rs10502172

Homo sapiens
C>T
TTC12 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0336 (10067/29910,GnomAD)
T=0279 (8147/29118,TOPMED)
T=0210 (1051/5008,1000G)
T=0494 (1902/3854,ALSPAC)
T=0477 (1768/3708,TWINSUK)
chr11:113328424 (GRCh38.p7) (11q23.2)
AD
GWASdb2
5   publication(s)
See rs on genome
239 Enhancers around
30 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.113328424C>T
GRCh37.p13 chr 11 fix patch HG306_PATCHNW_003871078.1:g.511150C>T
GRCh37.p13 chr 11NC_000011.9:g.113199146C>T

Gene: TTC12, tetratricopeptide repeat domain 12(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TTC12 transcript variant 1NM_001318533.1:c.N/AIntron Variant
TTC12 transcript variant 2NM_017868.3:c.N/AIntron Variant
TTC12 transcript variant X2XM_005271604.3:c.N/AIntron Variant
TTC12 transcript variant X11XM_011542890.2:c.N/AIntron Variant
TTC12 transcript variant X1XM_017017943.1:c.N/AIntron Variant
TTC12 transcript variant X3XM_017017944.1:c.N/AIntron Variant
TTC12 transcript variant X4XM_017017945.1:c.N/AIntron Variant
TTC12 transcript variant X5XM_017017946.1:c.N/AIntron Variant
TTC12 transcript variant X6XM_017017947.1:c.N/AIntron Variant
TTC12 transcript variant X7XM_017017948.1:c.N/AIntron Variant
TTC12 transcript variant X8XM_017017949.1:c.N/AIntron Variant
TTC12 transcript variant X9XM_017017950.1:c.N/AIntron Variant
TTC12 transcript variant X10XR_001747914.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.976T=0.024
1000GenomesAmericanSub694C=0.710T=0.290
1000GenomesEast AsianSub1008C=0.947T=0.053
1000GenomesEuropeSub1006C=0.522T=0.478
1000GenomesGlobalStudy-wide5008C=0.790T=0.210
1000GenomesSouth AsianSub978C=0.710T=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.506T=0.494
The Genome Aggregation DatabaseAfricanSub8704C=0.915T=0.085
The Genome Aggregation DatabaseAmericanSub834C=0.740T=0.260
The Genome Aggregation DatabaseEast AsianSub1622C=0.954T=0.046
The Genome Aggregation DatabaseEuropeSub18450C=0.518T=0.481
The Genome Aggregation DatabaseGlobalStudy-wide29910C=0.663T=0.336
The Genome Aggregation DatabaseOtherSub300C=0.470T=0.530
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.720T=0.279
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.523T=0.477
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
22492058A common genetic network underlies substance use disorders and disruptive or externalizing disorders.Arcos-Burgos MHum Genet
22640768The genetic basis of addictive disorders.Ducci FPsychiatr Clin North Am
21168125TTC12-ANKK1-DRD2 and CHRNA5-CHRNA3-CHRNB4 influence different pathways leading to smoking behavior from adolescence to mid-adulthood.Ducci FBiol Psychiatry
27166759Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.Yang JMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs105021720.00021Alcohol dependence (early age of onset)20201924
rs105021720.0007alcohol dependence20201924

eQTL of rs10502172 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr11:113199146TTC12ENSG00000149292.12C>T3.5021e-1013895Cerebellum
Chr11:113199146RP11-159N11.4ENSG00000270179.1C>T4.5301e-3-40153Cerebellum
Chr11:113199146TTC12ENSG00000149292.12C>T3.5274e-1513895Frontal_Cortex_BA9
Chr11:113199146RP11-159N11.4ENSG00000270179.1C>T1.4464e-3-40153Frontal_Cortex_BA9
Chr11:113199146TTC12ENSG00000149292.12C>T1.3401e-1113895Hypothalamus
Chr11:113199146TTC12ENSG00000149292.12C>T2.0791e-1313895Cortex
Chr11:113199146TTC12ENSG00000149292.12C>T4.2684e-613895Cerebellar_Hemisphere
Chr11:113199146TTC12ENSG00000149292.12C>T1.0753e-1013895Caudate_basal_ganglia
Chr11:113199146RP11-159N11.4ENSG00000270179.1C>T2.2067e-4-40153Caudate_basal_ganglia
Chr11:113199146TTC12ENSG00000149292.12C>T3.5059e-913895Brain_Spinal_cord_cervical
Chr11:113199146TTC12ENSG00000149292.12C>T1.8208e-913895Hippocampus
Chr11:113199146TTC12ENSG00000149292.12C>T1.0004e-1013895Substantia_nigra
Chr11:113199146TTC12ENSG00000149292.12C>T6.3264e-813895Putamen_basal_ganglia
Chr11:113199146TTC12ENSG00000149292.12C>T6.6390e-1113895Anterior_cingulate_cortex
Chr11:113199146TTC12ENSG00000149292.12C>T6.0798e-1013895Nucleus_accumbens_basal_ganglia
Chr11:113199146RP11-159N11.4ENSG00000270179.1C>T2.6018e-3-40153Nucleus_accumbens_basal_ganglia
Chr11:113199146TTC12ENSG00000149292.12C>T1.8966e-1113895Amygdala

meQTL of rs10502172 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 )
chr11470287470555E067-40595
chr11476036476111E067-35039
chr11476189476245E067-34905
chr11476501476590E067-34560
chr11476777476837E067-34313
chr11477085477135E067-34015
chr11477159477329E067-33821
chr11477457477585E067-33565
chr11479158479332E067-31818
chr11479455479574E067-31576
chr11494512494631E067-16519
chr11494697495232E067-15918
chr11495269495499E067-15651
chr11495547495630E067-15520
chr11495663496075E067-15075
chr11496162496265E067-14885
chr11496298496347E067-14803
chr11499603499701E067-11449
chr11499719499778E067-11372
chr11499830499904E067-11246
chr11501848501898E067-9252
chr11502035502126E067-9024
chr11502174502387E067-8763
chr11502430502826E067-8324
chr11502859503105E067-8045
chr11534033534130E06722883
chr11468203468961E068-42189
chr11468994469034E068-42116
chr11494370494468E068-16682
chr11494512494631E068-16519
chr11494697495232E068-15918
chr11495269495499E068-15651
chr11495547495630E068-15520
chr11501478501825E068-9325
chr11501848501898E068-9252
chr11502035502126E068-9024
chr11502174502387E068-8763
chr11502430502826E068-8324
chr11502859503105E068-8045
chr11476036476111E069-35039
chr11476189476245E069-34905
chr11476501476590E069-34560
chr11476777476837E069-34313
chr11477085477135E069-34015
chr11477159477329E069-33821
chr11477457477585E069-33565
chr11477755477862E069-33288
chr11479158479332E069-31818
chr11479455479574E069-31576
chr11493906494047E069-17103
chr11494058494130E069-17020
chr11494241494313E069-16837
chr11494370494468E069-16682
chr11494512494631E069-16519
chr11494697495232E069-15918
chr11495269495499E069-15651
chr11495547495630E069-15520
chr11495663496075E069-15075
chr11496162496265E069-14885
chr11496298496347E069-14803
chr11498278498426E069-12724
chr11498451498524E069-12626
chr11498529498628E069-12522
chr11498693499250E069-11900
chr11499324499461E069-11689
chr11499488499581E069-11569
chr11499603499701E069-11449
chr11499719499778E069-11372
chr11499830499904E069-11246
chr11500379500437E069-10713
chr11501848501898E069-9252
chr11502174502387E069-8763
chr11502859503105E069-8045
chr11534033534130E06922883
chr11534156534220E06923006
chr11468203468961E070-42189
chr11533116533378E07021966
chr11468203468961E071-42189
chr11476501476590E071-34560
chr11476777476837E071-34313
chr11477085477135E071-34015
chr11477159477329E071-33821
chr11477457477585E071-33565
chr11478958479092E071-32058
chr11479158479332E071-31818
chr11479455479574E071-31576
chr11493906494047E071-17103
chr11494058494130E071-17020
chr11494241494313E071-16837
chr11494370494468E071-16682
chr11494512494631E071-16519
chr11494697495232E071-15918
chr11495269495499E071-15651
chr11495547495630E071-15520
chr11495663496075E071-15075
chr11496162496265E071-14885
chr11496298496347E071-14803
chr11500023500103E071-11047
chr11500150500204E071-10946
chr11500300500354E071-10796
chr11500379500437E071-10713
chr11500499500850E071-10300
chr11501049501247E071-9903
chr11501292501441E071-9709
chr11501478501825E071-9325
chr11501848501898E071-9252
chr11502035502126E071-9024
chr11502174502387E071-8763
chr11502859503105E071-8045
chr11533451533607E07122301
chr11533791534008E07122641
chr11534033534130E07122883
chr11534156534220E07123006
chr11468203468961E072-42189
chr11468994469034E072-42116
chr11469139469267E072-41883
chr11472227472287E072-38863
chr11472344472499E072-38651
chr11476189476245E072-34905
chr11476501476590E072-34560
chr11476777476837E072-34313
chr11477085477135E072-34015
chr11477159477329E072-33821
chr11477457477585E072-33565
chr11477755477862E072-33288
chr11478958479092E072-32058
chr11479158479332E072-31818
chr11479455479574E072-31576
chr11483789483839E072-27311
chr11488166488295E072-22855
chr11488364488445E072-22705
chr11488497488547E072-22603
chr11488609488670E072-22480
chr11489126489403E072-21747
chr11489467489517E072-21633
chr11489720489770E072-21380
chr11490602490804E072-20346
chr11490808490965E072-20185
chr11491061491286E072-19864
chr11493906494047E072-17103
chr11494058494130E072-17020
chr11494241494313E072-16837
chr11494370494468E072-16682
chr11494512494631E072-16519
chr11494697495232E072-15918
chr11495269495499E072-15651
chr11495547495630E072-15520
chr11495663496075E072-15075
chr11496162496265E072-14885
chr11496298496347E072-14803
chr11496501496598E072-14552
chr11496751497301E072-13849
chr11497354497462E072-13688
chr11497599498241E072-12909
chr11498278498426E072-12724
chr11498451498524E072-12626
chr11498529498628E072-12522
chr11498693499250E072-11900
chr11499324499461E072-11689
chr11499488499581E072-11569
chr11501049501247E072-9903
chr11501292501441E072-9709
chr11501478501825E072-9325
chr11501848501898E072-9252
chr11502035502126E072-9024
chr11502174502387E072-8763
chr11502430502826E072-8324
chr11502859503105E072-8045
chr11533791534008E07222641
chr11534033534130E07222883
chr11534156534220E07223006
chr11476777476837E073-34313
chr11477085477135E073-34015
chr11477159477329E073-33821
chr11477457477585E073-33565
chr11479158479332E073-31818
chr11479455479574E073-31576
chr11494370494468E073-16682
chr11494512494631E073-16519
chr11494697495232E073-15918
chr11495269495499E073-15651
chr11495547495630E073-15520
chr11495663496075E073-15075
chr11496162496265E073-14885
chr11496298496347E073-14803
chr11501478501825E073-9325
chr11501848501898E073-9252
chr11502035502126E073-9024
chr11502174502387E073-8763
chr11502430502826E073-8324
chr11502859503105E073-8045
chr11533451533607E07322301
chr11533791534008E07322641
chr11468203468961E074-42189
chr11468994469034E074-42116
chr11469139469267E074-41883
chr11469367469461E074-41689
chr11476501476590E074-34560
chr11476777476837E074-34313
chr11477085477135E074-34015
chr11477159477329E074-33821
chr11477457477585E074-33565
chr11478958479092E074-32058
chr11479158479332E074-31818
chr11479455479574E074-31576
chr11493906494047E074-17103
chr11494058494130E074-17020
chr11494241494313E074-16837
chr11494370494468E074-16682
chr11494512494631E074-16519
chr11494697495232E074-15918
chr11495269495499E074-15651
chr11495547495630E074-15520
chr11495663496075E074-15075
chr11496162496265E074-14885
chr11496298496347E074-14803
chr11499603499701E074-11449
chr11499719499778E074-11372
chr11499830499904E074-11246
chr11500023500103E074-11047
chr11500150500204E074-10946
chr11500300500354E074-10796
chr11500379500437E074-10713
chr11500499500850E074-10300
chr11501049501247E074-9903
chr11501292501441E074-9709
chr11501478501825E074-9325
chr11501848501898E074-9252
chr11502035502126E074-9024
chr11502174502387E074-8763
chr11502430502826E074-8324
chr11502859503105E074-8045
chr11534033534130E07422883
chr11534156534220E07423006
chr11533116533378E08121966
chr11533451533607E08122301
chr11533791534008E08122641
chr11534033534130E08122883
chr11534156534220E08123006









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11506103508291E067-2859
chr11518423519269E0677273
chr11534247538855E06723097
chr11506103508291E068-2859
chr11518423519269E0687273
chr11534247538855E06823097
chr11506103508291E069-2859
chr11518423519269E0697273
chr11534247538855E06923097
chr11506103508291E070-2859
chr11534247538855E07023097
chr11554567555883E07043417
chr11506103508291E071-2859
chr11518423519269E0717273
chr11534247538855E07123097
chr11506103508291E072-2859
chr11518423519269E0727273
chr11534247538855E07223097
chr11506103508291E073-2859
chr11534247538855E07323097
chr11506103508291E074-2859
chr11518423519269E0747273
chr11534247538855E07423097
chr11506103508291E081-2859
chr11506103508291E082-2859
chr11518423519269E0827273
chr11534247538855E08223097
chr11554567555883E08243417
chr11555966556159E08244816
chr11556174556843E08245024