rs4620789

Homo sapiens
G>T
TMTC2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0169 (5082/29944,GnomAD)
G==0190 (5535/29118,TOPMED)
G==0245 (1226/5008,1000G)
G==0117 (449/3854,ALSPAC)
G==0114 (422/3708,TWINSUK)
chr12:82714616 (GRCh38.p7) (12q21.31)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.82714616G>T
GRCh37.p13 chr 12NC_000012.11:g.83108395G>T

Gene: TMTC2, transmembrane and tetratricopeptide repeat containing 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TMTC2 transcript variant 2NM_001320321.1:c.N/AIntron Variant
TMTC2 transcript variant 3NM_001320322.1:c.N/AIntron Variant
TMTC2 transcript variant 1NM_152588.2:c.N/AIntron Variant
TMTC2 transcript variant X1XM_017018884.1:c.N/AIntron Variant
TMTC2 transcript variant X3XR_001748601.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.275T=0.725
1000GenomesAmericanSub694G=0.230T=0.770
1000GenomesEast AsianSub1008G=0.364T=0.636
1000GenomesEuropeSub1006G=0.134T=0.866
1000GenomesGlobalStudy-wide5008G=0.245T=0.755
1000GenomesSouth AsianSub978G=0.210T=0.790
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.117T=0.883
The Genome Aggregation DatabaseAfricanSub8704G=0.234T=0.766
The Genome Aggregation DatabaseAmericanSub834G=0.210T=0.790
The Genome Aggregation DatabaseEast AsianSub1610G=0.384T=0.616
The Genome Aggregation DatabaseEuropeSub18494G=0.118T=0.881
The Genome Aggregation DatabaseGlobalStudy-wide29944G=0.169T=0.830
The Genome Aggregation DatabaseOtherSub302G=0.180T=0.820
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.190T=0.809
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.114T=0.886
PMID Title Author Journal
23089632A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.Wang JCMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs46207899.63E-06alcohol dependence23089632

eQTL of rs4620789 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 rs4620789 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 )
chr128308461183084661E067-23734
chr128308480583084859E067-23536
chr128308489583084945E067-23450
chr128308529683085598E067-22797
chr128308584483086057E067-22338
chr128308645183086506E067-21889
chr128309264983092732E067-15663
chr128310178883102841E067-5554
chr128312670283126742E06718307
chr128312735283127402E06718957
chr128313874983139207E06730354
chr128313930083139355E06730905
chr128313938583139441E06730990
chr128313965183139759E06731256
chr128314052883140734E06732133
chr128314079283140939E06732397
chr128314275783142818E06734362
chr128314284383142997E06734448
chr128314867483148977E06740279
chr128314898083149030E06740585
chr128315020683150379E06741811
chr128315077183150862E06742376
chr128315217883152228E06743783
chr128315265183152813E06744256
chr128315282183153005E06744426
chr128315306583153431E06744670
chr128315371283153762E06745317
chr128315402583154112E06745630
chr128315418983154243E06745794
chr128315426983154499E06745874
chr128315451683154576E06746121
chr128315494883155080E06746553
chr128315708083157301E06748685
chr128315757583157634E06749180
chr128307596383076003E068-32392
chr128307606783076422E068-31973
chr128307655183076950E068-31445
chr128308584483086057E068-22338
chr128308645183086506E068-21889
chr128308942783089523E068-18872
chr128308952983089650E068-18745
chr128308970383089759E068-18636
chr128310059983100649E068-7746
chr128310069483100744E068-7651
chr128310093983101300E068-7095
chr128310139683101633E068-6762
chr128310178883102841E068-5554
chr128310289583102978E068-5417
chr128311501483115064E0686619
chr128313874983139207E06830354
chr128313930083139355E06830905
chr128313938583139441E06830990
chr128313965183139759E06831256
chr128313976083139824E06831365
chr128314019483140289E06831799
chr128314052883140734E06832133
chr128314079283140939E06832397
chr128314145683141510E06833061
chr128314157483141635E06833179
chr128314867483148977E06840279
chr128314898083149030E06840585
chr128314935883149572E06840963
chr128315077183150862E06842376
chr128315089483151108E06842499
chr128315114883151271E06842753
chr128315131683151356E06842921
chr128315144483151793E06843049
chr128315217883152228E06843783
chr128315265183152813E06844256
chr128315282183153005E06844426
chr128315306583153431E06844670
chr128315371283153762E06845317
chr128315402583154112E06845630
chr128315418983154243E06845794
chr128315426983154499E06845874
chr128315451683154576E06846121
chr128315494883155080E06846553
chr128307564183075695E069-32700
chr128307596383076003E069-32392
chr128307606783076422E069-31973
chr128307655183076950E069-31445
chr128308461183084661E069-23734
chr128308480583084859E069-23536
chr128308489583084945E069-23450
chr128309210783092306E069-16089
chr128309264983092732E069-15663
chr128309277183092837E069-15558
chr128310139683101633E069-6762
chr128310178883102841E069-5554
chr128310289583102978E069-5417
chr128310319383103239E069-5156
chr128310328683103406E069-4989
chr128310369283104106E069-4289
chr128311489583114970E0696500
chr128311501483115064E0696619
chr128313848583138589E06930090
chr128313868783138737E06930292
chr128313874983139207E06930354
chr128313930083139355E06930905
chr128313938583139441E06930990
chr128313965183139759E06931256
chr128313976083139824E06931365
chr128314019483140289E06931799
chr128314052883140734E06932133
chr128314079283140939E06932397
chr128314145683141510E06933061
chr128314157483141635E06933179
chr128314215783142207E06933762
chr128314228283142367E06933887
chr128314275783142818E06934362
chr128314284383142997E06934448
chr128314867483148977E06940279
chr128314898083149030E06940585
chr128314935883149572E06940963
chr128315020683150379E06941811
chr128315051683150670E06942121
chr128315077183150862E06942376
chr128315089483151108E06942499
chr128315114883151271E06942753
chr128315131683151356E06942921
chr128315144483151793E06943049
chr128315217883152228E06943783
chr128315265183152813E06944256
chr128315426983154499E06945874
chr128315451683154576E06946121
chr128315494883155080E06946553
chr128315757583157634E06949180
chr128307596383076003E070-32392
chr128307606783076422E070-31973
chr128307655183076950E070-31445
chr128308461183084661E070-23734
chr128308480583084859E070-23536
chr128308489583084945E070-23450
chr128308529683085598E070-22797
chr128308584483086057E070-22338
chr128308645183086506E070-21889
chr128310178883102841E070-5554
chr128312573483125819E07017339
chr128312648583126539E07018090
chr128312670283126742E07018307
chr128312735283127402E07018957
chr128313848583138589E07030090
chr128313868783138737E07030292
chr128313874983139207E07030354
chr128313930083139355E07030905
chr128313938583139441E07030990
chr128313965183139759E07031256
chr128313976083139824E07031365
chr128314019483140289E07031799
chr128314052883140734E07032133
chr128314079283140939E07032397
chr128305922083059363E071-49032
chr128308584483086057E071-22338
chr128308881483089100E071-19295
chr128308942783089523E071-18872
chr128308952983089650E071-18745
chr128309210783092306E071-16089
chr128309264983092732E071-15663
chr128310093983101300E071-7095
chr128310139683101633E071-6762
chr128310178883102841E071-5554
chr128310289583102978E071-5417
chr128310319383103239E071-5156
chr128311489583114970E0716500
chr128311501483115064E0716619
chr128313868783138737E07130292
chr128313874983139207E07130354
chr128313930083139355E07130905
chr128313938583139441E07130990
chr128313965183139759E07131256
chr128313976083139824E07131365
chr128314019483140289E07131799
chr128314052883140734E07132133
chr128314079283140939E07132397
chr128314145683141510E07133061
chr128314157483141635E07133179
chr128314275783142818E07134362
chr128314284383142997E07134448
chr128314335883143522E07134963
chr128314662683146805E07138231
chr128315051683150670E07142121
chr128315077183150862E07142376
chr128315089483151108E07142499
chr128315114883151271E07142753
chr128315131683151356E07142921
chr128315144483151793E07143049
chr128315217883152228E07143783
chr128315265183152813E07144256
chr128315282183153005E07144426
chr128315306583153431E07144670
chr128315402583154112E07145630
chr128315418983154243E07145794
chr128315426983154499E07145874
chr128315451683154576E07146121
chr128315494883155080E07146553
chr128315708083157301E07148685
chr128315757583157634E07149180
chr128306696583067196E072-41199
chr128307596383076003E072-32392
chr128307606783076422E072-31973
chr128307655183076950E072-31445
chr128308942783089523E072-18872
chr128309210783092306E072-16089
chr128309942683099466E072-8929
chr128310139683101633E072-6762
chr128310178883102841E072-5554
chr128310289583102978E072-5417
chr128313813983138299E07229744
chr128313848583138589E07230090
chr128313868783138737E07230292
chr128313874983139207E07230354
chr128313930083139355E07230905
chr128313938583139441E07230990
chr128313965183139759E07231256
chr128314052883140734E07232133
chr128314079283140939E07232397
chr128314145683141510E07233061
chr128314157483141635E07233179
chr128314275783142818E07234362
chr128314284383142997E07234448
chr128314335883143522E07234963
chr128315426983154499E07245874
chr128315451683154576E07246121
chr128315494883155080E07246553
chr128309210783092306E073-16089
chr128309264983092732E073-15663
chr128310178883102841E073-5554
chr128315144483151793E07343049
chr128315217883152228E07343783
chr128315265183152813E07344256
chr128315282183153005E07344426
chr128306696583067196E074-41199
chr128307596383076003E074-32392
chr128307606783076422E074-31973
chr128307655183076950E074-31445
chr128308584483086057E074-22338
chr128308645183086506E074-21889
chr128308881483089100E074-19295
chr128308942783089523E074-18872
chr128308952983089650E074-18745
chr128308970383089759E074-18636
chr128309210783092306E074-16089
chr128309264983092732E074-15663
chr128309277183092837E074-15558
chr128309942683099466E074-8929
chr128309968683099756E074-8639
chr128309982383099883E074-8512
chr128310059983100649E074-7746
chr128310069483100744E074-7651
chr128310093983101300E074-7095
chr128310139683101633E074-6762
chr128310178883102841E074-5554
chr128310289583102978E074-5417
chr128310319383103239E074-5156
chr128310328683103406E074-4989
chr128310369283104106E074-4289
chr128312464383125157E07416248
chr128312520683125404E07416811
chr128312550683125631E07417111
chr128313813983138299E07429744
chr128313848583138589E07430090
chr128313868783138737E07430292
chr128313874983139207E07430354
chr128313930083139355E07430905
chr128313938583139441E07430990
chr128313965183139759E07431256
chr128313976083139824E07431365
chr128314019483140289E07431799
chr128314052883140734E07432133
chr128314079283140939E07432397
chr128314145683141510E07433061
chr128314157483141635E07433179
chr128314275783142818E07434362
chr128314284383142997E07434448
chr128314335883143522E07434963
chr128314867483148977E07440279
chr128314898083149030E07440585
chr128314935883149572E07440963
chr128315020683150379E07441811
chr128315051683150670E07442121
chr128315077183150862E07442376
chr128315089483151108E07442499
chr128315114883151271E07442753
chr128315131683151356E07442921
chr128315144483151793E07443049
chr128315217883152228E07443783
chr128315265183152813E07444256
chr128315282183153005E07444426
chr128315306583153431E07444670
chr128315371283153762E07445317
chr128315402583154112E07445630
chr128315418983154243E07445794
chr128315426983154499E07445874
chr128307564183075695E081-32700
chr128307596383076003E081-32392
chr128307606783076422E081-31973
chr128308584483086057E081-22338
chr128315131683151356E08142921
chr128307606783076422E082-31973
chr128307655183076950E082-31445
chr128308584483086057E082-22338
chr128309277183092837E082-15558
chr128314019483140289E08231799
chr128314145683141510E08233061










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr128307931283082294E067-26101
chr128308229583082382E067-26013
chr128308245483082679E067-25716
chr128308269083082846E067-25549
chr128308319283083515E067-24880
chr128308363683083923E067-24472
chr128308395683084174E067-24221
chr128309288183093376E067-15019
chr128307931283082294E068-26101
chr128308229583082382E068-26013
chr128308245483082679E068-25716
chr128308269083082846E068-25549
chr128308319283083515E068-24880
chr128308363683083923E068-24472
chr128308395683084174E068-24221
chr128309288183093376E068-15019
chr128307931283082294E069-26101
chr128308229583082382E069-26013
chr128308245483082679E069-25716
chr128308269083082846E069-25549
chr128308319283083515E069-24880
chr128308363683083923E069-24472
chr128308395683084174E069-24221
chr128309288183093376E069-15019
chr128307931283082294E070-26101
chr128308229583082382E070-26013
chr128308245483082679E070-25716
chr128308269083082846E070-25549
chr128308319283083515E070-24880
chr128308363683083923E070-24472
chr128308395683084174E070-24221
chr128309288183093376E070-15019
chr128307931283082294E071-26101
chr128308229583082382E071-26013
chr128308245483082679E071-25716
chr128308269083082846E071-25549
chr128308319283083515E071-24880
chr128308363683083923E071-24472
chr128308395683084174E071-24221
chr128309288183093376E071-15019
chr128307931283082294E072-26101
chr128308229583082382E072-26013
chr128308245483082679E072-25716
chr128308269083082846E072-25549
chr128308319283083515E072-24880
chr128308363683083923E072-24472
chr128308395683084174E072-24221
chr128309288183093376E072-15019
chr128307931283082294E073-26101
chr128308229583082382E073-26013
chr128308245483082679E073-25716
chr128308269083082846E073-25549
chr128308319283083515E073-24880
chr128308363683083923E073-24472
chr128308395683084174E073-24221
chr128309288183093376E073-15019
chr128307931283082294E074-26101
chr128308229583082382E074-26013
chr128308245483082679E074-25716
chr128308269083082846E074-25549
chr128308319283083515E074-24880
chr128308363683083923E074-24472
chr128308395683084174E074-24221
chr128309288183093376E074-15019
chr128307931283082294E081-26101
chr128308229583082382E081-26013
chr128308245483082679E081-25716
chr128308269083082846E081-25549
chr128307931283082294E082-26101
chr128308229583082382E082-26013
chr128308245483082679E082-25716
chr128308269083082846E082-25549
chr128308319283083515E082-24880
chr128308363683083923E082-24472
chr128308395683084174E082-24221