SNP Detail Info-rs40200

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

AGXT2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0158 (4740/29902,GnomAD)
A==0166 (4845/29118,TOPMED)
A==0242 (1210/5008,1000G)
A==0101 (391/3854,ALSPAC)
A==0092 (340/3708,TWINSUK)

Position: chr5:35045640 (GRCh38.p7) (5p13.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 19 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.35045640A>G
GRCh37.p13 chr 5	NC_000005.9:g.35045745A>G

Molecule type	Change	Amino acid[Codon]	SO Term
AGXT2 transcript variant 2	NM_001306173.1:c.	N/A	Intron Variant
AGXT2 transcript variant 1	NM_031900.3:c.	N/A	Intron Variant
AGXT2 transcript variant X1	XM_005248337.2:c.	N/A	Intron Variant
AGXT2 transcript variant X2	XM_005248338.2:c.	N/A	Intron Variant
AGXT2 transcript variant X3	XM_017009748.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.206	G=0.794
1000Genomes	American	Sub	694	A=0.300	G=0.700
1000Genomes	East Asian	Sub	1008	A=0.458	G=0.542
1000Genomes	Europe	Sub	1006	A=0.088	G=0.912
1000Genomes	Global	Study-wide	5008	A=0.242	G=0.758
1000Genomes	South Asian	Sub	978	A=0.180	G=0.820
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.101	G=0.899
The Genome Aggregation Database	African	Sub	8698	A=0.208	G=0.792
The Genome Aggregation Database	American	Sub	838	A=0.300	G=0.700
The Genome Aggregation Database	East Asian	Sub	1610	A=0.461	G=0.539
The Genome Aggregation Database	Europe	Sub	18454	A=0.102	G=0.897
The Genome Aggregation Database	Global	Study-wide	29902	A=0.158	G=0.841
The Genome Aggregation Database	Other	Sub	302	A=0.110	G=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.166	G=0.833
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.092	G=0.908

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
rs40200	3.65E-05	alcohol and nictotine co-dependence	20158304

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr5	34998293	34998407	E070	-47338
chr5	35043661	35043736	E070	-2009
chr5	35043871	35044302	E070	-1443
chr5	35032570	35032723	E081	-13022
chr5	35038988	35039716	E081	-6029
chr5	35040294	35040383	E081	-5362
chr5	35041159	35041242	E081	-4503
chr5	35041354	35041419	E081	-4326
chr5	35041525	35041660	E081	-4085
chr5	35041730	35041780	E081	-3965
chr5	35042209	35042433	E081	-3312
chr5	35042988	35043288	E081	-2457
chr5	35043661	35043736	E081	-2009
chr5	35043871	35044302	E081	-1443
chr5	35094539	35094667	E081	48794
chr5	35095165	35095430	E081	49420
chr5	35095668	35095722	E081	49923
chr5	35043661	35043736	E082	-2009
chr5	35043871	35044302	E082	-1443

rs40200