rs6005754

Homo sapiens
T>C
TTC28 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0444 (13303/29914,GnomAD)
T==0490 (14285/29116,TOPMED)
T==0476 (2383/5008,1000G)
T==0400 (1540/3854,ALSPAC)
T==0396 (1470/3708,TWINSUK)
chr22:28286628 (GRCh38.p7) (22q12.1)
ND
GWASdb2
1   publication(s)
See rs on genome
205 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 22NC_000022.11:g.28286628T>C
GRCh37.p13 chr 22NC_000022.10:g.28682616T>C

Gene: TTC28, tetratricopeptide repeat domain 28(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TTC28 transcriptNM_001145418.1:c.N/AIntron Variant
TTC28 transcript variant X1XM_005261405.2:c.N/AIntron Variant
TTC28 transcript variant X4XM_006724171.3:c.N/AIntron Variant
TTC28 transcript variant X2XM_011530018.2:c.N/AIntron Variant
TTC28 transcript variant X5XM_011530019.2:c.N/AIntron Variant
TTC28 transcript variant X6XM_011530020.1:c.N/AIntron Variant
TTC28 transcript variant X8XM_011530021.2:c.N/AIntron Variant
TTC28 transcript variant X7XM_011530022.1:c.N/AIntron Variant
TTC28 transcript variant X3XM_017028673.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.626C=0.374
1000GenomesAmericanSub694T=0.510C=0.490
1000GenomesEast AsianSub1008T=0.505C=0.495
1000GenomesEuropeSub1006T=0.412C=0.588
1000GenomesGlobalStudy-wide5008T=0.476C=0.524
1000GenomesSouth AsianSub978T=0.290C=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.400C=0.600
The Genome Aggregation DatabaseAfricanSub8706T=0.576C=0.424
The Genome Aggregation DatabaseAmericanSub836T=0.470C=0.530
The Genome Aggregation DatabaseEast AsianSub1616T=0.507C=0.493
The Genome Aggregation DatabaseEuropeSub18454T=0.377C=0.622
The Genome Aggregation DatabaseGlobalStudy-wide29914T=0.444C=0.555
The Genome Aggregation DatabaseOtherSub302T=0.360C=0.640
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.490C=0.509
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.396C=0.604
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs60057541.62E-05nicotine dependence (smoking)22377092

eQTL of rs6005754 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr22:28682616TTC28ENSG00000100154.10T>C3.2006e-9-393237Cerebellum

meQTL of rs6005754 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 )
chr222863979228639907E067-42709
chr222863998328640700E067-41916
chr222864078328641182E067-41434
chr222864313628643517E067-39099
chr222864361728643970E067-38646
chr222864399228644292E067-38324
chr222864445928644513E067-38103
chr222865571928656306E067-26310
chr222865680428656917E067-25699
chr222866412528664250E067-18366
chr222866429728664409E067-18207
chr222866447028664803E067-17813
chr222869323828693278E06710622
chr222869435128694429E06711735
chr222869451228694618E06711896
chr222869571428696105E06713098
chr222869676328696817E06714147
chr222872533928725477E06742723
chr222872558628725686E06742970
chr222872570628726091E06743090
chr222872889528728955E06746279
chr222872905528729155E06746439
chr222872924728729502E06746631
chr222863998328640700E068-41916
chr222864277728642851E068-39765
chr222864285228642991E068-39625
chr222864313628643517E068-39099
chr222864361728643970E068-38646
chr222864399228644292E068-38324
chr222864445928644513E068-38103
chr222864460528644693E068-37923
chr222864478628644958E068-37658
chr222865571928656306E068-26310
chr222869302828693090E06810412
chr222869323828693278E06810622
chr222869435128694429E06811735
chr222869533028695439E06812714
chr222869545228695566E06812836
chr222869559028695673E06812974
chr222869571428696105E06813098
chr222872533928725477E06842723
chr222872558628725686E06842970
chr222872570628726091E06843090
chr222872853128728651E06845915
chr222872877828728880E06846162
chr222872889528728955E06846279
chr222872905528729155E06846439
chr222872924728729502E06846631
chr222863998328640700E069-41916
chr222864078328641182E069-41434
chr222864313628643517E069-39099
chr222864361728643970E069-38646
chr222864399228644292E069-38324
chr222865571928656306E069-26310
chr222866412528664250E069-18366
chr222866429728664409E069-18207
chr222869302828693090E06910412
chr222869323828693278E06910622
chr222869435128694429E06911735
chr222869533028695439E06912714
chr222869545228695566E06912836
chr222869559028695673E06912974
chr222869571428696105E06913098
chr222872533928725477E06942723
chr222872558628725686E06942970
chr222872570628726091E06943090
chr222864811828648168E070-34448
chr222864844528648833E070-33783
chr222864886828648939E070-33677
chr222870498628705036E07022370
chr222870528828705338E07022672
chr222870550928705549E07022893
chr222871625028716300E07033634
chr222871630628716513E07033690
chr222872640228726452E07043786
chr222864078328641182E071-41434
chr222864135528641472E071-41144
chr222864313628643517E071-39099
chr222864361728643970E071-38646
chr222864399228644292E071-38324
chr222864445928644513E071-38103
chr222864460528644693E071-37923
chr222864478628644958E071-37658
chr222864516028645240E071-37376
chr222865571928656306E071-26310
chr222865680428656917E071-25699
chr222866412528664250E071-18366
chr222866429728664409E071-18207
chr222866447028664803E071-17813
chr222869302828693090E07110412
chr222869323828693278E07110622
chr222869350428694002E07110888
chr222869408528694225E07111469
chr222869435128694429E07111735
chr222869451228694618E07111896
chr222869484528694899E07112229
chr222869533028695439E07112714
chr222869545228695566E07112836
chr222869559028695673E07112974
chr222869571428696105E07113098
chr222869676328696817E07114147
chr222870467428704736E07122058
chr222870498628705036E07122370
chr222872558628725686E07142970
chr222872570628726091E07143090
chr222872763528727689E07145019
chr222872770328727753E07145087
chr222872797828728073E07145362
chr222872853128728651E07145915
chr222872877828728880E07146162
chr222872889528728955E07146279
chr222864078328641182E072-41434
chr222864313628643517E072-39099
chr222864361728643970E072-38646
chr222864399228644292E072-38324
chr222864445928644513E072-38103
chr222864460528644693E072-37923
chr222864478628644958E072-37658
chr222865571928656306E072-26310
chr222866500328665070E072-17546
chr222866507628665239E072-17377
chr222866541628665517E072-17099
chr222866561828665674E072-16942
chr222869302828693090E07210412
chr222869323828693278E07210622
chr222869435128694429E07211735
chr222869451228694618E07211896
chr222869533028695439E07212714
chr222869545228695566E07212836
chr222869559028695673E07212974
chr222869571428696105E07213098
chr222872533928725477E07242723
chr222872558628725686E07242970
chr222872570628726091E07243090
chr222864078328641182E073-41434
chr222864399228644292E073-38324
chr222864932528649714E073-32902
chr222866500328665070E073-17546
chr222866507628665239E073-17377
chr222866561828665674E073-16942
chr222872853128728651E07345915
chr222863998328640700E074-41916
chr222864078328641182E074-41434
chr222864135528641472E074-41144
chr222864161728642018E074-40598
chr222864277728642851E074-39765
chr222864285228642991E074-39625
chr222864313628643517E074-39099
chr222864361728643970E074-38646
chr222864399228644292E074-38324
chr222864445928644513E074-38103
chr222865571928656306E074-26310
chr222865680428656917E074-25699
chr222869302828693090E07410412
chr222869323828693278E07410622
chr222869435128694429E07411735
chr222869451228694618E07411896
chr222869484528694899E07412229
chr222869533028695439E07412714
chr222869545228695566E07412836
chr222869559028695673E07412974
chr222869571428696105E07413098
chr222869676328696817E07414147
chr222872533928725477E07442723
chr222872558628725686E07442970
chr222872570628726091E07443090
chr222872797828728073E07445362
chr222872853128728651E07445915
chr222872877828728880E07446162
chr222872889528728955E07446279
chr222863931528639426E081-43190
chr222863946228639513E081-43103
chr222863952628639784E081-42832
chr222863979228639907E081-42709
chr222863998328640700E081-41916
chr222864078328641182E081-41434
chr222864844528648833E081-33783
chr222865571928656306E081-26310
chr222865680428656917E081-25699
chr222867840628678710E081-3906
chr222867875328678907E081-3709
chr222867902728679215E081-3401
chr222867930128679550E081-3066
chr222868107228681170E081-1446
chr222869571428696105E08113098
chr222872533928725477E08142723
chr222872558628725686E08142970
chr222872570628726091E08143090
chr222872640228726452E08143786
chr222865571928656306E082-26310
chr222869533028695439E08212714
chr222869545228695566E08212836
chr222869559028695673E08212974
chr222869571428696105E08213098
chr222870408528704163E08221469
chr222871594228716082E08233326
chr222871609928716186E08233483
chr222871618828716247E08233572
chr222871625028716300E08233634
chr222871630628716513E08233690
chr222872484028725007E08242224
chr222872533928725477E08242723
chr222872558628725686E08242970
chr222872570628726091E08243090
chr222872640228726452E08243786










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr222870051028700665E06817894
chr222870070428700799E06818088