rs11086862

Homo sapiens
T>C
PTPRT : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0086 (2582/29968,GnomAD)
C=0092 (2704/29118,TOPMED)
C=0128 (641/5008,1000G)
C=0041 (158/3854,ALSPAC)
C=0047 (174/3708,TWINSUK)
chr20:43125961 (GRCh38.p7) (20q13.11)
AD
GWASCatalog
1   publication(s)
See rs on genome
90 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.43125961T>C
GRCh37.p13 chr 20NC_000020.10:g.41754601T>C
PTPRT RefSeqGeneNG_033880.1:g.68957A>G

Gene: PTPRT, protein tyrosine phosphatase, receptor type T(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PTPRT transcript variant 2NM_007050.5:c.N/AIntron Variant
PTPRT transcript variant 1NM_133170.3:c.N/AIntron Variant
PTPRT transcript variant X2XM_017027611.1:c.N/AGenic Upstream Transcript Variant
PTPRT transcript variant X3XM_017027612.1:c.N/AGenic Upstream Transcript Variant
PTPRT transcript variant X4XM_017027613.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.844C=0.156
1000GenomesAmericanSub694T=0.950C=0.050
1000GenomesEast AsianSub1008T=0.756C=0.244
1000GenomesEuropeSub1006T=0.950C=0.050
1000GenomesGlobalStudy-wide5008T=0.872C=0.128
1000GenomesSouth AsianSub978T=0.900C=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.959C=0.041
The Genome Aggregation DatabaseAfricanSub8716T=0.856C=0.144
The Genome Aggregation DatabaseAmericanSub838T=0.950C=0.050
The Genome Aggregation DatabaseEast AsianSub1612T=0.738C=0.262
The Genome Aggregation DatabaseEuropeSub18500T=0.954C=0.045
The Genome Aggregation DatabaseGlobalStudy-wide29968T=0.913C=0.086
The Genome Aggregation DatabaseOtherSub302T=0.930C=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.907C=0.092
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.953C=0.047
PMID Title Author Journal
29082582Problematic alcohol use associates with sodium channel and clathrin linker 1 (SCLT1) in trauma-exposed populations.Almli LMAddict Biol

P-Value

SNP ID p-value Traits Study
rs110868625E-06alcohol dependence29082582

eQTL of rs11086862 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 rs11086862 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 )
chr204172479941725850E067-28751
chr204177555041775613E06720949
chr204172479941725850E068-28751
chr204176624041766319E06811639
chr204176654341766587E06811942
chr204176696541767036E06812364
chr204176710141767151E06812500
chr204177421041774439E06819609
chr204177449741774743E06819896
chr204177531741775367E06820716
chr204177555041775613E06820949
chr204178866441789081E06834063
chr204180073541800819E06846134
chr204180083541800910E06846234
chr204172479941725850E069-28751
chr204176654341766587E06911942
chr204176696541767036E06912364
chr204176710141767151E06912500
chr204177484341775187E06920242
chr204177531741775367E06920716
chr204177555041775613E06920949
chr204180073541800819E06946134
chr204180083541800910E06946234
chr204172479941725850E070-28751
chr204172479941725850E071-28751
chr204172619441726479E071-28122
chr204172659641726697E071-27904
chr204176654341766587E07111942
chr204176696541767036E07112364
chr204176710141767151E07112500
chr204176930541769394E07114704
chr204177421041774439E07119609
chr204177449741774743E07119896
chr204177484341775187E07120242
chr204177531741775367E07120716
chr204177555041775613E07120949
chr204180073541800819E07146134
chr204180083541800910E07146234
chr204172479941725850E072-28751
chr204176696541767036E07212364
chr204176710141767151E07212500
chr204176821141768271E07213610
chr204177421041774439E07219609
chr204177449741774743E07219896
chr204177531741775367E07220716
chr204177555041775613E07220949
chr204180083541800910E07246234
chr204172479941725850E073-28751
chr204172619441726479E073-28122
chr204176654341766587E07311942
chr204176696541767036E07312364
chr204176710141767151E07312500
chr204172479941725850E074-28751
chr204172619441726479E074-28122
chr204172659641726697E074-27904
chr204176624041766319E07411639
chr204176654341766587E07411942
chr204176696541767036E07412364
chr204176710141767151E07412500
chr204176791241767956E07413311
chr204176821141768271E07413610
chr204177421041774439E07419609
chr204177449741774743E07419896
chr204177484341775187E07420242
chr204177531741775367E07420716
chr204177555041775613E07420949
chr204180073541800819E07446134
chr204180083541800910E07446234
chr204172479941725850E081-28751
chr204175303441753146E081-1455
chr204176654341766587E08111942
chr204176821141768271E08113610
chr204178495241785002E08130351
chr204178814141788264E08133540
chr204178866441789081E08134063
chr204178911441789172E08134513
chr204178933541789399E08134734
chr204178961841790719E08135017
chr204172367241723747E082-30854
chr204172479941725850E082-28751
chr204178495241785002E08230351
chr204178526941785382E08230668
chr204178814141788264E08233540
chr204178866441789081E08234063
chr204178911441789172E08234513
chr204178933541789399E08234734
chr204178961841790719E08235017
chr204179100741791057E08236406
chr204179115341791207E08236552
chr204179140141791611E08236800