rs3789373

Homo sapiens
C>T
XPR1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0348 (10409/29870,GnomAD)
T=0328 (9576/29118,TOPMED)
T=0289 (1447/5008,1000G)
T=0406 (1566/3854,ALSPAC)
T=0405 (1500/3708,TWINSUK)
chr1:180804994 (GRCh38.p7) (1q25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
46 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.180804994C>T
GRCh37.p13 chr 1NC_000001.10:g.180774130C>T

Gene: XPR1, xenotropic and polytropic retrovirus receptor 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
XPR1 transcript variant 2NM_001135669.1:c.N/AIntron Variant
XPR1 transcript variant 1NM_004736.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.750T=0.250
1000GenomesAmericanSub694C=0.670T=0.330
1000GenomesEast AsianSub1008C=0.845T=0.155
1000GenomesEuropeSub1006C=0.597T=0.403
1000GenomesGlobalStudy-wide5008C=0.711T=0.289
1000GenomesSouth AsianSub978C=0.670T=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.594T=0.406
The Genome Aggregation DatabaseAfricanSub8690C=0.720T=0.280
The Genome Aggregation DatabaseAmericanSub832C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1610C=0.871T=0.129
The Genome Aggregation DatabaseEuropeSub18436C=0.599T=0.400
The Genome Aggregation DatabaseGlobalStudy-wide29870C=0.651T=0.348
The Genome Aggregation DatabaseOtherSub302C=0.640T=0.360
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.671T=0.328
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.595T=0.405
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
rs37893730.000952alcohol dependence21314694

eQTL of rs3789373 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 rs3789373 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 )
chr1180823306180823492E06849176
chr1180823590180824126E06849460
chr1180810715180810901E06936585
chr1180811730180811852E06937600
chr1180812009180812092E06937879
chr1180812113180812344E06937983
chr1180805579180805865E07031449
chr1180806227180806458E07032097
chr1180810715180810901E07036585
chr1180810985180811035E07036855
chr1180811314180811466E07037184
chr1180811730180811852E07037600
chr1180812009180812092E07037879
chr1180812113180812344E07037983
chr1180812442180812537E07038312
chr1180813801180813877E07039671
chr1180823066180823139E07048936
chr1180823306180823492E07049176
chr1180751052180751106E072-23024
chr1180811314180811466E07237184
chr1180811730180811852E07237600
chr1180812009180812092E07237879
chr1180812113180812344E07237983
chr1180811730180811852E07437600
chr1180812009180812092E07437879
chr1180812113180812344E07437983
chr1180754558180754724E081-19406
chr1180755059180755154E081-18976
chr1180755448180755527E081-18603
chr1180755721180756171E081-17959
chr1180810715180810901E08136585
chr1180810985180811035E08136855
chr1180811314180811466E08137184
chr1180811730180811852E08137600
chr1180812009180812092E08137879
chr1180812113180812344E08137983
chr1180734325180734637E082-39493
chr1180751052180751106E082-23024
chr1180755059180755154E082-18976
chr1180805579180805865E08231449
chr1180806227180806458E08232097
chr1180810985180811035E08236855
chr1180811314180811466E08237184
chr1180811730180811852E08237600
chr1180812009180812092E08237879
chr1180812113180812344E08237983