rs2283839

Homo sapiens
A>C
TPST2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0412 (12327/29890,GnomAD)
C=0361 (10516/29116,TOPMED)
A==0472 (2363/5008,1000G)
C=0421 (1622/3854,ALSPAC)
C=0424 (1573/3708,TWINSUK)
chr22:26573096 (GRCh38.p7) (22q12.1)
AD
GWASdb2
2   publication(s)
See rs on genome
133 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 22NC_000022.11:g.26573096A>C
GRCh37.p13 chr 22NC_000022.10:g.26969061A>C

Gene: TPST2, tyrosylprotein sulfotransferase 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TPST2 transcript variant 2NM_003595.3:c.N/AIntron Variant
TPST2 transcript variant 1NM_001008566.1:c.N/AGenic Upstream Transcript Variant
TPST2 transcript variant X1XM_006724338.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.781C=0.219
1000GenomesAmericanSub694A=0.390C=0.610
1000GenomesEast AsianSub1008A=0.268C=0.732
1000GenomesEuropeSub1006A=0.546C=0.454
1000GenomesGlobalStudy-wide5008A=0.472C=0.528
1000GenomesSouth AsianSub978A=0.250C=0.750
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.579C=0.421
The Genome Aggregation DatabaseAfricanSub8694A=0.744C=0.256
The Genome Aggregation DatabaseAmericanSub838A=0.380C=0.620
The Genome Aggregation DatabaseEast AsianSub1616A=0.246C=0.754
The Genome Aggregation DatabaseEuropeSub18442A=0.554C=0.445
The Genome Aggregation DatabaseGlobalStudy-wide29890A=0.587C=0.412
The Genome Aggregation DatabaseOtherSub300A=0.480C=0.520
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.638C=0.361
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.576C=0.424
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
17384212Single nucleotide polymorphism profiling assay to confirm the identity of human tissues.Huijsmans RJ Mol Diagn

P-Value

SNP ID p-value Traits Study
rs22838390.000766alcohol dependence21314694

eQTL of rs2283839 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 rs2283839 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 )
chr222694240826942627E067-26434
chr222694264626942706E067-26355
chr222694293626942990E067-26071
chr222694307626943169E067-25892
chr222695279126953283E067-15778
chr222695350926953626E067-15435
chr222695463426954910E067-14151
chr222695500526955081E067-13980
chr222695785426957995E067-11066
chr222695800826958648E067-10413
chr222696390626964849E067-4212
chr222696612026966404E067-2657
chr222696643126966683E067-2378
chr222696674326966900E067-2161
chr222698088226981692E06711821
chr222698249426983060E06713433
chr222698307426983146E06714013
chr222698315926983373E06714098
chr222700619327006794E06737132
chr222700682027006879E06737759
chr222694189726942024E068-27037
chr222694216826942273E068-26788
chr222694240826942627E068-26434
chr222694264626942706E068-26355
chr222694293626942990E068-26071
chr222694614326947058E068-22003
chr222694721926947588E068-21473
chr222695007826950180E068-18881
chr222695018626950428E068-18633
chr222695047126950599E068-18462
chr222695071626950766E068-18295
chr222695088826951342E068-17719
chr222695785426957995E068-11066
chr222696390626964849E068-4212
chr222696643126966683E068-2378
chr222696674326966900E068-2161
chr222700682027006879E06837759
chr222700696827007447E06837907
chr222701522227015323E06846161
chr222694240826942627E069-26434
chr222694264626942706E069-26355
chr222694614326947058E069-22003
chr222694809226948153E069-20908
chr222695088826951342E069-17719
chr222695147526951713E069-17348
chr222695177426951953E069-17108
chr222695279126953283E069-15778
chr222696643126966683E069-2378
chr222696674326966900E069-2161
chr222697002926970079E069968
chr222697036826970750E0691307
chr222698088226981692E06911821
chr222700619327006794E06937132
chr222700682027006879E06937759
chr222700696827007447E06937907
chr222695088826951342E070-17719
chr222695147526951713E070-17348
chr222695177426951953E070-17108
chr222692363626924410E071-44651
chr222695422926954410E071-14651
chr222695447826954591E071-14470
chr222695463426954910E071-14151
chr222695785426957995E071-11066
chr222695800826958648E071-10413
chr222696390626964849E071-4212
chr222696521126965361E071-3700
chr222698088226981692E07111821
chr222700619327006794E07137132
chr222700682027006879E07137759
chr222700696827007447E07137907
chr222701230827012418E07143247
chr222701245927012499E07143398
chr222694216826942273E072-26788
chr222694240826942627E072-26434
chr222694264626942706E072-26355
chr222694293626942990E072-26071
chr222695147526951713E072-17348
chr222695177426951953E072-17108
chr222695279126953283E072-15778
chr222695422926954410E072-14651
chr222695447826954591E072-14470
chr222695463426954910E072-14151
chr222695800826958648E072-10413
chr222696390626964849E072-4212
chr222696612026966404E072-2657
chr222696643126966683E072-2378
chr222696674326966900E072-2161
chr222696700226967074E072-1987
chr222696714426967329E072-1732
chr222698088226981692E07211821
chr222698795326988852E07218892
chr222698885426988950E07219793
chr222700682027006879E07237759
chr222692336226923520E073-45541
chr222692363626924410E073-44651
chr222694264626942706E073-26355
chr222694614326947058E073-22003
chr222695147526951713E073-17348
chr222695177426951953E073-17108
chr222695279126953283E073-15778
chr222695422926954410E073-14651
chr222695447826954591E073-14470
chr222695463426954910E073-14151
chr222695599726956352E073-12709
chr222695785426957995E073-11066
chr222695800826958648E073-10413
chr222695891526958968E073-10093
chr222695898826959304E073-9757
chr222696348526963535E073-5526
chr222696390626964849E073-4212
chr222696612026966404E073-2657
chr222696643126966683E073-2378
chr222696674326966900E073-2161
chr222696862426968674E073-387
chr222696867826968728E073-333
chr222698088226981692E07311821
chr222698307426983146E07314013
chr222700619327006794E07337132
chr222700682027006879E07337759
chr222700696827007447E07337907
chr222695007826950180E074-18881
chr222695018626950428E074-18633
chr222695047126950599E074-18462
chr222695071626950766E074-18295
chr222695088826951342E074-17719
chr222695147526951713E074-17348
chr222695177426951953E074-17108
chr222700682027006879E07437759
chr222692336226923520E081-45541
chr222692363626924410E081-44651
chr222696612026966404E081-2657
chr222696643126966683E081-2378
chr222696674326966900E081-2161









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr222698455426986979E06715493
chr222698455426986979E06815493
chr222698455426986979E06915493
chr222698455426986979E07015493
chr222698455426986979E07115493
chr222698455426986979E07215493
chr222698455426986979E07315493
chr222698455426986979E07415493
chr222698455426986979E08115493
chr222698455426986979E08215493