rs16859177

Homo sapiens
C>T
TLK1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0127 (3829/29944,GnomAD)
T=0194 (5648/29118,TOPMED)
T=0130 (651/5008,1000G)
T=0081 (312/3854,ALSPAC)
T=0082 (304/3708,TWINSUK)
chr2:171150066 (GRCh38.p7) (2q31.1)
AD
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
28 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.171150066C>T
GRCh37.p13 chr 2NC_000002.11:g.172006576C>T

Gene: TLK1, tousled like kinase 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TLK1 transcript variant 2NM_001136554.1:c.N/AIntron Variant
TLK1 transcript variant 1NM_012290.4:c.N/AIntron Variant
TLK1 transcript variant 3NM_001136555.1:c.N/AGenic Upstream Transcript Variant
TLK1 transcript variant X1XM_011512238.2:c.N/AIntron Variant
TLK1 transcript variant X2XM_017005421.1:c.N/AIntron Variant
TLK1 transcript variant X3XM_017005422.1:c.N/AIntron Variant
TLK1 transcript variant X4XR_001739084.1:n.N/AIntron Variant
TLK1 transcript variant X5XR_001739085.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.619T=0.381
1000GenomesAmericanSub694C=0.910T=0.090
1000GenomesEast AsianSub1008C=1.000T=0.000
1000GenomesEuropeSub1006C=0.927T=0.073
1000GenomesGlobalStudy-wide5008C=0.870T=0.130
1000GenomesSouth AsianSub978C=0.990T=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.919T=0.081
The Genome Aggregation DatabaseAfricanSub8698C=0.683T=0.317
The Genome Aggregation DatabaseAmericanSub838C=0.920T=0.080
The Genome Aggregation DatabaseEast AsianSub1622C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18486C=0.946T=0.053
The Genome Aggregation DatabaseGlobalStudy-wide29944C=0.872T=0.127
The Genome Aggregation DatabaseOtherSub300C=0.950T=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.806T=0.194
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.918T=0.082
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
rs168591770.000404alcohol dependence21314694

eQTL of rs16859177 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 rs16859177 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 )
chr2171997986171998186E067-8390
chr2171997986171998186E068-8390
chr2172003252172003443E071-3133
chr2171989698171989753E072-16823
chr2172003252172003443E072-3133
chr2172013042172013145E0826466





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2172015372172018100E0678796
chr2172018102172018174E06711526
chr2172018219172018269E06711643
chr2172015372172018100E0688796
chr2172018102172018174E06811526
chr2172018219172018269E06811643
chr2172015372172018100E0698796
chr2172018102172018174E06911526
chr2172018219172018269E06911643
chr2172015372172018100E0708796
chr2172018102172018174E07011526
chr2172018219172018269E07011643
chr2172015372172018100E0718796
chr2172018102172018174E07111526
chr2172018219172018269E07111643
chr2172015372172018100E0728796
chr2172018102172018174E07211526
chr2172015372172018100E0738796
chr2172018102172018174E07311526
chr2172015372172018100E0748796
chr2172018102172018174E07411526
chr2172018219172018269E07411643
chr2172015372172018100E0818796
chr2172018102172018174E08111526
chr2172018219172018269E08111643
chr2172015372172018100E0828796
chr2172018102172018174E08211526
chr2172018219172018269E08211643