rs9823402

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PEX5L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0293 (8786/29930,GnomAD)
G==0265 (7730/29118,TOPMED)
G==0250 (1250/5008,1000G)
G==0352 (1355/3854,ALSPAC)
G==0350 (1296/3708,TWINSUK)

Position: chr3:179851760 (GRCh38.p7) (3q26.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 76 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.179851760G>A
GRCh37.p13 chr 3	NC_000003.11:g.179569548G>A

Gene: PEX5L, peroxisomal biogenesis factor 5-like(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PEX5L transcript variant 2	NM_001256750.1:c.	N/A	Intron Variant
PEX5L transcript variant 3	NM_001256751.1:c.	N/A	Intron Variant
PEX5L transcript variant 4	NM_001256752.1:c.	N/A	Intron Variant
PEX5L transcript variant 5	NM_001256753.1:c.	N/A	Intron Variant
PEX5L transcript variant 6	NM_001256754.1:c.	N/A	Intron Variant
PEX5L transcript variant 7	NM_001256755.1:c.	N/A	Intron Variant
PEX5L transcript variant 8	NM_001256756.1:c.	N/A	Intron Variant
PEX5L transcript variant 1	NM_016559.2:c.	N/A	Intron Variant
PEX5L transcript variant X1	XM_011512882.2:c.	N/A	Intron Variant
PEX5L transcript variant X2	XM_011512884.2:c.	N/A	Intron Variant
PEX5L transcript variant X3	XM_011512885.2:c.	N/A	Intron Variant
PEX5L transcript variant X4	XM_011512886.2:c.	N/A	Intron Variant
PEX5L transcript variant X5	XM_011512887.2:c.	N/A	Intron Variant
PEX5L transcript variant X4	XM_011512888.2:c.	N/A	Intron Variant
PEX5L transcript variant X6	XM_011512891.2:c.	N/A	Intron Variant
PEX5L transcript variant X9	XM_011512892.2:c.	N/A	Intron Variant
PEX5L transcript variant X6	XM_017006601.1:c.	N/A	Intron Variant
PEX5L transcript variant X7	XM_017006602.1:c.	N/A	Intron Variant
PEX5L transcript variant X9	XM_017006603.1:c.	N/A	Intron Variant
PEX5L transcript variant X10	XM_017006604.1:c.	N/A	Intron Variant
PEX5L transcript variant X11	XM_017006605.1:c.	N/A	Intron Variant
PEX5L transcript variant X13	XM_017006606.1:c.	N/A	Intron Variant
PEX5L transcript variant X7	XM_017006607.1:c.	N/A	Intron Variant
PEX5L transcript variant X8	XM_017006608.1:c.	N/A	Intron Variant
PEX5L transcript variant X16	XM_017006609.1:c.	N/A	Intron Variant
PEX5L transcript variant X17	XM_017006610.1:c.	N/A	Intron Variant
PEX5L transcript variant X18	XM_017006611.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.114	A=0.886
1000Genomes	American	Sub	694	G=0.310	A=0.690
1000Genomes	East Asian	Sub	1008	G=0.199	A=0.801
1000Genomes	Europe	Sub	1006	G=0.370	A=0.630
1000Genomes	Global	Study-wide	5008	G=0.250	A=0.750
1000Genomes	South Asian	Sub	978	G=0.320	A=0.680
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.352	A=0.648
The Genome Aggregation Database	African	Sub	8714	G=0.161	A=0.839
The Genome Aggregation Database	American	Sub	838	G=0.330	A=0.670
The Genome Aggregation Database	East Asian	Sub	1614	G=0.200	A=0.800
The Genome Aggregation Database	Europe	Sub	18462	G=0.358	A=0.641
The Genome Aggregation Database	Global	Study-wide	29930	G=0.293	A=0.706
The Genome Aggregation Database	Other	Sub	302	G=0.520	A=0.480
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.265	A=0.734
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.350	A=0.650

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs9823402	4.73E-05	alcohol consumption	23743675

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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	179529118	179529795	E067	-39753
chr3	179537253	179537495	E067	-32053
chr3	179537787	179537923	E067	-31625
chr3	179537967	179538092	E067	-31456
chr3	179543804	179543898	E067	-25650
chr3	179544115	179544301	E067	-25247
chr3	179552701	179553468	E067	-16080
chr3	179599147	179599288	E067	29599
chr3	179599744	179599839	E067	30196
chr3	179600132	179600409	E067	30584
chr3	179529118	179529795	E068	-39753
chr3	179537253	179537495	E068	-32053
chr3	179599744	179599839	E068	30196
chr3	179600132	179600409	E068	30584
chr3	179600440	179600558	E068	30892
chr3	179600599	179600680	E068	31051
chr3	179600786	179600863	E068	31238
chr3	179529118	179529795	E069	-39753
chr3	179537253	179537495	E069	-32053
chr3	179537787	179537923	E069	-31625
chr3	179598773	179599003	E069	29225
chr3	179599147	179599288	E069	29599
chr3	179599744	179599839	E069	30196
chr3	179600132	179600409	E069	30584
chr3	179600440	179600558	E069	30892
chr3	179600599	179600680	E069	31051
chr3	179537253	179537495	E070	-32053
chr3	179537787	179537923	E070	-31625
chr3	179537967	179538092	E070	-31456
chr3	179599744	179599839	E070	30196
chr3	179600132	179600409	E070	30584
chr3	179529118	179529795	E071	-39753
chr3	179537787	179537923	E071	-31625
chr3	179537967	179538092	E071	-31456
chr3	179543804	179543898	E071	-25650
chr3	179544115	179544301	E071	-25247
chr3	179552701	179553468	E071	-16080
chr3	179598773	179599003	E071	29225
chr3	179599147	179599288	E071	29599
chr3	179599744	179599839	E071	30196
chr3	179600132	179600409	E071	30584
chr3	179600440	179600558	E071	30892
chr3	179600599	179600680	E071	31051
chr3	179600786	179600863	E071	31238
chr3	179529118	179529795	E072	-39753
chr3	179537253	179537495	E072	-32053
chr3	179537787	179537923	E072	-31625
chr3	179537967	179538092	E072	-31456
chr3	179543804	179543898	E072	-25650
chr3	179544115	179544301	E072	-25247
chr3	179552701	179553468	E072	-16080
chr3	179599744	179599839	E072	30196
chr3	179600132	179600409	E072	30584
chr3	179600440	179600558	E072	30892
chr3	179600599	179600680	E072	31051
chr3	179600786	179600863	E072	31238
chr3	179529118	179529795	E074	-39753
chr3	179537253	179537495	E074	-32053
chr3	179537787	179537923	E074	-31625
chr3	179537967	179538092	E074	-31456
chr3	179538787	179539319	E074	-30229
chr3	179543804	179543898	E074	-25650
chr3	179544115	179544301	E074	-25247
chr3	179552701	179553468	E074	-16080
chr3	179553911	179554080	E074	-15468
chr3	179598773	179599003	E074	29225
chr3	179599147	179599288	E074	29599
chr3	179599744	179599839	E074	30196
chr3	179600132	179600409	E074	30584
chr3	179600440	179600558	E074	30892
chr3	179600599	179600680	E074	31051
chr3	179600786	179600863	E074	31238
chr3	179599744	179599839	E082	30196
chr3	179600132	179600409	E082	30584
chr3	179600440	179600558	E082	30892
chr3	179600599	179600680	E082	31051

rs9823402

Genomic Coordinates

Gene: PEX5L, peroxisomal biogenesis factor 5-like(minus strand)

Population Frequency

P-Value

eQTL of rs9823402 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs9823402 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)