SNP Detail Info-rs3219123

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

PARP1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0039 (1181/29994,GnomAD)
A=0034 (1012/29116,TOPMED)
G==0044 (574/13006,GO-ESP)
A=0027 (133/5008,1000G)
A=0053 (205/3854,ALSPAC)
A=0056 (209/3708,TWINSUK)

Position: chr1:226367647 (GRCh38.p7) (1q42.12)

Phenotype: ND

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.226367647G>A
GRCh38.p7 chr 1	NC_000001.11:g.226367647G>T
GRCh37.p13 chr 1	NC_000001.10:g.226555348G>A
GRCh37.p13 chr 1	NC_000001.10:g.226555348G>T

Gene: PARP1, poly (ADP-ribose) polymerase 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PARP1 transcript	NM_001618.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.998	A=0.002
1000Genomes	American	Sub	694	G=0.960	A=0.040
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.933	A=0.067
1000Genomes	Global	Study-wide	5008	G=0.973	A=0.027
1000Genomes	South Asian	Sub	978	G=0.960	A=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.947	A=0.053
The Genome Aggregation Database	African	Sub	8734	G=0.991	A=0.009
The Genome Aggregation Database	American	Sub	838	G=0.970	A=0.030
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18500	G=0.943	A=0.056
The Genome Aggregation Database	Global	Study-wide	29994	G=0.960	A=0.039
The Genome Aggregation Database	Other	Sub	302	G=0.900	A=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.965	A=0.034
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.944	A=0.056

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet
21767974	Association analysis of PARP1 polymorphisms with Parkinson's disease.	Brighina L	Parkinsonism Relat Disord
21537398	Telomere length and variation in telomere biology genes in individuals with osteosarcoma.	Mirabello L	Int J Mol Epidemiol Genet

P-Value

SNP ID	p-value	Traits	Study
rs3219123	6.23E-06	alcohol and nictotine co-dependence	20158304

eQTL of rs3219123 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 rs3219123 in Fetal Brain

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	5159013	5159684	E069	16342
chr1	5159013	5159684	E070	16342
chr1	5159706	5159903	E070	17035
chr1	5179945	5180204	E071	37274
chr1	5179369	5179873	E074	36698
chr1	5179945	5180204	E074	37274
chr1	5159013	5159684	E081	16342
chr1	5159706	5159903	E081	17035
chr1	5189877	5190338	E081	47206

rs3219123

Genomic Coordinates

Gene: PARP1, poly (ADP-ribose) polymerase 1(minus strand)

Population Frequency

P-Value

eQTL of rs3219123 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs3219123 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)