rs7639979

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PRSS46 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0224 (6726/29944,GnomAD)
G=0273 (7952/29118,TOPMED)
G=0257 (1287/5008,1000G)
G=0138 (531/3854,ALSPAC)
G=0137 (508/3708,TWINSUK)

Position: chr3:46733286 (GRCh38.p7) (3p21.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 53 Enhancers around

Promoter: 13 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.46733286A>G
GRCh37.p13 chr 3	NC_000003.11:g.46774776A>G

Gene: PRSS46, protease, serine 46(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PRSS46 transcript	NM_001205271.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.542	G=0.458
1000Genomes	American	Sub	694	A=0.790	G=0.210
1000Genomes	East Asian	Sub	1008	A=0.847	G=0.153
1000Genomes	Europe	Sub	1006	A=0.857	G=0.143
1000Genomes	Global	Study-wide	5008	A=0.743	G=0.257
1000Genomes	South Asian	Sub	978	A=0.750	G=0.250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.862	G=0.138
The Genome Aggregation Database	African	Sub	8704	A=0.593	G=0.407
The Genome Aggregation Database	American	Sub	836	A=0.770	G=0.230
The Genome Aggregation Database	East Asian	Sub	1616	A=0.868	G=0.132
The Genome Aggregation Database	Europe	Sub	18486	A=0.851	G=0.148
The Genome Aggregation Database	Global	Study-wide	29944	A=0.775	G=0.224
The Genome Aggregation Database	Other	Sub	302	A=0.850	G=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.726	G=0.273
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.863	G=0.137

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
20220758	Understanding mechanisms underlying human gene expression variation with RNA sequencing.	Pickrell JK	Nature

P-Value

SNP ID	p-value	Traits	Study
rs7639979	0.000317	alcohol dependence	20201924

eQTL of rs7639979 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:46774776	PRSS45	ENSG00000188086.8	A>G	8.0486e-7	-78430	Nucleus_accumbens_basal_ganglia

meQTL of rs7639979 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	46735904	46735978	E067	-38798
chr3	46736055	46736398	E067	-38378
chr3	46736428	46738419	E067	-36357
chr3	46741224	46741391	E067	-33385
chr3	46741396	46741758	E067	-33018
chr3	46741831	46741886	E067	-32890
chr3	46742249	46742627	E067	-32149
chr3	46736428	46738419	E068	-36357
chr3	46738459	46738584	E068	-36192
chr3	46741224	46741391	E068	-33385
chr3	46741396	46741758	E068	-33018
chr3	46741831	46741886	E068	-32890
chr3	46742249	46742627	E068	-32149
chr3	46743779	46743866	E068	-30910
chr3	46743917	46743991	E068	-30785
chr3	46736428	46738419	E069	-36357
chr3	46741831	46741886	E069	-32890
chr3	46742249	46742627	E069	-32149
chr3	46743779	46743866	E069	-30910
chr3	46743917	46743991	E069	-30785
chr3	46746375	46747178	E069	-27598
chr3	46767055	46767135	E069	-7641
chr3	46767219	46767423	E069	-7353
chr3	46743779	46743866	E070	-30910
chr3	46743917	46743991	E070	-30785
chr3	46736428	46738419	E071	-36357
chr3	46738459	46738584	E071	-36192
chr3	46741224	46741391	E071	-33385
chr3	46741396	46741758	E071	-33018
chr3	46741831	46741886	E071	-32890
chr3	46743779	46743866	E071	-30910
chr3	46743917	46743991	E071	-30785
chr3	46735904	46735978	E072	-38798
chr3	46736055	46736398	E072	-38378
chr3	46736428	46738419	E072	-36357
chr3	46741224	46741391	E072	-33385
chr3	46741396	46741758	E072	-33018
chr3	46741831	46741886	E072	-32890
chr3	46735904	46735978	E073	-38798
chr3	46736055	46736398	E073	-38378
chr3	46736428	46738419	E073	-36357
chr3	46738459	46738584	E073	-36192
chr3	46741396	46741758	E073	-33018
chr3	46741831	46741886	E073	-32890
chr3	46742249	46742627	E073	-32149
chr3	46746375	46747178	E073	-27598
chr3	46741396	46741758	E074	-33018
chr3	46741831	46741886	E074	-32890
chr3	46742249	46742627	E074	-32149
chr3	46743779	46743866	E074	-30910
chr3	46742249	46742627	E081	-32149
chr3	46743779	46743866	E081	-30910
chr3	46743917	46743991	E081	-30785

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	46734032	46735874	E067	-38902
chr3	46734032	46735874	E068	-38902
chr3	46734032	46735874	E069	-38902
chr3	46734032	46735874	E070	-38902
chr3	46742732	46742842	E070	-31934
chr3	46734032	46735874	E071	-38902
chr3	46742732	46742842	E071	-31934
chr3	46734032	46735874	E072	-38902
chr3	46742732	46742842	E072	-31934
chr3	46734032	46735874	E073	-38902
chr3	46742732	46742842	E073	-31934
chr3	46734032	46735874	E074	-38902
chr3	46742732	46742842	E082	-31934