.175165541A>G
GRCh37.p13 chr 1	NC_000001.10:g.175134677A>G

Molecule type	Change	Amino acid[Codon]	SO Term
KIAA0040 transcript variant 1	NM_001162893.1:c.	N/A	Intron Variant
KIAA0040 transcript variant 3	NM_001162894.1:c.	N/A	Intron Variant
KIAA0040 transcript variant 4	NM_001162895.1:c.	N/A	Intron Variant
KIAA0040 transcript variant 5	NM_001319230.1:c.	N/A	Intron Variant
KIAA0040 transcript variant 6	NM_001319231.1:c.	N/A	Intron Variant
KIAA0040 transcript variant 2	NM_014656.2:c.	N/A	Intron Variant
KIAA0040 transcript variant X1	XM_017002909.1:c.	N/A	Intron Variant
KIAA0040 transcript variant X2	XM_017002910.1:c.	N/A	Intron Variant
KIAA0040 transcript variant X3	XM_017002911.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.385	G=0.615
1000Genomes	American	Sub	694	A=0.340	G=0.660
1000Genomes	East Asian	Sub	1008	A=0.148	G=0.852
1000Genomes	Europe	Sub	1006	A=0.476	G=0.524
1000Genomes	Global	Study-wide	5008	A=0.333	G=0.667
1000Genomes	South Asian	Sub	978	A=0.300	G=0.700
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.504	G=0.496
The Genome Aggregation Database	African	Sub	8696	A=0.417	G=0.583
The Genome Aggregation Database	American	Sub	836	A=0.310	G=0.690
The Genome Aggregation Database	East Asian	Sub	1614	A=0.134	G=0.866
The Genome Aggregation Database	Europe	Sub	18440	A=0.490	G=0.509
The Genome Aggregation Database	Global	Study-wide	29888	A=0.442	G=0.557
The Genome Aggregation Database	Other	Sub	302	A=0.290	G=0.710
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.423	G=0.576
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.511	G=0.489

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
rs10489326	4.9E-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	-7039
chr1	175127726	175127793	E067	-6884
chr1	175121212	175121706	E069	-12971
chr1	175138495	175138718	E069	3818
chr1	175117508	175117593	E070	-17084
chr1	175131566	175131616	E070	-3061
chr1	175131702	175131793	E070	-2884
chr1	175131845	175132044	E070	-2633
chr1	175132208	175132358	E070	-2319
chr1	175169465	175169525	E071	34788
chr1	175169774	175170871	E071	35097
chr1	175121212	175121706	E072	-12971
chr1	175173548	175173704	E073	38871
chr1	175173714	175173889	E073	39037
chr1	175115170	175115364	E081	-19313
chr1	175115429	175115500	E081	-19177
chr1	175115737	175116333	E081	-18344
chr1	175116438	175116534	E081	-18143
chr1	175116763	175117071	E081	-17606
chr1	175117325	175117401	E081	-17276
chr1	175117508	175117593	E081	-17084
chr1	175120951	175121040	E081	-13637
chr1	175121212	175121706	E081	-12971
chr1	175127262	175127638	E082	-7039
chr1	175127726	175127793	E082	-6884
chr1	175173548	175173704	E082	38871
chr1	175173714	175173889	E082	39037

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	175160861	175163201	E067	26184
chr1	175160861	175163201	E068	26184
chr1	175160861	175163201	E069	26184
chr1	175160861	175163201	E071	26184
chr1	175160861	175163201	E072	26184
chr1	175160861	175163201	E073	26184
chr1	175160861	175163201	E074	26184
chr1	175160861	175163201	E082	26184

rs10489326