rs12953717

Homo sapiens
C>T
SMAD7 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0358 (10711/29902,GnomAD)
T=0351 (10238/29118,TOPMED)
T=0305 (1526/5008,1000G)
T=0427 (1645/3854,ALSPAC)
T=0449 (1666/3708,TWINSUK)
chr18:48927559 (GRCh38.p7) (18q21.1)
AD
GWASdb2
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.48927559C>T
GRCh37.p13 chr 18NC_000018.9:g.46453929C>T
SMAD7 RefSeqGeneNG_023330.1:g.28153G>A

Gene: SMAD7, SMAD family member 7(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SMAD7 transcript variant 2NM_001190821.1:c.N/AIntron Variant
SMAD7 transcript variant 3NM_001190822.1:c.N/AIntron Variant
SMAD7 transcript variant 4NM_001190823.1:c.N/AIntron Variant
SMAD7 transcript variant 1NM_005904.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.775T=0.225
1000GenomesAmericanSub694C=0.680T=0.320
1000GenomesEast AsianSub1008C=0.693T=0.307
1000GenomesEuropeSub1006C=0.552T=0.448
1000GenomesGlobalStudy-wide5008C=0.695T=0.305
1000GenomesSouth AsianSub978C=0.750T=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.573T=0.427
The Genome Aggregation DatabaseAfricanSub8708C=0.748T=0.252
The Genome Aggregation DatabaseAmericanSub834C=0.710T=0.290
The Genome Aggregation DatabaseEast AsianSub1612C=0.697T=0.303
The Genome Aggregation DatabaseEuropeSub18446C=0.585T=0.414
The Genome Aggregation DatabaseGlobalStudy-wide29902C=0.641T=0.358
The Genome Aggregation DatabaseOtherSub302C=0.550T=0.450
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.648T=0.351
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.551T=0.449
PMID Title Author Journal
19843678Enrichment of low penetrance susceptibility loci in a Dutch familial colorectal cancer cohort.Middeldorp ACancer Epidemiol Biomarkers Prev
18231913Lack of a relationship between the common 18q24 variant rs12953717 and risk of chronic lymphocytic leukemia.Broderick PLeuk Lymphoma
24764655Genetic variations in colorectal cancer risk and clinical outcome.Zhang KWorld J Gastroenterol
21387313Genetic variation in bone morphogenetic protein and colon and rectal cancer.Slattery MLInt J Cancer
21365634Genetic variation in the transforming growth factor-beta signaling pathway and survival after diagnosis with colon and rectal cancer.Slattery MLCancer
27186328Genes, environment and gene expression in colon tissue: a pathway approach to determining functionality.Slattery MLInt J Mol Epidemiol Genet
22848671Association of eleven common, low-penetrance colorectal cancer susceptibility genetic variants at six risk loci with clinical outcome.Hoskins JMPLoS One
20124488Increased risk of colon cancer associated with a genetic polymorphism of SMAD7.Slattery MLCancer Res
21179028Replication study of SNP associations for colorectal cancer in Hong Kong Chinese.Ho JWBr J Cancer
23949881SMAD7 rs12953717 polymorphism contributes to increased risk of colorectal cancer.Hu YTumour Biol
19395656The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression.Pittman AMGenome Res
18372901Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.Tenesa ANat Genet
21221812A risk-associated single nucleotide polymorphism of SMAD7 is common to colorectal, gastric, and lung cancers in a Han Chinese population.Li XMol Biol Rep
21036793Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field.Ogino SGut
21068203Genetic variation in the TGF-beta signaling pathway and colon and rectal cancer risk.Slattery MLCancer Epidemiol Biomarkers Prev
19155440Meta association of colorectal cancer confirms risk alleles at 8q24 and 18q21.Curtin KCancer Epidemiol Biomarkers Prev
19357349Association of common genetic variants in SMAD7 and risk of colon cancer.Thompson CLCarcinogenesis
20659471Genetic heterogeneity in colorectal cancer associations between African and European americans.Kupfer SSGastroenterology
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res
24448986Genome-wide association study identifies a new SMAD7 risk variant associated with colorectal cancer risk in East Asians.Zhang BInt J Cancer
19562778Wnt antagonist gene polymorphisms and renal cancer.Hirata HCancer
21088106Associations between genetic variation in RUNX1, RUNX2, RUNX3, MAPK1 and eIF4E and riskof colon and rectal cancer: additional support for a TGF-beta-signaling pathway.Slattery MLCarcinogenesis
19011631Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer.Houlston RSNat Genet

P-Value

SNP ID p-value Traits Study
rs129537177.04E-05alcohol consumption23953852

eQTL of rs12953717 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 rs12953717 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 )
chr184641550446415626E067-38303
chr184641563146416236E067-37693
chr184642781846427898E067-26031
chr184642794046428014E067-25915
chr184642810846429237E067-24692
chr184644522046445816E067-8113
chr184644584346446059E067-7870
chr184644606246446186E067-7743
chr184644626746446311E067-7618
chr184644726846447378E067-6551
chr184644757446448109E067-5820
chr184644812246448177E067-5752
chr184644818446448269E067-5660
chr184644833746448442E067-5487
chr184644865346448833E067-5096
chr184644888446450560E067-3369
chr184645062746451701E067-2228
chr184645172246452088E067-1841
chr184645239546452435E067-1494
chr184645248146452601E067-1328
chr184645261346453409E067-520
chr184645343246453512E067-417
chr184645358046453719E067-210
chr184645372546453843E067-86
chr184645387046453977E0670
chr184645400546454457E06776
chr184645457046454617E067641
chr184645464346454797E067714
chr184645486046454907E067931
chr184645495146457607E0671022
chr184645777046457915E0673841
chr184645798146462426E0674052
chr184646250946462711E0678580
chr184646455446464679E06710625
chr184646468446464969E06710755
chr184646498846466909E06711059
chr184646695946467064E06713030
chr184646706546470420E06713136
chr184647045946471001E06716530
chr184647107246471558E06717143
chr184647184446471896E06717915
chr184647194346472059E06718014
chr184641379946413849E068-40080
chr184641385446414233E068-39696
chr184641430846414366E068-39563
chr184641437946414718E068-39211
chr184641489546415087E068-38842
chr184641516346415215E068-38714
chr184641522746415303E068-38626
chr184641550446415626E068-38303
chr184641563146416236E068-37693
chr184641624946416823E068-37106
chr184642290546424253E068-29676
chr184642794046428014E068-25915
chr184642810846429237E068-24692
chr184642938746429933E068-23996
chr184643034346430397E068-23532
chr184643042346430789E068-23140
chr184644522046445816E068-8113
chr184644584346446059E068-7870
chr184644606246446186E068-7743
chr184644626746446311E068-7618
chr184644668846447267E068-6662
chr184644726846447378E068-6551
chr184644757446448109E068-5820
chr184644812246448177E068-5752
chr184644818446448269E068-5660
chr184644833746448442E068-5487
chr184645062746451701E068-2228
chr184645172246452088E068-1841
chr184645261346453409E068-520
chr184645343246453512E068-417
chr184645358046453719E068-210
chr184645372546453843E068-86
chr184645387046453977E0680
chr184645400546454457E06876
chr184645457046454617E068641
chr184645464346454797E068714
chr184645486046454907E068931
chr184645495146457607E0681022
chr184645777046457915E0683841
chr184645798146462426E0684052
chr184646250946462711E0688580
chr184646281446462878E0688885
chr184646292946463000E0689000
chr184646304246463110E0689113
chr184646331846463407E0689389
chr184646351846464542E0689589
chr184646695946467064E06813030
chr184646706546470420E06813136
chr184647045946471001E06816530
chr184647184446471896E06817915
chr184648122646483089E06827297
chr184641385446414233E069-39696
chr184641430846414366E069-39563
chr184641437946414718E069-39211
chr184641489546415087E069-38842
chr184641516346415215E069-38714
chr184641522746415303E069-38626
chr184641550446415626E069-38303
chr184641563146416236E069-37693
chr184641624946416823E069-37106
chr184641696046417045E069-36884
chr184641721246417262E069-36667
chr184641729246417376E069-36553
chr184641743146417622E069-36307
chr184641972046419760E069-34169
chr184641983846419948E069-33981
chr184641997146420536E069-33393
chr184642062846420699E069-33230
chr184642290546424253E069-29676
chr184642794046428014E069-25915
chr184642810846429237E069-24692
chr184644072746441730E069-12199
chr184644522046445816E069-8113
chr184644584346446059E069-7870
chr184644606246446186E069-7743
chr184644626746446311E069-7618
chr184644668846447267E069-6662
chr184644726846447378E069-6551
chr184644757446448109E069-5820
chr184644812246448177E069-5752
chr184644818446448269E069-5660
chr184644833746448442E069-5487
chr184645062746451701E069-2228
chr184645172246452088E069-1841
chr184645239546452435E069-1494
chr184645248146452601E069-1328
chr184645261346453409E069-520
chr184645343246453512E069-417
chr184645358046453719E069-210
chr184645372546453843E069-86
chr184645387046453977E0690
chr184645400546454457E06976
chr184645457046454617E069641
chr184645464346454797E069714
chr184645486046454907E069931
chr184645495146457607E0691022
chr184645777046457915E0693841
chr184645798146462426E0694052
chr184646351846464542E0699589
chr184646455446464679E06910625
chr184646468446464969E06910755
chr184646498846466909E06911059
chr184646695946467064E06913030
chr184646706546470420E06913136
chr184647045946471001E06916530
chr184647107246471558E06917143
chr184647184446471896E06917915
chr184647194346472059E06918014
chr184641120046411377E070-42552
chr184641379946413849E070-40080
chr184641385446414233E070-39696
chr184641430846414366E070-39563
chr184641437946414718E070-39211
chr184641489546415087E070-38842
chr184641516346415215E070-38714
chr184641522746415303E070-38626
chr184641550446415626E070-38303
chr184641563146416236E070-37693
chr184641624946416823E070-37106
chr184641721246417262E070-36667
chr184641729246417376E070-36553
chr184641743146417622E070-36307
chr184641810246418142E070-35787
chr184641819146418263E070-35666
chr184641832346418392E070-35537
chr184641843446418484E070-35445
chr184641867246418716E070-35213
chr184641874546419201E070-34728
chr184641928646419464E070-34465
chr184641972046419760E070-34169
chr184641983846419948E070-33981
chr184641997146420536E070-33393
chr184642290546424253E070-29676
chr184642794046428014E070-25915
chr184642810846429237E070-24692
chr184642927246429369E070-24560
chr184644059146440649E070-13280
chr184644072746441730E070-12199
chr184644668846447267E070-6662
chr184644726846447378E070-6551
chr184644757446448109E070-5820
chr184644812246448177E070-5752
chr184644818446448269E070-5660
chr184644833746448442E070-5487
chr184644865346448833E070-5096
chr184644888446450560E070-3369
chr184645062746451701E070-2228
chr184645172246452088E070-1841
chr184645261346453409E070-520
chr184645343246453512E070-417
chr184645358046453719E070-210
chr184645372546453843E070-86
chr184645387046453977E0700
chr184645400546454457E07076
chr184645457046454617E070641
chr184645464346454797E070714
chr184645486046454907E070931
chr184645495146457607E0701022
chr184645798146462426E0704052
chr184646351846464542E0709589
chr184646455446464679E07010625
chr184646468446464969E07010755
chr184646498846466909E07011059
chr184646695946467064E07013030
chr184649487646495449E07040947
chr184649553646495596E07041607
chr184650351646503601E07049587
chr184650363846503705E07049709
chr184641379946413849E071-40080
chr184641385446414233E071-39696
chr184641430846414366E071-39563
chr184641437946414718E071-39211
chr184641489546415087E071-38842
chr184641516346415215E071-38714
chr184641522746415303E071-38626
chr184641550446415626E071-38303
chr184641563146416236E071-37693
chr184641624946416823E071-37106
chr184641997146420536E071-33393
chr184642747246427533E071-26396
chr184642760446427707E071-26222
chr184642781846427898E071-26031
chr184642794046428014E071-25915
chr184642810846429237E071-24692
chr184642927246429369E071-24560
chr184643254146432641E071-21288
chr184643279546432839E071-21090
chr184644072746441730E071-12199
chr184644522046445816E071-8113
chr184644584346446059E071-7870
chr184644606246446186E071-7743
chr184644626746446311E071-7618
chr184644668846447267E071-6662
chr184644726846447378E071-6551
chr184644757446448109E071-5820
chr184644812246448177E071-5752
chr184644818446448269E071-5660
chr184644833746448442E071-5487
chr184644865346448833E071-5096
chr184644888446450560E071-3369
chr184645062746451701E071-2228
chr184645172246452088E071-1841
chr184645239546452435E071-1494
chr184645248146452601E071-1328
chr184645261346453409E071-520
chr184645343246453512E071-417
chr184645358046453719E071-210
chr184645372546453843E071-86
chr184645387046453977E0710
chr184645400546454457E07176
chr184645457046454617E071641
chr184645464346454797E071714
chr184645486046454907E071931
chr184645495146457607E0711022
chr184645777046457915E0713841
chr184646250946462711E0718580
chr184646281446462878E0718885
chr184646292946463000E0719000
chr184646304246463110E0719113
chr184646331846463407E0719389
chr184646351846464542E0719589
chr184646455446464679E07110625
chr184646468446464969E07110755
chr184646498846466909E07111059
chr184646695946467064E07113030
chr184646706546470420E07113136
chr184647184446471896E07117915
chr184641550446415626E072-38303
chr184641563146416236E072-37693
chr184641983846419948E072-33981
chr184641997146420536E072-33393
chr184642290546424253E072-29676
chr184642781846427898E072-26031
chr184642794046428014E072-25915
chr184642810846429237E072-24692
chr184642927246429369E072-24560
chr184643279546432839E072-21090
chr184644072746441730E072-12199
chr184644584346446059E072-7870
chr184644606246446186E072-7743
chr184644626746446311E072-7618
chr184644668846447267E072-6662
chr184644726846447378E072-6551
chr184644757446448109E072-5820
chr184644812246448177E072-5752
chr184644818446448269E072-5660
chr184644833746448442E072-5487
chr184644865346448833E072-5096
chr184644888446450560E072-3369
chr184645062746451701E072-2228
chr184645172246452088E072-1841
chr184645248146452601E072-1328
chr184645261346453409E072-520
chr184645343246453512E072-417
chr184645358046453719E072-210
chr184645372546453843E072-86
chr184645387046453977E0720
chr184645400546454457E07276
chr184645457046454617E072641
chr184645464346454797E072714
chr184645486046454907E072931
chr184645495146457607E0721022
chr184645777046457915E0723841
chr184645798146462426E0724052
chr184646250946462711E0728580
chr184646281446462878E0728885
chr184646292946463000E0729000
chr184646351846464542E0729589
chr184646455446464679E07210625
chr184646468446464969E07210755
chr184646498846466909E07211059
chr184646695946467064E07213030
chr184646706546470420E07213136
chr184647045946471001E07216530
chr184647184446471896E07217915
chr184647194346472059E07218014
chr184641430846414366E073-39563
chr184641437946414718E073-39211
chr184641489546415087E073-38842
chr184641516346415215E073-38714
chr184641522746415303E073-38626
chr184641550446415626E073-38303
chr184641563146416236E073-37693
chr184641624946416823E073-37106
chr184641983846419948E073-33981
chr184641997146420536E073-33393
chr184642109346421133E073-32796
chr184642129746421418E073-32511
chr184642144046421507E073-32422
chr184642152246421618E073-32311
chr184642290546424253E073-29676
chr184642794046428014E073-25915
chr184642810846429237E073-24692
chr184642927246429369E073-24560
chr184644072746441730E073-12199
chr184644522046445816E073-8113
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chr184644668846447267E073-6662
chr184644726846447378E073-6551
chr184644757446448109E073-5820
chr184644812246448177E073-5752
chr184644818446448269E073-5660
chr184644833746448442E073-5487
chr184644865346448833E073-5096
chr184644888446450560E073-3369
chr184645062746451701E073-2228
chr184645172246452088E073-1841
chr184645239546452435E073-1494
chr184645248146452601E073-1328
chr184645261346453409E073-520
chr184645343246453512E073-417
chr184645358046453719E073-210
chr184645372546453843E073-86
chr184645387046453977E0730
chr184645400546454457E07376
chr184645457046454617E073641
chr184645464346454797E073714
chr184645486046454907E073931
chr184645495146457607E0731022
chr184645777046457915E0733841
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chr184646250946462711E0738580
chr184646351846464542E0739589
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chr184646468446464969E07310755
chr184646498846466909E07311059
chr184646695946467064E07313030
chr184646706546470420E07313136
chr184647045946471001E07316530
chr184647107246471558E07317143
chr184647184446471896E07317915
chr184647194346472059E07318014
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chr184641563146416236E074-37693
chr184641624946416823E074-37106
chr184641696046417045E074-36884
chr184641997146420536E074-33393
chr184642495046425035E074-28894
chr184642781846427898E074-26031
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chr184642938746429933E074-23996
chr184644072746441730E074-12199
chr184644522046445816E074-8113
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chr184644668846447267E074-6662
chr184644726846447378E074-6551
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chr184644812246448177E074-5752
chr184644818446448269E074-5660
chr184644833746448442E074-5487
chr184644865346448833E074-5096
chr184644888446450560E074-3369
chr184645062746451701E074-2228
chr184645172246452088E074-1841
chr184645239546452435E074-1494
chr184645248146452601E074-1328
chr184645261346453409E074-520
chr184645343246453512E074-417
chr184645358046453719E074-210
chr184645372546453843E074-86
chr184645387046453977E0740
chr184645400546454457E07476
chr184645457046454617E074641
chr184645464346454797E074714
chr184645486046454907E074931
chr184645495146457607E0741022
chr184645777046457915E0743841
chr184645798146462426E0744052
chr184646250946462711E0748580
chr184646281446462878E0748885
chr184646292946463000E0749000
chr184646304246463110E0749113
chr184646331846463407E0749389
chr184646351846464542E0749589
chr184646455446464679E07410625
chr184646468446464969E07410755
chr184646498846466909E07411059
chr184646695946467064E07413030
chr184646706546470420E07413136
chr184647045946471001E07416530
chr184647107246471558E07417143
chr184647184446471896E07417915
chr184647194346472059E07418014
chr184647977646479882E07425847
chr184647991446480069E07425985
chr184641430846414366E081-39563
chr184641437946414718E081-39211
chr184641489546415087E081-38842
chr184641516346415215E081-38714
chr184641522746415303E081-38626
chr184641550446415626E081-38303
chr184641563146416236E081-37693
chr184641624946416823E081-37106
chr184641696046417045E081-36884
chr184641867246418716E081-35213
chr184641874546419201E081-34728
chr184641928646419464E081-34465
chr184642144046421507E081-32422
chr184642794046428014E081-25915
chr184642810846429237E081-24692
chr184644072746441730E081-12199
chr184644726846447378E081-6551
chr184644757446448109E081-5820
chr184644888446450560E081-3369
chr184645062746451701E081-2228
chr184645172246452088E081-1841
chr184645239546452435E081-1494
chr184645248146452601E081-1328
chr184645261346453409E081-520
chr184645343246453512E081-417
chr184645358046453719E081-210
chr184645372546453843E081-86
chr184645387046453977E0810
chr184645495146457607E0811022
chr184646455446464679E08110625
chr184646468446464969E08110755
chr184646498846466909E08111059
chr184646695946467064E08113030
chr184646706546470420E08113136
chr184647045946471001E08116530
chr184647107246471558E08117143
chr184647184446471896E08117915
chr184647194346472059E08118014
chr184647977646479882E08125847
chr184647991446480069E08125985
chr184641437946414718E082-39211
chr184641489546415087E082-38842
chr184641516346415215E082-38714
chr184641522746415303E082-38626
chr184641550446415626E082-38303
chr184641563146416236E082-37693
chr184641743146417622E082-36307
chr184641810246418142E082-35787
chr184641819146418263E082-35666
chr184641832346418392E082-35537
chr184641843446418484E082-35445
chr184641867246418716E082-35213
chr184641874546419201E082-34728
chr184641928646419464E082-34465
chr184641972046419760E082-34169
chr184641983846419948E082-33981
chr184641997146420536E082-33393
chr184642290546424253E082-29676
chr184644888446450560E082-3369
chr184645062746451701E082-2228
chr184645172246452088E082-1841
chr184645457046454617E082641
chr184645464346454797E082714
chr184645486046454907E082931
chr184646455446464679E08210625
chr184646468446464969E08210755
chr184646498846466909E08211059










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr184647387646479746E06719947
chr184649991346503178E06745984
chr184647387646479746E06819947
chr184649991346503178E06845984
chr184647387646479746E06919947
chr184649991346503178E06945984
chr184647387646479746E07019947
chr184649991346503178E07045984
chr184647387646479746E07119947
chr184649991346503178E07145984
chr184647387646479746E07219947
chr184647387646479746E07319947
chr184649991346503178E07345984
chr184647387646479746E07419947
chr184647387646479746E08119947
chr184647387646479746E08219947
chr184649991346503178E08245984