SNP Detail Info-rs12129498

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SLC30A10 : Intron Variant
LOC107985281 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0083 (2513/29968,GnomAD)
G=0075 (2188/29116,TOPMED)
G=0074 (370/5008,1000G)
G=0116 (447/3854,ALSPAC)
G=0126 (468/3708,TWINSUK)

Position: chr1:219934575 (GRCh38.p7) (1q41)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 37 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.219934575A>G
GRCh37.p13 chr 1	NC_000001.10:g.220107917A>G

Molecule type	Change	Amino acid[Codon]	SO Term
SLC30A10 transcript variant 1	NM_018713.2:c.	N/A	Genic Upstream Transcript Variant
SLC30A10 transcript variant 2	NR_046437.1:n.	N/A	Genic Upstream Transcript Variant
SLC30A10 transcript variant X1	XM_006711437.3:c.	N/A	Intron Variant
SLC30A10 transcript variant X2	XM_017001684.1:c.	N/A	Genic Upstream Transcript Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985281 transcript	XR_001738476.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.997	G=0.003
1000Genomes	American	Sub	694	A=0.930	G=0.070
1000Genomes	East Asian	Sub	1008	A=0.839	G=0.161
1000Genomes	Europe	Sub	1006	A=0.877	G=0.123
1000Genomes	Global	Study-wide	5008	A=0.926	G=0.074
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=0.884	G=0.116
The Genome Aggregation Database	African	Sub	8734	A=0.978	G=0.022
The Genome Aggregation Database	American	Sub	832	A=0.920	G=0.080
The Genome Aggregation Database	East Asian	Sub	1616	A=0.819	G=0.181
The Genome Aggregation Database	Europe	Sub	18486	A=0.895	G=0.104
The Genome Aggregation Database	Global	Study-wide	29968	A=0.916	G=0.083
The Genome Aggregation Database	Other	Sub	300	A=0.900	G=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.924	G=0.075
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.874	G=0.126

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
rs12129498	2.71E-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 )
chr1	220097565	220098281	E069	-9636
chr1	220086810	220086968	E081	-20949

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	220099789	220100428	E067	-7489
chr1	220100536	220100643	E067	-7274
chr1	220100783	220100912	E067	-7005
chr1	220101046	220102474	E067	-5443
chr1	220099789	220100428	E068	-7489
chr1	220100536	220100643	E068	-7274
chr1	220100783	220100912	E068	-7005
chr1	220101046	220102474	E068	-5443
chr1	220099789	220100428	E069	-7489
chr1	220100536	220100643	E069	-7274
chr1	220100783	220100912	E069	-7005
chr1	220101046	220102474	E069	-5443
chr1	220099789	220100428	E070	-7489
chr1	220100536	220100643	E070	-7274
chr1	220100783	220100912	E070	-7005
chr1	220101046	220102474	E070	-5443
chr1	220099789	220100428	E071	-7489
chr1	220100536	220100643	E071	-7274
chr1	220100783	220100912	E071	-7005
chr1	220101046	220102474	E071	-5443
chr1	220099789	220100428	E072	-7489
chr1	220100536	220100643	E072	-7274
chr1	220100783	220100912	E072	-7005
chr1	220101046	220102474	E072	-5443
chr1	220099789	220100428	E073	-7489
chr1	220100536	220100643	E073	-7274
chr1	220100783	220100912	E073	-7005
chr1	220101046	220102474	E073	-5443
chr1	220099789	220100428	E074	-7489
chr1	220100536	220100643	E074	-7274
chr1	220100783	220100912	E074	-7005
chr1	220101046	220102474	E074	-5443
chr1	220100536	220100643	E081	-7274
chr1	220100783	220100912	E081	-7005
chr1	220100536	220100643	E082	-7274
chr1	220100783	220100912	E082	-7005
chr1	220101046	220102474	E082	-5443

rs12129498