rs1567449

Homo sapiens
C>T
SPATA17 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0206 (6171/29896,GnomAD)
C==0185 (5394/29116,TOPMED)
C==0299 (1496/5008,1000G)
C==0169 (651/3854,ALSPAC)
C==0179 (665/3708,TWINSUK)
chr1:217845614 (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.217845614C>T
GRCh37.p13 chr 1NC_000001.10:g.218018956C>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=0.208T=0.792
1000GenomesAmericanSub694C=0.180T=0.820
1000GenomesEast AsianSub1008C=0.534T=0.466
1000GenomesEuropeSub1006C=0.150T=0.850
1000GenomesGlobalStudy-wide5008C=0.299T=0.701
1000GenomesSouth AsianSub978C=0.420T=0.580
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.169T=0.831
The Genome Aggregation DatabaseAfricanSub8710C=0.212T=0.788
The Genome Aggregation DatabaseAmericanSub836C=0.200T=0.800
The Genome Aggregation DatabaseEast AsianSub1562C=0.571T=0.429
The Genome Aggregation DatabaseEuropeSub18486C=0.173T=0.826
The Genome Aggregation DatabaseGlobalStudy-wide29896C=0.206T=0.793
The Genome Aggregation DatabaseOtherSub302C=0.200T=0.800
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.185T=0.814
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.179T=0.821
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
rs15674490.00068alcohol consumption (maxi-drinks)24277619

eQTL of rs1567449 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 rs1567449 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 )
chr1218030432218030913E07011476
chr1218031012218031108E07012056
chr1218031175218031284E07012219