rs3799861

Homo sapiens
T>C
PLA2G7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0176 (5273/29910,GnomAD)
T==0187 (5468/29118,TOPMED)
T==0149 (745/5008,1000G)
T==0206 (793/3854,ALSPAC)
T==0194 (718/3708,TWINSUK)
chr6:46721792 (GRCh38.p7) (6p12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
12 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.46721792T>C
GRCh37.p13 chr 6NC_000006.11:g.46689529T>C
PLA2G7 RefSeqGeneNG_016204.1:g.18902A>G

Gene: PLA2G7, phospholipase A2 group VII(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PLA2G7 transcript variant 2NM_001168357.1:c.N/AIntron Variant
PLA2G7 transcript variant 1NM_005084.3:c.N/AIntron Variant
PLA2G7 transcript variant X1XM_005249408.4:c.N/AIntron Variant
PLA2G7 transcript variant X2XR_001743639.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.143C=0.857
1000GenomesAmericanSub694T=0.160C=0.840
1000GenomesEast AsianSub1008T=0.091C=0.909
1000GenomesEuropeSub1006T=0.244C=0.756
1000GenomesGlobalStudy-wide5008T=0.149C=0.851
1000GenomesSouth AsianSub978T=0.110C=0.890
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.206C=0.794
The Genome Aggregation DatabaseAfricanSub8688T=0.142C=0.858
The Genome Aggregation DatabaseAmericanSub838T=0.160C=0.840
The Genome Aggregation DatabaseEast AsianSub1620T=0.127C=0.873
The Genome Aggregation DatabaseEuropeSub18462T=0.197C=0.802
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.176C=0.823
The Genome Aggregation DatabaseOtherSub302T=0.160C=0.840
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.187C=0.812
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.194C=0.806
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
rs37998610.000749alcohol dependence24277619

eQTL of rs3799861 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 rs3799861 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 )
chr64667245646672670E068-16859
chr64668691646687132E068-2397
chr64664197046642744E069-46785
chr64664480846644913E070-44616
chr64664491546645010E070-44519
chr64664506646645253E070-44276
chr64664144146641555E071-47974
chr64664197046642744E071-46785
chr64667245646672670E073-16859
chr64664197046642744E074-46785
chr64664480846644913E082-44616
chr64664491546645010E082-44519







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr64670167946702160E06712150
chr64670221046702345E06712681
chr64670237046702461E06712841
chr64670249646703621E06712967
chr64670221046702345E06812681
chr64670237046702461E06812841
chr64670249646703621E06812967
chr64670221046702345E06912681
chr64670237046702461E06912841
chr64670249646703621E06912967
chr64670221046702345E07012681
chr64670237046702461E07012841
chr64670249646703621E07012967
chr64670167946702160E07112150
chr64670221046702345E07112681
chr64670237046702461E07112841
chr64670249646703621E07112967
chr64670221046702345E07212681
chr64670237046702461E07212841
chr64670249646703621E07212967
chr64670221046702345E07312681
chr64670237046702461E07312841
chr64670249646703621E07312967
chr64670221046702345E07412681
chr64670237046702461E07412841
chr64670249646703621E07412967
chr64670221046702345E08212681
chr64670237046702461E08212841
chr64670249646703621E08212967