Table 1

Case-control association results obtained by logistic regression analyses

SNP*RegionNearby geneVariant typeRisk alleleRAF cases/controlsOR95% CIP value
rs120809291p33SLC5A9Intronic variantT0.73/0.711.086(0.85 to 1.39)0.5093
rs726474841p36.12CDC42/WNTIntergenic variantC0.08/0.081.096(0.72 to 1.66)0.6656
rs109112511q25.3LAMC1Intronic variantA0.58/0.590.9767(0.78 to 1.23)0.8409
rs66911701q41DUSP10Intergenic variantT0.34/0.360.9123(0.72 to 1.15)0.4376
rs119037572q32.3NABP1Intergenic variantC0.13/0.150.8341(0.61 to 1.15)0.2653
rs9921572q35PNKD/TMBIM1Intronic variantA0.58/0.51.36(1.09 to 1.7)0.007454
rs116763482q35CXCR2Intergenic variantT0.49/0.540.8345(0.67 to 1.03)0.09742
rs8124813p14.1LRIG1Intronic variantG0.53/0.521.022(0.82 to 1.28)0.8472
rs353603283p22.1CTNNB1intergenic variantA0.14/0.140.9986(0.72 to 1.38)0.9931
rs109365993q26.2TERCSynonymous variantC0.78/0.751.174(0.89 to 1.54)0.2474
rs71367024q13.2LARP4/DIP2BIntergenic variantT0.32/0.340.9124(0.72 to 1.16)0.4501
rs39874q26NDST3Intergenic variantG0.45/0.460.9761(0.78 to 1.22)0.831
rs27361005p15.33TERTIntronic variantA0.5/0.520.9495(0.76 to 1.19)0.6472
rs6471615q31.1PITX1Intronic variantA0.73/0.691.196(0.94 to 1.52)0.1458
rs13213116p1.2CDKN1AIntergenic variantA0.29/0.271.086(0.84 to 1.4)0.527
rs47116896p21.1TFEBIntronic variantA0.54/0.541.01(0.81 to 1.27)0.9282
rs119871938p12DUSP4Intergenic variantC0.7/0.740.8091(0.63 to 1.05)0.1055
rs168927668q23.3EIF3HIntergenic variantC0.08/0.051.686(1.09 to 2.62)0.01959
rs64696568q23.3EIF3HIntragenic variantA0.9/0.891.112(0.78 to 1.58)0.5505
rs69832678q24.21MYCNon-coding transcript variant/intronic variantG0.54/0.511.099(0.88 to 1.37)0.4035
rs7197259p24TPD52L3/UHRF2Intronic variantA0.62/0.581.198(0.95 to 1.51)0.1215
rs1079566810p14ARN5SP299/GATA3Intronic variantA0.3/0.330.8803(0.69 to 1.12)0.2995
rs70401710q22.3ZMIZ1-AS1Intronic variantG0.57/0.51.307(1.04 to 1.64)0.02218
rs103520910q24.2ABCC2/MRP2Intergenic variantT0.16/0.160.9457(0.7 to 1.28)0.7188
rs1119016410q24.2SLC25A28Intergenic variantG0.2/0.230.8207(0.62 to 1.08)0.1657
rs1119617210q25.2TCF7L2Intronic variantA0.11/0.170.648(0.46 to 0.91)0.01186
rs1224100810q25.2VTI1AIntronic variantC0.11/0.091.272(0.87 to 1.86)0.2129
rs424621511q12.2FEN13'-UTR variantT0.3/0.330.8561(0.67 to 1.09)0.2136
rs17453711q12.2MYRFIntronic variantG0.7/0.671.161(0.91 to 1.48)0.226
rs153511q12.2FADS2Intronic variantA0.69/0.661.168(0.92 to 1.49)0.206
rs17455011q12.2FADS1Intronic variantT0.69/0.671.124(0.88 to 1.43)0.3422
rs382499911q13.4POLD3Intronic variantG0.53/0.491.146(0.92 to 1.43)0.2257
rs380284211q23.1COLCA1/COLCA2Intronic variantC0.26/0.260.9952(0.78 to 1.28)0.9696
rs223812612p13.2ETV6Intronic variantG0.14/0.160.8391(0.61 to 1.15)0.2764
rs1084943212p13.31CD9Intronic variantT0.88/0.881.065(0.75 to 1.52)0.7295
rs1106443712p13.31SPSB2Splice acceptor variantC1/0.992.453(0.57 to 10.48)0.2256
rs321790112p13.32CCND2Intronic variantG0.38/0.341.162(0.92 to 1.47)0.2046
rs1077421412p13.32CCND2Intronic variantT0.37/0.351.125(0.89 to 1.42)0.3242
rs321781012p13.32CCND2Intronic variantT0.12/0.081.686(1.16 to 2.45)0.006237
rs1116955212q13.12DIP2B/ATF1Intergenic variantC0.76/0.760.9557(0.74 to 1.24)0.7319
rs318450412q24.12SH2B3Mis-sense variantC0.58/0.561.066(0.85 to 1.33)0.5737
rs5933612q24.21TBX3Intronic variantT0.54/0.521.092(0.87 to 1.37)0.4528
rs7320812012q24.22NOS1Intronic variantG0.06/0.051.053(0.64 to 1.74)0.8393
rs444423514q22.2BMP4Intergenic variantC0.56/0.551.036(0.83 to 1.3)0.7544
rs195763614q22.2BMP4Intronic variantT0.41/0.41.044(0.83 to 1.31)0.7078
rs1709498314q23.1RTN1Intergenic variantG0.86/0.860.9959(0.72 to 1.38)0.9803
rs477958415q13.3GREM1Intergenic variantT0.25/0.171.573(1.21 to 2.04)0.0006432
rs992921816q22.1CDH1Intronic variantG0.72/0.691.169(0.91 to 1.49)0.212
rs1694183516q24.1FOXL1Intergenic variantC0.17/0.180.9193(0.68 to 1.24)0.5842
rs1260352617q13.3NXNIntronic variantC0.01/0.011.368(0.45 to 4.13)0.5786
rs493982718q21.1SMAD7Intronic variantT0.56/0.551.063(0.85 to 1.33)0.5909
rs1297029118q22.3TSHZ1Intergenic variantA0.04/0.031.127(0.6 to 2.12)0.7105
rs1041121019q13.11RHPN2Intronic variantC0.87/0.870.9811(0.71 to 1.36)0.9099
rs224171419q13.2B9D2Mis-sense variant/2 kb upstream variantC0.67/0.651.096(0.86 to 1.39)0.4517
rs180046919q13.2TGFB12 kb upstream variant/0.5 kb downstream variantG0.67/0.651.102(0.87 to 1.4)0.4215
rs242327920p12.3HAQ1Intergenic variantC0.28/0.310.8595(0.67 to 1.1)0.2333
rs96125320p12.3BMP2Intergenic variantA0.34/0.321.085(0.86 to 1.37)0.4941
rs481380220p12.3BMP2Regulatory region variant?G0.36/0.321.216(0.96 to 1.54)0.1046
rs606682520q13.13PREX1Intronic variantA0.6/0.581.113(0.89 to 1.39)0.3445
rs606123120q13.33LAMA5Intergenic variantC0.78/0.721.412(1.08 to 1.85)0.01189
rs492538620q13.33LAMA5Intronic variantC0.73/0.681.261(0.98 to 1.62)0.06688
rs5934683Xp22.2SHROOM2Intronic variantC0.59/0.610.9276(0.71 to 1.22)0.5873
  • Association results for 216 SPS cases and 526 controls. Results are based on the reported risk allele from previous CRC GWAS. Statistically significant associations are denoted in bold (p value <0.05).

  • *SNPs with genotyping success rate below 90% were removed from subsequent analyses (including rs7229639, rs3764482). We also removed a monomorphic SNP (rs10904849).

  • CRC, colorectal cancer; GWAS, genome-wide association studies; RAF, risk allele frequency; SPS, serrated polyposis syndrome; UTR, untranslated region.