rs12759918

Homo sapiens
C>T
SPATA17 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0376 (11232/29846,GnomAD)
C==0410 (11939/29116,TOPMED)
C==0469 (2348/5008,1000G)
C==0336 (1295/3854,ALSPAC)
C==0351 (1302/3708,TWINSUK)
chr1:217847795 (GRCh38.p7) (1q41)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.217847795C>T
GRCh37.p13 chr 1NC_000001.10:g.218021137C>T

Gene: SPATA17, spermatogenesis associated 17(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SPATA17 transcriptNM_138796.3:c.N/AIntron Variant
SPATA17 transcript variant X1XM_005273052.1:c.N/AIntron Variant
SPATA17 transcript variant X2XM_006711165.3:c.N/AIntron Variant
SPATA17 transcript variant X3XM_011509194.2:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.449T=0.551
1000GenomesAmericanSub694C=0.430T=0.570
1000GenomesEast AsianSub1008C=0.619T=0.381
1000GenomesEuropeSub1006C=0.322T=0.678
1000GenomesGlobalStudy-wide5008C=0.469T=0.531
1000GenomesSouth AsianSub978C=0.520T=0.480
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.336T=0.664
The Genome Aggregation DatabaseAfricanSub8686C=0.443T=0.557
The Genome Aggregation DatabaseAmericanSub838C=0.410T=0.590
The Genome Aggregation DatabaseEast AsianSub1588C=0.646T=0.354
The Genome Aggregation DatabaseEuropeSub18432C=0.319T=0.681
The Genome Aggregation DatabaseGlobalStudy-wide29846C=0.376T=0.623
The Genome Aggregation DatabaseOtherSub302C=0.460T=0.540
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.410T=0.590
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.351T=0.649
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs127599180.000667alcohol consumption (maxi-drinks)24277619

eQTL of rs12759918 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 rs12759918 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 )
chr1218030432218030913E0709295
chr1218031012218031108E0709875
chr1218031175218031284E07010038