rs10446425

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

ULK4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0457 (13695/29940,GnomAD)
C==0439 (12784/29118,TOPMED)
C==0413 (2069/5008,1000G)
A=0475 (1829/3854,ALSPAC)
A=0475 (1762/3708,TWINSUK)

Position: chr3:41443340 (GRCh38.p7) (3p22.1)

Phenotype: AD | ND

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.41443340C>A
GRCh37.p13 chr 3	NC_000003.11:g.41484831C>A

Gene: ULK4, unc-51 like kinase 4(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ULK4 transcript variant 2	NM_001322500.1:c.	N/A	Intron Variant
ULK4 transcript variant 3	NM_001322501.1:c.	N/A	Intron Variant
ULK4 transcript variant 1	NM_017886.3:c.	N/A	Intron Variant
ULK4 transcript variant 4	NR_136342.1:n.	N/A	Intron Variant
ULK4 transcript variant X1	XM_011533874.2:c.	N/A	Intron Variant
ULK4 transcript variant X7	XM_011533880.2:c.	N/A	Intron Variant
ULK4 transcript variant X2	XM_017006711.1:c.	N/A	Intron Variant
ULK4 transcript variant X3	XM_017006712.1:c.	N/A	Intron Variant
ULK4 transcript variant X4	XR_001740188.1:n.	N/A	Genic Downstream Transcript Variant
ULK4 transcript variant X6	XR_001740189.1:n.	N/A	Genic Downstream Transcript Variant
ULK4 transcript variant X5	XR_427279.3:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.315	A=0.685
1000Genomes	American	Sub	694	C=0.540	A=0.460
1000Genomes	East Asian	Sub	1008	C=0.327	A=0.673
1000Genomes	Europe	Sub	1006	C=0.521	A=0.479
1000Genomes	Global	Study-wide	5008	C=0.413	A=0.587
1000Genomes	South Asian	Sub	978	C=0.430	A=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.525	A=0.475
The Genome Aggregation Database	African	Sub	8718	C=0.353	A=0.647
The Genome Aggregation Database	American	Sub	836	C=0.570	A=0.430
The Genome Aggregation Database	East Asian	Sub	1614	C=0.297	A=0.703
The Genome Aggregation Database	Europe	Sub	18470	C=0.514	A=0.485
The Genome Aggregation Database	Global	Study-wide	29940	C=0.457	A=0.542
The Genome Aggregation Database	Other	Sub	302	C=0.530	A=0.470
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.439	A=0.561
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.525	A=0.475

PMID	Title	Author	Journal
22096494	A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.	Zuo L	PLoS One
22488850	Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.	Zuo L	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs10446425	0.0000034	alcohol dependence	22096494
rs10446425	0.0000083	alcohol and nictotine co-dependence	22488850

eQTL of rs10446425 in Brain tissues (GTEx Analysis Release V7)

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

meQTL of rs10446425 in Fetal Brain

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

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr3	41478511	41478790	E070	-6041
chr3	41478511	41478790	E081	-6041