rs17815700

Homo sapiens
T>C
ATP2C2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0101 (3046/29938,GnomAD)
C=0089 (2610/29118,TOPMED)
C=0051 (257/5008,1000G)
C=0162 (625/3854,ALSPAC)
C=0154 (570/3708,TWINSUK)
chr16:84455427 (GRCh38.p7) (16q24.1)
AD
GWASdb2
1   publication(s)
See rs on genome
46 Enhancers around
25 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.84455427T>C
GRCh37.p13 chr 16NC_000016.9:g.84489033T>C

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
1000GenomesAfricanSub1322T=0.981C=0.019
1000GenomesAmericanSub694T=0.910C=0.090
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.846C=0.154
1000GenomesGlobalStudy-wide5008T=0.949C=0.051
1000GenomesSouth AsianSub978T=0.980C=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.838C=0.162
The Genome Aggregation DatabaseAfricanSub8718T=0.962C=0.038
The Genome Aggregation DatabaseAmericanSub838T=0.920C=0.080
The Genome Aggregation DatabaseEast AsianSub1622T=1.000C=0.000
The Genome Aggregation DatabaseEuropeSub18458T=0.857C=0.142
The Genome Aggregation DatabaseGlobalStudy-wide29938T=0.898C=0.101
The Genome Aggregation DatabaseOtherSub302T=0.920C=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.910C=0.089
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.846C=0.154
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
rs178157000.00068Alcohol dependence (early age of onset)20201924
rs178157000.00071alcohol dependence20201924

eQTL of rs17815700 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 rs17815700 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 )
chr168453685084537014E06747817
chr168448051784480592E068-8441
chr168451429884514412E06825265
chr168451447484514544E06825441
chr168451498984515151E06825956
chr168451520684515256E06826173
chr168451554784516071E06826514
chr168451612684516441E06827093
chr168451650984516559E06827476
chr168451816984518582E06829136
chr168453685084537014E06847817
chr168444078684440840E069-48193
chr168447277484472932E069-16101
chr168451554784516071E06926514
chr168451612684516441E06927093
chr168451650984516559E06927476
chr168451756184517648E06928528
chr168451774084517790E06928707
chr168451816984518582E06929136
chr168453685084537014E06947817
chr168451816984518582E07029136
chr168453573684536202E07046703
chr168453629784536577E07047264
chr168453667084536795E07047637
chr168451498984515151E07125956
chr168451520684515256E07126173
chr168451554784516071E07126514
chr168451612684516441E07127093
chr168453685084537014E07147817
chr168451498984515151E07225956
chr168451520684515256E07226173
chr168451554784516071E07226514
chr168451612684516441E07227093
chr168451774084517790E07228707
chr168451816984518582E07229136
chr168451867584518844E07229642
chr168453685084537014E07247817
chr168451554784516071E07326514
chr168451612684516441E07327093
chr168451650984516559E07327476
chr168453685084537014E07347817
chr168444078684440840E074-48193
chr168451554784516071E07426514
chr168451612684516441E07427093
chr168453685084537014E08147817
chr168453667084536795E08247637










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr168443976984439906E067-49127
chr168443992784440262E067-48771
chr168445670684456877E067-32156
chr168445694984456999E067-32034
chr168445714884457448E067-31585
chr168443976984439906E068-49127
chr168443992784440262E068-48771
chr168445714884457448E068-31585
chr168443976984439906E069-49127
chr168443992784440262E069-48771
chr168443992784440262E070-48771
chr168443976984439906E071-49127
chr168443992784440262E071-48771
chr168445670684456877E071-32156
chr168445694984456999E071-32034
chr168445714884457448E071-31585
chr168443976984439906E072-49127
chr168443992784440262E072-48771
chr168445714884457448E072-31585
chr168443976984439906E073-49127
chr168443992784440262E073-48771
chr168445714884457448E073-31585
chr168443976984439906E074-49127
chr168443992784440262E074-48771
chr168443976984439906E082-49127