rs12682807

Homo sapiens
A>C
SPATA6L : Intron Variant
SLC1A1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0103 (12559/121296,ExAC)
C=0095 (2850/29982,GnomAD)
C=0063 (1850/29116,TOPMED)
A==0077 (1005/13006,GO-ESP)
C=0106 (533/5008,1000G)
C=0113 (436/3854,ALSPAC)
C=0122 (453/3708,TWINSUK)
chr9:4574022 (GRCh38.p7) (9p24.2)
AD
GWASdb2
3   publication(s)
See rs on genome
47 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.4574022A>C
GRCh37.p13 chr 9NC_000009.11:g.4574022A>C
SLC1A1 RefSeqGeneNG_017044.1:g.88596A>C

Gene: SLC1A1, solute carrier family 1 member 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC1A1 transcriptNM_004170.5:c.N/AIntron Variant
SLC1A1 transcript variant X1XM_011518007.1:c.N/AIntron Variant
SLC1A1 transcript variant X2XM_011518008.2:c.N/AIntron Variant
SLC1A1 transcript variant X4XM_011518009.2:c.N/AIntron Variant
SLC1A1 transcript variant X6XM_011518010.1:c.N/AIntron Variant
SLC1A1 transcript variant X3XM_017015042.1:c.N/AIntron Variant
SLC1A1 transcript variant X5XM_017015043.1:c.N/AIntron Variant

Gene: SPATA6L, spermatogenesis associated 6 like(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SPATA6L transcript variant 5NM_001039395.3:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X6XM_017014882.1:c.N/AIntron Variant
SPATA6L transcript variant X1XM_006716795.2:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X5XM_006716798.3:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X9XM_006716799.3:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X10XM_006716800.2:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X14XM_006716801.2:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X11XM_011517952.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X15XM_011517954.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X22XM_011517956.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X20XM_011517957.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X21XM_011517958.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X2XM_017014881.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X7XM_017014883.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X12XM_017014884.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X11XM_017014885.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X18XM_017014886.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X19XM_017014887.1:c.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X3XR_001746335.1:n.N/AIntron Variant
SPATA6L transcript variant X3XR_001746336.1:n.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X7XR_001746337.1:n.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X12XR_001746338.1:n.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X13XR_001746339.1:n.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X17XR_001746340.1:n.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X18XR_001746341.1:n.N/AGenic Downstream Transcript Variant
SPATA6L transcript variant X25XR_001746342.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.995C=0.005
1000GenomesAmericanSub694A=0.900C=0.100
1000GenomesEast AsianSub1008A=0.745C=0.255
1000GenomesEuropeSub1006A=0.881C=0.119
1000GenomesGlobalStudy-wide5008A=0.894C=0.106
1000GenomesSouth AsianSub978A=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.887C=0.113
The Exome Aggregation ConsortiumAmericanSub21926A=0.932C=0.067
The Exome Aggregation ConsortiumAsianSub25138A=0.873C=0.126
The Exome Aggregation ConsortiumEuropeSub73326A=0.893C=0.106
The Exome Aggregation ConsortiumGlobalStudy-wide121296A=0.896C=0.103
The Exome Aggregation ConsortiumOtherSub906A=0.900C=0.100
The Genome Aggregation DatabaseAfricanSub8726A=0.977C=0.023
The Genome Aggregation DatabaseAmericanSub838A=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1620A=0.726C=0.274
The Genome Aggregation DatabaseEuropeSub18496A=0.885C=0.114
The Genome Aggregation DatabaseGlobalStudy-wide29982A=0.904C=0.095
The Genome Aggregation DatabaseOtherSub302A=0.970C=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.936C=0.063
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.878C=0.122
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res
17894418Association of the SLC1A1 glutamate transporter gene and obsessive-compulsive disorder.Stewart SEAm J Med Genet B Neuropsychiatr Genet
23606572Meta-analysis of association between obsessive-compulsive disorder and the 3' region of neuronal glutamate transporter gene SLC1A1.Stewart SEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs126828070.000549alcohol dependence21314694

eQTL of rs12682807 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 rs12682807 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 )
chr945508624551481E067-22541
chr945515124551791E067-22231
chr945550844555220E067-18802
chr945552504555448E067-18574
chr945303594530795E068-43227
chr945550844555220E068-18802
chr945552504555448E068-18574
chr945554704555545E068-18477
chr945556704555720E068-18302
chr945557914555857E068-18165
chr945676834567776E068-6246
chr945678544567904E068-6118
chr945679344568025E068-5997
chr945905154591433E06816493
chr945303594530795E069-43227
chr945508624551481E069-22541
chr945515124551791E069-22231
chr945668484567216E069-6806
chr945676834567776E069-6246
chr945915554591605E06917533
chr945917744591837E06917752
chr945872864587461E07013264
chr945303594530795E071-43227
chr945308684531135E071-42887
chr945668484567216E071-6806
chr945722284572278E071-1744
chr945303594530795E072-43227
chr945508624551481E072-22541
chr945740414574240E07219
chr945505144550801E073-23221
chr945508624551481E073-22541
chr945738624574023E0730
chr945740414574240E07319
chr945743094574414E073287
chr945748464574911E073824
chr945749444574998E073922
chr945905154591433E07316493
chr945915554591605E07317533
chr945917744591837E07317752
chr945508624551481E074-22541
chr945515124551791E074-22231
chr945905154591433E07416493
chr945790164579452E0814994
chr945795794579652E0815557
chr945799384580024E0815916
chr945801514580214E0816129
chr945790164579452E0824994