rs198966

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

KLK4 : Synonymous Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0009 (1200/121240,ExAC)
A=0031 (932/29910,GnomAD)
A=0050 (1462/29118,TOPMED)
A=0034 (168/5008,1000G)

Position: chr19:50908754 (GRCh38.p7) (19q13.41)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.50908754G>A
GRCh37.p13 chr 19	NC_000019.9:g.51412010G>A
KLK4 RefSeqGene	NG_012154.2:g.6985C>T

Gene: KLK4, kallikrein related peptidase 4(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KLK4 transcript variant 1	NM_004917.4:c.300C>T	S [AGC]> S [AGT]	Coding Sequence Variant
kallikrein-4 isoform 1 preproprotein	NP_004908.4:p.Ser...NP_004908.4:p.Ser100=	S [Ser]> S [Ser]	Synonymous Variant
KLK4 transcript variant 2	NM_001302961.1:c....NM_001302961.1:c.15C>T	S [AGC]> S [AGT]	Coding Sequence Variant
kallikrein-4 isoform 2	NP_001289890.1:p....NP_001289890.1:p.Ser5=	S [Ser]> S [Ser]	Synonymous Variant
KLK4 transcript variant 3	NR_126566.1:n.293C>T	C>T	Non Coding Transcript Variant
KLK4 transcript variant X1	XM_011527545.2:c....XM_011527545.2:c.300C>T	S [AGC]> S [AGT]	Coding Sequence Variant
kallikrein-4 isoform X1	XP_011525847.1:p....XP_011525847.1:p.Ser100=	S [Ser]> S [Ser]	Synonymous Variant
KLK4 transcript variant X2	XM_005259441.4:c....XM_005259441.4:c.15C>T	S [AGC]> S [AGT]	Coding Sequence Variant
kallikrein-4 isoform X2	XP_005259498.2:p....XP_005259498.2:p.Ser5=	S [Ser]> S [Ser]	Synonymous Variant
KLK4 transcript variant X3	XM_011527546.2:c....XM_011527546.2:c.300C>T	S [AGC]> S [AGT]	Coding Sequence Variant
kallikrein-4 isoform X3	XP_011525848.1:p....XP_011525848.1:p.Ser100=	S [Ser]> S [Ser]	Synonymous Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.878	A=0.122
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.998	A=0.002
1000Genomes	Global	Study-wide	5008	G=0.966	A=0.034
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Exome Aggregation Consortium	American	Sub	21954	G=0.946	A=0.053
The Exome Aggregation Consortium	Asian	Sub	25156	G=1.000	A=0.000
The Exome Aggregation Consortium	Europe	Sub	73224	G=0.999	A=0.000
The Exome Aggregation Consortium	Global	Study-wide	121240	G=0.990	A=0.009
The Exome Aggregation Consortium	Other	Sub	906	G=1.000	A=0.000
The Genome Aggregation Database	African	Sub	8708	G=0.894	A=0.106
The Genome Aggregation Database	American	Sub	836	G=1.000	A=0.000
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18444	G=0.999	A=0.000
The Genome Aggregation Database	Global	Study-wide	29910	G=0.968	A=0.031
The Genome Aggregation Database	Other	Sub	302	G=1.000	A=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.949	A=0.050

PMID	Title	Author	Journal
22481050	Genetic influences on craving for alcohol.	Agrawal A	Addict Behav
22970239	Genetic association of the KLK4 locus with risk of prostate cancer.	Lose F	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs198966	2.61E-05	alcohol craving with or without dependence	22481050

eQTL of rs198966 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 rs198966 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 )
chr19	51432726	51432821	E071	20716