rs4135275

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PPARG : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0166 (4977/29908,GnomAD)
G=0137 (4000/29118,TOPMED)
G=0274 (1373/5008,1000G)
G=0198 (765/3854,ALSPAC)
G=0204 (758/3708,TWINSUK)

Position: chr3:12402345 (GRCh38.p7) (3p25.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 5 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.12402345A>G
GRCh37.p13 chr 3	NC_000003.11:g.12443844A>G
PPARG RefSeqGene	NG_011749.1:g.119496A>G

Gene: PPARG, peroxisome proliferator activated receptor gamma(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PPARG transcript variant 4	NM_005037.5:c.	N/A	Intron Variant
PPARG transcript variant 2	NM_015869.4:c.	N/A	Intron Variant
PPARG transcript variant 3	NM_138711.3:c.	N/A	Intron Variant
PPARG transcript variant 1	NM_138712.3:c.	N/A	Intron Variant
PPARG transcript variant X1	XM_011533841.2:c.	N/A	Intron Variant
PPARG transcript variant X4	XM_011533842.2:c.	N/A	Intron Variant
PPARG transcript variant X5	XM_011533843.2:c.	N/A	Intron Variant
PPARG transcript variant X6	XM_011533844.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.961	G=0.039
1000Genomes	American	Sub	694	A=0.770	G=0.230
1000Genomes	East Asian	Sub	1008	A=0.511	G=0.489
1000Genomes	Europe	Sub	1006	A=0.810	G=0.190
1000Genomes	Global	Study-wide	5008	A=0.726	G=0.274
1000Genomes	South Asian	Sub	978	A=0.510	G=0.490
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.802	G=0.198
The Genome Aggregation Database	African	Sub	8712	A=0.935	G=0.065
The Genome Aggregation Database	American	Sub	836	A=0.740	G=0.260
The Genome Aggregation Database	East Asian	Sub	1610	A=0.514	G=0.486
The Genome Aggregation Database	Europe	Sub	18448	A=0.817	G=0.182
The Genome Aggregation Database	Global	Study-wide	29908	A=0.833	G=0.166
The Genome Aggregation Database	Other	Sub	302	A=0.870	G=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.862	G=0.137
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.796	G=0.204

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
24843374	Association of the PPAR-gamma Gene with Altered Glucose Levels and Psychosis Profile in Schizophrenia Patients Exposed to Antipsychotics.	Liu YR	Psychiatry Investig
25549360	Placental genome and maternal-placental genetic interactions: a genome-wide and candidate gene association study of placental abruption.	Denis M	PLoS One
22301832	Genetic variation in peroxisome proliferator-activated receptor gamma, soy, and mammographic density in Singapore Chinese women.	Lee E	Cancer Epidemiol Biomarkers Prev

P-Value

SNP ID	p-value	Traits	Study
rs4135275	0.000135	alcohol dependence	20201924

eQTL of rs4135275 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 rs4135275 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	12483062	12483169	E069	39218
chr3	12483292	12483347	E069	39448
chr3	12483569	12483632	E069	39725
chr3	12465493	12465750	E071	21649
chr3	12465817	12466145	E071	21973