rs16914086

Homo sapiens
G>A
TBC1D2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0096 (2886/29962,GnomAD)
A=0073 (2132/29118,TOPMED)
A=0091 (456/5008,1000G)
A=0127 (488/3854,ALSPAC)
A=0140 (518/3708,TWINSUK)
chr9:98226195 (GRCh38.p7) (9q22.33)
ND
GWASdb2
4   publication(s)
See rs on genome
47 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.98226195G>A
GRCh37.p13 chr 9NC_000009.11:g.100988477G>A

Gene: TBC1D2, TBC1 domain family member 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TBC1D2 transcript variant 1NM_001267571.1:c.N/AIntron Variant
TBC1D2 transcript variant 2NM_018421.3:c.N/AIntron Variant
TBC1D2 transcript variant 3NM_001267572.1:c.N/AGenic Upstream Transcript Variant
TBC1D2 transcript variant 4NR_051978.1:n.N/AIntron Variant
TBC1D2 transcript variant X4XM_011518844.2:c.N/AIntron Variant
TBC1D2 transcript variant X2XM_017014899.1:c.N/AIntron Variant
TBC1D2 transcript variant X3XM_011518843.1:c.N/AGenic Upstream Transcript Variant
TBC1D2 transcript variant X1XR_929823.1:n.N/AIntron Variant
TBC1D2 transcript variant X5XR_929824.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.995A=0.005
1000GenomesAmericanSub694G=0.840A=0.160
1000GenomesEast AsianSub1008G=0.909A=0.091
1000GenomesEuropeSub1006G=0.868A=0.132
1000GenomesGlobalStudy-wide5008G=0.909A=0.091
1000GenomesSouth AsianSub978G=0.890A=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.873A=0.127
The Genome Aggregation DatabaseAfricanSub8722G=0.975A=0.025
The Genome Aggregation DatabaseAmericanSub836G=0.870A=0.130
The Genome Aggregation DatabaseEast AsianSub1614G=0.877A=0.123
The Genome Aggregation DatabaseEuropeSub18488G=0.874A=0.126
The Genome Aggregation DatabaseGlobalStudy-wide29962G=0.903A=0.096
The Genome Aggregation DatabaseOtherSub302G=0.910A=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.926A=0.073
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.860A=0.140
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend
19010793Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.Baranzini SEHum Mol Genet
22411505Replication study of multiple sclerosis (MS) susceptibility alleles and correlation of DNA-variants with disease features in a cohort of Austrian MS patients.Schmied MCNeurogenetics
20944657Replication of top markers of a genome-wide association study in multiple sclerosis in Spain.Cavanillas MLGenes Immun

P-Value

SNP ID p-value Traits Study
rs169140866.6E-05nicotine dependence (smoking)22377092

eQTL of rs16914086 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 rs16914086 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 )
chr9100977277100977530E067-10947
chr9100977643100977889E067-10588
chr9100977915100978148E067-10329
chr9100994198100994367E0675721
chr9100994419100994618E0675942
chr9100994659100994741E0676182
chr9101015533101015593E06827056
chr9101015624101015707E06827147
chr9101015744101016071E06827267
chr9100977643100977889E069-10588
chr9100977915100978148E069-10329
chr9101015533101015593E06927056
chr9101015624101015707E06927147
chr9101015744101016071E06927267
chr9101016109101016231E06927632
chr9101016287101016374E06927810
chr9101019560101019615E06931083
chr9101004830101005051E07016353
chr9101005159101005218E07016682
chr9100956029100956069E071-32408
chr9100956089100956266E071-32211
chr9100977090100977159E071-11318
chr9100977277100977530E071-10947
chr9100994198100994367E0715721
chr9100994419100994618E0715942
chr9100994659100994741E0716182
chr9100994928100995030E0716451
chr9101015744101016071E07127267
chr9101016109101016231E07127632
chr9101016287101016374E07127810
chr9100977277100977530E072-10947
chr9100977643100977889E072-10588
chr9101016109101016231E07227632
chr9101016287101016374E07227810
chr9100956029100956069E073-32408
chr9100956089100956266E073-32211
chr9101015744101016071E07327267
chr9101016109101016231E07327632
chr9101016287101016374E07327810
chr9101013406101013655E07424929
chr9101013689101014275E07425212
chr9101016109101016231E07427632
chr9101016287101016374E07427810
chr9100956029100956069E081-32408
chr9100956089100956266E081-32211
chr9100956029100956069E082-32408
chr9100956089100956266E082-32211










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr9100953433100955958E067-32519
chr9101016455101019486E06727978
chr9100953433100955958E068-32519
chr9101016455101019486E06827978
chr9100953433100955958E069-32519
chr9101016455101019486E06927978
chr9100953433100955958E070-32519
chr9101016455101019486E07027978
chr9100953433100955958E071-32519
chr9101016455101019486E07127978
chr9100953433100955958E072-32519
chr9101016455101019486E07227978
chr9100953433100955958E073-32519
chr9101016455101019486E07327978
chr9100953433100955958E074-32519
chr9101016455101019486E07427978
chr9101016455101019486E08127978
chr9100953433100955958E082-32519
chr9101016455101019486E08227978