SNP Detail Info-rs3213609

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PEX1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0063 (6165/97702,ExAC)
G=0055 (1674/29990,GnomAD)
G=0069 (2026/29118,TOPMED)
A==0040 (528/12976,GO-ESP)
G=0106 (530/5008,1000G)
G=0017 (64/3854,ALSPAC)
G=0019 (71/3708,TWINSUK)

Position: chr7:92501715 (GRCh38.p7) (7q21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 30 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.92501715A>G
GRCh37.p13 chr 7	NC_000007.13:g.92131029A>G
PEX1 RefSeqGene	NG_008341.1:g.31817T>C

Gene: PEX1, peroxisomal biogenesis factor 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PEX1 transcript variant 1	NM_000466.2:c.	N/A	Intron Variant
PEX1 transcript variant 2	NM_001282677.1:c.	N/A	Intron Variant
PEX1 transcript variant 3	NM_001282678.1:c.	N/A	Intron Variant
PEX1 transcript variant X2	XM_017012319.1:c.	N/A	Intron Variant
PEX1 transcript variant X3	XR_001744808.1:n.	N/A	Intron Variant
PEX1 transcript variant X1	XR_242246.4:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.901	G=0.099
1000Genomes	American	Sub	694	A=0.900	G=0.100
1000Genomes	East Asian	Sub	1008	A=0.725	G=0.275
1000Genomes	Europe	Sub	1006	A=0.981	G=0.019
1000Genomes	Global	Study-wide	5008	A=0.894	G=0.106
1000Genomes	South Asian	Sub	978	A=0.970	G=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.983	G=0.017
The Exome Aggregation Consortium	American	Sub	17726	A=0.861	G=0.138
The Exome Aggregation Consortium	Asian	Sub	20856	A=0.887	G=0.112
The Exome Aggregation Consortium	Europe	Sub	58310	A=0.977	G=0.022
The Exome Aggregation Consortium	Global	Study-wide	97702	A=0.936	G=0.063
The Exome Aggregation Consortium	Other	Sub	810	A=0.960	G=0.040
The Genome Aggregation Database	African	Sub	8736	A=0.908	G=0.092
The Genome Aggregation Database	American	Sub	838	A=0.870	G=0.130
The Genome Aggregation Database	East Asian	Sub	1612	A=0.708	G=0.292
The Genome Aggregation Database	Europe	Sub	18502	A=0.985	G=0.014
The Genome Aggregation Database	Global	Study-wide	29990	A=0.944	G=0.055
The Genome Aggregation Database	Other	Sub	302	A=0.920	G=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.930	G=0.069
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.981	G=0.019

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs3213609	0.0005	alcohol dependence	20201924

eQTL of rs3213609 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr7:92131029	RBM48	ENSG00000127993.10	A>G	2.2782e-4	-27058	Hypothalamus

meQTL of rs3213609 in Fetal Brain

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr7	92081595	92081651	E067	-49378
chr7	92163834	92163874	E067	32805
chr7	92163923	92164003	E067	32894
chr7	92164048	92164147	E067	33019
chr7	92164803	92164887	E067	33774
chr7	92155227	92155275	E068	24198
chr7	92155287	92155347	E068	24258
chr7	92163834	92163874	E069	32805
chr7	92163923	92164003	E069	32894
chr7	92164048	92164147	E069	33019
chr7	92164803	92164887	E069	33774
chr7	92165533	92165573	E069	34504
chr7	92154840	92154904	E070	23811
chr7	92155227	92155275	E070	24198
chr7	92155287	92155347	E070	24258
chr7	92155426	92155482	E070	24397
chr7	92155227	92155275	E071	24198
chr7	92155287	92155347	E071	24258
chr7	92155426	92155482	E071	24397
chr7	92155227	92155275	E072	24198
chr7	92155287	92155347	E072	24258
chr7	92155426	92155482	E072	24397
chr7	92163923	92164003	E072	32894
chr7	92164048	92164147	E072	33019
chr7	92155227	92155275	E073	24198
chr7	92155287	92155347	E073	24258
chr7	92155426	92155482	E073	24397
chr7	92163834	92163874	E074	32805
chr7	92163923	92164003	E074	32894
chr7	92164048	92164147	E074	33019

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	92156745	92158674	E067	25716
chr7	92158721	92158793	E067	27692
chr7	92156745	92158674	E068	25716
chr7	92158721	92158793	E068	27692
chr7	92156745	92158674	E069	25716
chr7	92158721	92158793	E069	27692
chr7	92156745	92158674	E070	25716
chr7	92158721	92158793	E070	27692
chr7	92156745	92158674	E071	25716
chr7	92158721	92158793	E071	27692
chr7	92156745	92158674	E072	25716
chr7	92158721	92158793	E072	27692
chr7	92156745	92158674	E073	25716
chr7	92158721	92158793	E073	27692
chr7	92156745	92158674	E074	25716
chr7	92158721	92158793	E074	27692
chr7	92156745	92158674	E081	25716
chr7	92158721	92158793	E081	27692
chr7	92156745	92158674	E082	25716
chr7	92158721	92158793	E082	27692

rs3213609