rs2970888

Homo sapiens
C>A
SMYD1 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0250 (7486/29924,GnomAD)
C==0225 (6577/29116,TOPMED)
C==0208 (1042/5008,1000G)
C==0318 (1224/3854,ALSPAC)
C==0322 (1193/3708,TWINSUK)
chr2:88112274 (GRCh38.p7) (2p11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
73 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.88112274C>A
GRCh37.p13 chr 2NC_000002.11:g.88411793C>A

Gene: SMYD1, SET and MYND domain containing 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SMYD1 transcript variant 1NM_198274.3:c.N/A3 Prime UTR Variant
SMYD1 transcript variant X1XM_005264156.2:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.124A=0.876
1000GenomesAmericanSub694C=0.400A=0.600
1000GenomesEast AsianSub1008C=0.166A=0.834
1000GenomesEuropeSub1006C=0.282A=0.718
1000GenomesGlobalStudy-wide5008C=0.208A=0.792
1000GenomesSouth AsianSub978C=0.150A=0.850
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.318A=0.682
The Genome Aggregation DatabaseAfricanSub8704C=0.150A=0.850
The Genome Aggregation DatabaseAmericanSub836C=0.440A=0.560
The Genome Aggregation DatabaseEast AsianSub1614C=0.162A=0.838
The Genome Aggregation DatabaseEuropeSub18468C=0.296A=0.703
The Genome Aggregation DatabaseGlobalStudy-wide29924C=0.250A=0.749
The Genome Aggregation DatabaseOtherSub302C=0.240A=0.760
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.225A=0.774
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.322A=0.678
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
rs29708880.000989alcohol consumption (maxi-drinks)24277619

eQTL of rs2970888 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 rs2970888 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 )
chr28838151488381710E067-30083
chr28838187088381949E067-29844
chr28838198888382059E067-29734
chr28838242788382581E067-29212
chr28838515488385215E067-26578
chr28838523488385362E067-26431
chr28840006888400308E067-11485
chr28841434488415139E0672551
chr28843636288436591E06724569
chr28845947688459836E06747683
chr28838151488381710E068-30083
chr28838187088381949E068-29844
chr28838198888382059E068-29734
chr28838242788382581E068-29212
chr28840006888400308E068-11485
chr28841434488415139E0682551
chr28843636288436591E06824569
chr28837672788376896E069-34897
chr28837694788377239E069-34554
chr28838151488381710E069-30083
chr28838187088381949E069-29844
chr28838198888382059E069-29734
chr28838242788382581E069-29212
chr28838478588384880E069-26913
chr28839468788394811E069-16982
chr28839488888394938E069-16855
chr28839931988399916E069-11877
chr28840006888400308E069-11485
chr28841434488415139E0692551
chr28843636288436591E06924569
chr28838151488381710E071-30083
chr28838187088381949E071-29844
chr28838198888382059E071-29734
chr28838242788382581E071-29212
chr28839931988399916E071-11877
chr28840006888400308E071-11485
chr28841434488415139E0712551
chr28843420088434840E07122407
chr28843636288436591E07124569
chr28837672788376896E072-34897
chr28837694788377239E072-34554
chr28838151488381710E072-30083
chr28838187088381949E072-29844
chr28838198888382059E072-29734
chr28838242788382581E072-29212
chr28838478588384880E072-26913
chr28838515488385215E072-26578
chr28839468788394811E072-16982
chr28839488888394938E072-16855
chr28839931988399916E072-11877
chr28840006888400308E072-11485
chr28843636288436591E07224569
chr28838151488381710E073-30083
chr28838187088381949E073-29844
chr28838198888382059E073-29734
chr28838242788382581E073-29212
chr28838478588384880E073-26913
chr28838515488385215E073-26578
chr28838523488385362E073-26431
chr28839032388390524E073-21269
chr28839056188390626E073-21167
chr28840006888400308E073-11485
chr28838151488381710E074-30083
chr28838187088381949E074-29844
chr28838198888382059E074-29734
chr28838242788382581E074-29212
chr28838478588384880E074-26913
chr28838515488385215E074-26578
chr28838523488385362E074-26431
chr28839931988399916E074-11877
chr28840006888400308E074-11485
chr28841434488415139E0742551
chr28843636288436591E07424569