rs16973814

Homo sapiens
G>A / G>T
ATP2C2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0190 (5692/29960,GnomAD)
T=0129 (647/5008,1000G)
chr16:84446014 (GRCh38.p7) (16q24.1)
AD
GWASdb2
1   publication(s)
See rs on genome
12 Enhancers around
15 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.84446014G>A
GRCh38.p7 chr 16NC_000016.10:g.84446014G>T
GRCh37.p13 chr 16NC_000016.9:g.84479620G>A
GRCh37.p13 chr 16NC_000016.9:g.84479620G>T

Gene: ATP2C2, ATPase secretory pathway Ca2+ transporting 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ATP2C2 transcript variant 1NM_001286527.2:c.N/AIntron Variant
ATP2C2 transcript variant 3NM_001291454.1:c.N/AIntron Variant
ATP2C2 transcript variant 2NM_014861.3:c.N/AIntron Variant
ATP2C2 transcript variant X1XM_011523486.2:c.N/AIntron Variant
ATP2C2 transcript variant X3XM_011523487.2:c.N/AIntron Variant
ATP2C2 transcript variant X2XR_001752045.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.751T=0.249
1000GenomesAmericanSub694G=0.860T=0.140
1000GenomesEast AsianSub1008G=0.999T=0.001
1000GenomesEuropeSub1006G=0.825T=0.175
1000GenomesGlobalStudy-wide5008G=0.871T=0.129
1000GenomesSouth AsianSub978G=0.950T=0.050
The Genome Aggregation DatabaseAfricanSub8718G=0.712T=0.288
The Genome Aggregation DatabaseAmericanSub838G=0.900T=0.10,
The Genome Aggregation DatabaseEast AsianSub1622G=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18480G=0.835T=0.164
The Genome Aggregation DatabaseGlobalStudy-wide29960G=0.809T=0.190
The Genome Aggregation DatabaseOtherSub302G=0.850T=0.15,
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs169738140.00074alcohol dependence20201924

eQTL of rs16973814 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 rs16973814 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 )
chr167269756972697773E067-28174
chr167275603672756361E06730089
chr167275542172755621E06929474
chr167275640472756755E06930457
chr167275640472756755E07030457
chr167275996672760016E07034019
chr167269756972697773E071-28174
chr167275603672756361E07130089
chr167275640472756755E07130457
chr167275640472756755E07430457
chr167275698972757039E07431042
chr167269756972697773E082-28174






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr167269801072699658E067-26289
chr167269801072699658E068-26289
chr167269970672699806E068-26141
chr167269801072699658E069-26289
chr167269801072699658E070-26289
chr167269970672699806E070-26141
chr167269801072699658E071-26289
chr167269970672699806E071-26141
chr167269801072699658E072-26289
chr167269801072699658E073-26289
chr167269970672699806E073-26141
chr167269801072699658E074-26289
chr167269801072699658E081-26289
chr167269970672699806E081-26141
chr167269801072699658E082-26289