rs13378890

Homo sapiens
C>T
ATP8A2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0053 (1610/29978,GnomAD)
T=0062 (1826/29116,TOPMED)
T=0072 (360/5008,1000G)
chr13:25422552 (GRCh38.p7) (13q12.13)
AD
GWASdb2
1   publication(s)
See rs on genome
57 Enhancers around
22 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.25422552C>T
GRCh37.p13 chr 13NC_000013.10:g.25996690C>T
ATP8A2 RefSeqGeneNG_042855.1:g.55542C>T

Gene: ATP8A2, ATPase phospholipid transporting 8A2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
ATP8A2 transcript variant 1NM_016529.5:c.N/AIntron Variant
ATP8A2 transcript variant 2NM_001313741.1:c.N/AGenic Upstream Transcript Variant
ATP8A2 transcript variant X1XM_011535103.1:c.N/AIntron Variant
ATP8A2 transcript variant X4XM_011535106.1:c.N/AIntron Variant
ATP8A2 transcript variant X5XM_011535107.2:c.N/AIntron Variant
ATP8A2 transcript variant X8XM_011535113.2:c.N/AIntron Variant
ATP8A2 transcript variant X9XM_017020625.1:c.N/AIntron Variant
ATP8A2 transcript variant X10XM_017020626.1:c.N/AIntron Variant
ATP8A2 transcript variant X2XM_005266419.1:c.N/AGenic Upstream Transcript Variant
ATP8A2 transcript variant X3XM_011535104.2:c.N/AGenic Upstream Transcript Variant
ATP8A2 transcript variant X6XM_011535109.2:c.N/AGenic Upstream Transcript Variant
ATP8A2 transcript variant X7XM_011535112.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.859T=0.141
1000GenomesAmericanSub694C=0.980T=0.020
1000GenomesEast AsianSub1008C=0.992T=0.008
1000GenomesEuropeSub1006C=0.980T=0.020
1000GenomesGlobalStudy-wide5008C=0.928T=0.072
1000GenomesSouth AsianSub978C=0.870T=0.130
The Genome Aggregation DatabaseAfricanSub8728C=0.887T=0.113
The Genome Aggregation DatabaseAmericanSub838C=0.980T=0.020
The Genome Aggregation DatabaseEast AsianSub1620C=0.994T=0.006
The Genome Aggregation DatabaseEuropeSub18490C=0.968T=0.031
The Genome Aggregation DatabaseGlobalStudy-wide29978C=0.946T=0.053
The Genome Aggregation DatabaseOtherSub302C=0.940T=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.937T=0.062
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs133788900.00099alcohol dependence21314694

eQTL of rs13378890 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 rs13378890 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 )
chr132597504925975129E067-21561
chr132597485725974937E068-21753
chr132597504925975129E068-21561
chr132599079325990843E070-5847
chr132602808426028298E07031394
chr132602902326029063E07032333
chr132602927226029914E07032582
chr132603014026030184E07033450
chr132599250825992586E071-4104
chr132599276425993005E071-3685
chr132595443325954598E072-42092
chr132594774425947809E073-48881
chr132594794225948055E073-48635
chr132594845125948704E073-47986
chr132594774425947809E081-48881
chr132594794225948055E081-48635
chr132594832525948375E081-48315
chr132595174825952077E081-44613
chr132595228425952340E081-44350
chr132595277125952968E081-43722
chr132595317825953500E081-43190
chr132595389125953941E081-42749
chr132595422025954381E081-42309
chr132595443325954598E081-42092
chr132598944025989618E081-7072
chr132598964125989800E081-6890
chr132598986525989931E081-6759
chr132599079325990843E081-5847
chr132602754526027683E08130855
chr132602774626027796E08131056
chr132602789926027953E08131209
chr132602808426028298E08131394
chr132602902326029063E08132333
chr132602927226029914E08132582
chr132603014026030184E08133450
chr132603065126030717E08133961
chr132603081926030888E08134129
chr132603089126030945E08134201
chr132603168326032151E08134993
chr132603219626032317E08135506
chr132604213626042211E08145446
chr132604498826045038E08148298
chr132594774425947809E082-48881
chr132595144025951555E082-45135
chr132595174825952077E082-44613
chr132595228425952340E082-44350
chr132595277125952968E082-43722
chr132595317825953500E082-43190
chr132595389125953941E082-42749
chr132602789926027953E08231209
chr132602808426028298E08231394
chr132602902326029063E08232333
chr132602927226029914E08232582
chr132603014026030184E08233450
chr132603065126030717E08233961
chr132603081926030888E08234129
chr132603089126030945E08234201








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr132604241226043571E06745722
chr132604368926043748E06746999
chr132604376026043845E06747070
chr132604241226043571E06845722
chr132604241226043571E06945722
chr132604368926043748E06946999
chr132604376026043845E06947070
chr132604241226043571E07045722
chr132604368926043748E07046999
chr132604376026043845E07047070
chr132604241226043571E07145722
chr132604241226043571E07245722
chr132604368926043748E07246999
chr132604376026043845E07247070
chr132604241226043571E07345722
chr132604368926043748E07346999
chr132604376026043845E07347070
chr132604241226043571E07445722
chr132604368926043748E08146999
chr132604241226043571E08245722
chr132604368926043748E08246999
chr132604376026043845E08247070