rs3824339

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

PAX5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0260 (7806/29940,GnomAD)
A=0247 (7201/29118,TOPMED)
A=0315 (1577/5008,1000G)
A=0274 (1056/3854,ALSPAC)
A=0277 (1028/3708,TWINSUK)

Position: chr9:36885749 (GRCh38.p7) (9p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.36885749G>A
GRCh38.p7 chr 9	NC_000009.12:g.36885749G>T
GRCh37.p13 chr 9	NC_000009.11:g.36885746G>A
GRCh37.p13 chr 9	NC_000009.11:g.36885746G>T
PAX5 RefSeqGene	NG_033894.1:g.153731C>T
PAX5 RefSeqGene	NG_033894.1:g.153731C>A

Gene: PAX5, paired box 5(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PAX5 transcript variant 2	NM_001280547.1:c.	N/A	Intron Variant
PAX5 transcript variant 3	NM_001280548.1:c.	N/A	Intron Variant
PAX5 transcript variant 4	NM_001280549.1:c.	N/A	Intron Variant
PAX5 transcript variant 5	NM_001280550.1:c.	N/A	Intron Variant
PAX5 transcript variant 6	NM_001280551.1:c.	N/A	Intron Variant
PAX5 transcript variant 7	NM_001280552.1:c.	N/A	Intron Variant
PAX5 transcript variant 8	NM_001280553.1:c.	N/A	Intron Variant
PAX5 transcript variant 9	NM_001280554.1:c.	N/A	Intron Variant
PAX5 transcript variant 10	NM_001280555.1:c.	N/A	Intron Variant
PAX5 transcript variant 11	NM_001280556.1:c.	N/A	Intron Variant
PAX5 transcript variant 1	NM_016734.2:c.	N/A	Intron Variant
PAX5 transcript variant 12	NR_103999.1:n.	N/A	Intron Variant
PAX5 transcript variant 13	NR_104000.1:n.	N/A	Intron Variant
PAX5 transcript variant X3	XM_005251481.4:c.	N/A	Intron Variant
PAX5 transcript variant X1	XM_011517896.2:c.	N/A	Intron Variant
PAX5 transcript variant X2	XM_011517897.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.834	A=0.166
1000Genomes	American	Sub	694	G=0.610	A=0.390
1000Genomes	East Asian	Sub	1008	G=0.421	A=0.579
1000Genomes	Europe	Sub	1006	G=0.720	A=0.280
1000Genomes	Global	Study-wide	5008	G=0.685	A=0.315
1000Genomes	South Asian	Sub	978	G=0.780	A=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.726	A=0.274
The Genome Aggregation Database	African	Sub	8728	G=0.836	T=0.000
The Genome Aggregation Database	American	Sub	834	G=0.610	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1610	G=0.440	T=0.000
The Genome Aggregation Database	Europe	Sub	18466	G=0.725	T=0.000
The Genome Aggregation Database	Global	Study-wide	29940	G=0.739	T=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.760	T=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.752	A=0.247
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.723	A=0.277

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
rs3824339	0.000327	alcohol dependence	21314694

eQTL of rs3824339 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 rs3824339 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.