rs462145

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

WFDC3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0406 (12136/29890,GnomAD)
A==0458 (2296/5008,1000G)
A==0363 (1400/3854,ALSPAC)
A==0373 (1383/3708,TWINSUK)

Position: chr20:45749572 (GRCh38.p7) (20q13.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 16 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.45749572A>G
GRCh37.p13 chr 20	NC_000020.10:g.44378211A>G

Gene: WFDC3, WAP four-disulfide core domain 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
WFDC3 transcript	NM_080614.1:c.	N/A	Genic Downstream Transcript Variant
WFDC3 transcript variant X2	XM_017027668.1:c.	N/A	Intron Variant
WFDC3 transcript variant X1	XM_011528553.2:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.500	G=0.500
1000Genomes	American	Sub	694	A=0.300	G=0.700
1000Genomes	East Asian	Sub	1008	A=0.473	G=0.527
1000Genomes	Europe	Sub	1006	A=0.387	G=0.613
1000Genomes	Global	Study-wide	5008	A=0.458	G=0.542
1000Genomes	South Asian	Sub	978	A=0.570	G=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.363	G=0.637
The Genome Aggregation Database	African	Sub	8704	A=0.461	G=0.539
The Genome Aggregation Database	American	Sub	838	A=0.290	G=0.710
The Genome Aggregation Database	East Asian	Sub	1612	A=0.514	G=0.486
The Genome Aggregation Database	Europe	Sub	18434	A=0.373	G=0.626
The Genome Aggregation Database	Global	Study-wide	29890	A=0.406	G=0.594
The Genome Aggregation Database	Other	Sub	302	A=0.520	G=0.480
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.373	G=0.627

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs462145	0.000896	alcohol dependence	21314694

eQTL of rs462145 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	3.1956e-18	-42360	Cerebellum
Chr20:44378211	SNX21	ENSG00000124104.14	A>G	9.8821e-13	-84238	Cerebellum
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	6.7687e-18	-42360	Frontal_Cortex_BA9
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	7.2384e-17	-42360	Hypothalamus
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	2.0973e-22	-42360	Cortex
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	4.2979e-12	-42360	Cerebellar_Hemisphere
Chr20:44378211	SNX21	ENSG00000124104.14	A>G	1.0439e-10	-84238	Cerebellar_Hemisphere
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	3.9571e-23	-42360	Caudate_basal_ganglia
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	1.3786e-6	-42360	Brain_Spinal_cord_cervical
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	1.5287e-17	-42360	Hippocampus
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	2.3005e-9	-42360	Substantia_nigra
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	3.3630e-17	-42360	Putamen_basal_ganglia
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	1.0744e-18	-42360	Anterior_cingulate_cortex
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	1.0070e-19	-42360	Nucleus_accumbens_basal_ganglia
Chr20:44378211	WFDC3	ENSG00000124116.14	A>G	3.4559e-10	-42360	Amygdala

meQTL of rs462145 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg23252815	chr20:44420276	DNTTIP1\|WFDC3	-0.0428712520133914	8.4400e-13
cg14780681	chr20:44420720	DNTTIP1\|WFDC3	-0.00580149145749031	1.5064e-9

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 )
chr20	44406659	44408661	E067	28448
chr20	44406659	44408661	E068	28448
chr20	44399423	44400464	E069	21212
chr20	44406659	44408661	E069	28448
chr20	44399423	44400464	E070	21212
chr20	44400487	44400643	E070	22276
chr20	44399423	44400464	E071	21212
chr20	44406659	44408661	E072	28448
chr20	44399423	44400464	E073	21212
chr20	44400487	44400643	E073	22276
chr20	44406659	44408661	E073	28448
chr20	44399423	44400464	E074	21212
chr20	44406659	44408661	E074	28448
chr20	44419860	44419917	E074	41649
chr20	44399423	44400464	E082	21212
chr20	44402885	44402976	E082	24674

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	44420148	44421786	E067	41937
chr20	44420148	44421786	E068	41937
chr20	44420148	44421786	E069	41937
chr20	44420148	44421786	E070	41937
chr20	44420148	44421786	E071	41937
chr20	44420148	44421786	E072	41937
chr20	44420148	44421786	E073	41937
chr20	44420148	44421786	E074	41937
chr20	44420148	44421786	E081	41937
chr20	44420148	44421786	E082	41937