rs12129498

Homo sapiens
A>G
SLC30A10 : Intron Variant
LOC107985281 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
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)
chr1:219934575 (GRCh38.p7) (1q41)
ND
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around

Genomic Coordinates

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

Gene: SLC30A10, solute carrier family 30 member 10(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC30A10 transcript variant 1NM_018713.2:c.N/AGenic Upstream Transcript Variant
SLC30A10 transcript variant 2NR_046437.1:n.N/AGenic Upstream Transcript Variant
SLC30A10 transcript variant X1XM_006711437.3:c.N/AIntron Variant
SLC30A10 transcript variant X2XM_017001684.1:c.N/AGenic Upstream Transcript Variant

Gene: LOC107985281, uncharacterized LOC107985281(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107985281 transcriptXR_001738476.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.997G=0.003
1000GenomesAmericanSub694A=0.930G=0.070
1000GenomesEast AsianSub1008A=0.839G=0.161
1000GenomesEuropeSub1006A=0.877G=0.123
1000GenomesGlobalStudy-wide5008A=0.926G=0.074
1000GenomesSouth AsianSub978A=0.970G=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.884G=0.116
The Genome Aggregation DatabaseAfricanSub8734A=0.978G=0.022
The Genome Aggregation DatabaseAmericanSub832A=0.920G=0.080
The Genome Aggregation DatabaseEast AsianSub1616A=0.819G=0.181
The Genome Aggregation DatabaseEuropeSub18486A=0.895G=0.104
The Genome Aggregation DatabaseGlobalStudy-wide29968A=0.916G=0.083
The Genome Aggregation DatabaseOtherSub300A=0.900G=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.924G=0.075
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.874G=0.126
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs121294982.71E-05alcohol and nictotine co-dependence20158304

eQTL of rs12129498 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 rs12129498 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 )
chr1220097565220098281E069-9636
chr1220086810220086968E081-20949


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1220099789220100428E067-7489
chr1220100536220100643E067-7274
chr1220100783220100912E067-7005
chr1220101046220102474E067-5443
chr1220099789220100428E068-7489
chr1220100536220100643E068-7274
chr1220100783220100912E068-7005
chr1220101046220102474E068-5443
chr1220099789220100428E069-7489
chr1220100536220100643E069-7274
chr1220100783220100912E069-7005
chr1220101046220102474E069-5443
chr1220099789220100428E070-7489
chr1220100536220100643E070-7274
chr1220100783220100912E070-7005
chr1220101046220102474E070-5443
chr1220099789220100428E071-7489
chr1220100536220100643E071-7274
chr1220100783220100912E071-7005
chr1220101046220102474E071-5443
chr1220099789220100428E072-7489
chr1220100536220100643E072-7274
chr1220100783220100912E072-7005
chr1220101046220102474E072-5443
chr1220099789220100428E073-7489
chr1220100536220100643E073-7274
chr1220100783220100912E073-7005
chr1220101046220102474E073-5443
chr1220099789220100428E074-7489
chr1220100536220100643E074-7274
chr1220100783220100912E074-7005
chr1220101046220102474E074-5443
chr1220100536220100643E081-7274
chr1220100783220100912E081-7005
chr1220100536220100643E082-7274
chr1220100783220100912E082-7005
chr1220101046220102474E082-5443