SNP Detail Info-rs3813301

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

TNFAIP8 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0107 (3168/29564,GnomAD)
G=0120 (3510/29118,TOPMED)
G=0090 (453/5008,1000G)
G=0061 (237/3854,ALSPAC)
G=0066 (244/3708,TWINSUK)

Position: chr5:119339551 (GRCh38.p7) (5q23.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 4 Enhancers around

Promoter: 9 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.119339551A>G
GRCh37.p13 chr 5	NC_000005.9:g.118675246A>G

Molecule type	Change	Amino acid[Codon]	SO Term
TNFAIP8 transcript variant 2	NM_001077654.2:c.	N/A	Intron Variant
TNFAIP8 transcript variant 4	NM_001286814.1:c.	N/A	Intron Variant
TNFAIP8 transcript variant 5	NM_001286815.1:c.	N/A	Intron Variant
TNFAIP8 transcript variant 6	NM_001286817.1:c.	N/A	Intron Variant
TNFAIP8 transcript variant 3	NM_001286813.1:c.	N/A	Genic Upstream Transcript Variant
TNFAIP8 transcript variant 1	NM_014350.3:c.	N/A	Genic Upstream Transcript Variant
TNFAIP8 transcript variant X2	XM_017009328.1:c.	N/A	Intron Variant
TNFAIP8 transcript variant X1	XM_017009327.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.797	G=0.203
1000Genomes	American	Sub	694	A=0.910	G=0.090
1000Genomes	East Asian	Sub	1008	A=0.969	G=0.031
1000Genomes	Europe	Sub	1006	A=0.940	G=0.060
1000Genomes	Global	Study-wide	5008	A=0.910	G=0.090
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=0.939	G=0.061
The Genome Aggregation Database	African	Sub	8566	A=0.799	G=0.201
The Genome Aggregation Database	American	Sub	826	A=0.930	G=0.070
The Genome Aggregation Database	East Asian	Sub	1610	A=0.953	G=0.047
The Genome Aggregation Database	Europe	Sub	18260	A=0.930	G=0.069
The Genome Aggregation Database	Global	Study-wide	29564	A=0.892	G=0.107
The Genome Aggregation Database	Other	Sub	302	A=0.840	G=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.879	G=0.120
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.934	G=0.066

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

SNP ID	p-value	Traits	Study
rs3813301	5.41E-05	alcohol and nictotine co-dependence	20158304

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr5:118675246	TNFAIP8	ENSG00000145779.7	A>G	2.9197e-12	70859	Cerebellum
Chr5:118675246	TNFAIP8	ENSG00000145779.7	A>G	9.0479e-6	70859	Cerebellar_Hemisphere

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr5	118651198	118651839	E068	-23407
chr5	118693617	118693763	E070	18371
chr5	118651198	118651839	E071	-23407
chr5	118651198	118651839	E074	-23407

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	118690801	118692895	E067	15555
chr5	118690801	118692895	E068	15555
chr5	118690801	118692895	E069	15555
chr5	118690801	118692895	E070	15555
chr5	118690801	118692895	E071	15555
chr5	118690801	118692895	E072	15555
chr5	118690801	118692895	E073	15555
chr5	118690801	118692895	E074	15555
chr5	118690801	118692895	E081	15555

rs3813301