Case-control association results obtained by logistic regression analyses
| SNP* | Region | Nearby gene | Variant type | Risk allele | RAF cases/controls | OR | 95% CI | P value |
| rs12080929 | 1p33 | SLC5A9 | Intronic variant | T | 0.73/0.71 | 1.086 | (0.85 to 1.39) | 0.5093 |
| rs72647484 | 1p36.12 | CDC42/WNT | Intergenic variant | C | 0.08/0.08 | 1.096 | (0.72 to 1.66) | 0.6656 |
| rs10911251 | 1q25.3 | LAMC1 | Intronic variant | A | 0.58/0.59 | 0.9767 | (0.78 to 1.23) | 0.8409 |
| rs6691170 | 1q41 | DUSP10 | Intergenic variant | T | 0.34/0.36 | 0.9123 | (0.72 to 1.15) | 0.4376 |
| rs11903757 | 2q32.3 | NABP1 | Intergenic variant | C | 0.13/0.15 | 0.8341 | (0.61 to 1.15) | 0.2653 |
| rs992157 | 2q35 | PNKD/TMBIM1 | Intronic variant | A | 0.58/0.5 | 1.36 | (1.09 to1.7) | 0.007454 |
| rs11676348 | 2q35 | CXCR2 | Intergenic variant | T | 0.49/0.54 | 0.8345 | (0.67 to 1.03) | 0.09742 |
| rs812481 | 3p14.1 | LRIG1 | Intronic variant | G | 0.53/0.52 | 1.022 | (0.82 to 1.28) | 0.8472 |
| rs35360328 | 3p22.1 | CTNNB1 | intergenic variant | A | 0.14/0.14 | 0.9986 | (0.72 to 1.38) | 0.9931 |
| rs10936599 | 3q26.2 | TERC | Synonymous variant | C | 0.78/0.75 | 1.174 | (0.89 to 1.54) | 0.2474 |
| rs7136702 | 4q13.2 | LARP4/DIP2B | Intergenic variant | T | 0.32/0.34 | 0.9124 | (0.72 to 1.16) | 0.4501 |
| rs3987 | 4q26 | NDST3 | Intergenic variant | G | 0.45/0.46 | 0.9761 | (0.78 to 1.22) | 0.831 |
| rs2736100 | 5p15.33 | TERT | Intronic variant | A | 0.5/0.52 | 0.9495 | (0.76 to 1.19) | 0.6472 |
| rs647161 | 5q31.1 | PITX1 | Intronic variant | A | 0.73/0.69 | 1.196 | (0.94 to 1.52) | 0.1458 |
| rs1321311 | 6p1.2 | CDKN1A | Intergenic variant | A | 0.29/0.27 | 1.086 | (0.84 to 1.4) | 0.527 |
| rs4711689 | 6p21.1 | TFEB | Intronic variant | A | 0.54/0.54 | 1.01 | (0.81 to 1.27) | 0.9282 |
| rs11987193 | 8p12 | DUSP4 | Intergenic variant | C | 0.7/0.74 | 0.8091 | (0.63 to 1.05) | 0.1055 |
| rs16892766 | 8q23.3 | EIF3H | Intergenic variant | C | 0.08/0.05 | 1.686 | (1.09 to2.62) | 0.01959 |
| rs6469656 | 8q23.3 | EIF3H | Intragenic variant | A | 0.9/0.89 | 1.112 | (0.78 to 1.58) | 0.5505 |
| rs6983267 | 8q24.21 | MYC | Non-coding transcript variant/intronic variant | G | 0.54/0.51 | 1.099 | (0.88 to 1.37) | 0.4035 |
| rs719725 | 9p24 | TPD52L3/UHRF2 | Intronic variant | A | 0.62/0.58 | 1.198 | (0.95 to 1.51) | 0.1215 |
| rs10795668 | 10p14 | ARN5SP299/GATA3 | Intronic variant | A | 0.3/0.33 | 0.8803 | (0.69 to 1.12) | 0.2995 |
| rs704017 | 10q22.3 | ZMIZ1-AS1 | Intronic variant | G | 0.57/0.5 | 1.307 | (1.04 to1.64) | 0.02218 |
| rs1035209 | 10q24.2 | ABCC2/MRP2 | Intergenic variant | T | 0.16/0.16 | 0.9457 | (0.7 to 1.28) | 0.7188 |
| rs11190164 | 10q24.2 | SLC25A28 | Intergenic variant | G | 0.2/0.23 | 0.8207 | (0.62 to 1.08) | 0.1657 |
| rs11196172 | 10q25.2 | TCF7L2 | Intronic variant | A | 0.11/0.17 | 0.648 | (0.46 to0.91) | 0.01186 |
| rs12241008 | 10q25.2 | VTI1A | Intronic variant | C | 0.11/0.09 | 1.272 | (0.87 to 1.86) | 0.2129 |
| rs4246215 | 11q12.2 | FEN1 | 3'-UTR variant | T | 0.3/0.33 | 0.8561 | (0.67 to 1.09) | 0.2136 |
| rs174537 | 11q12.2 | MYRF | Intronic variant | G | 0.7/0.67 | 1.161 | (0.91 to 1.48) | 0.226 |
| rs1535 | 11q12.2 | FADS2 | Intronic variant | A | 0.69/0.66 | 1.168 | (0.92 to 1.49) | 0.206 |
| rs174550 | 11q12.2 | FADS1 | Intronic variant | T | 0.69/0.67 | 1.124 | (0.88 to 1.43) | 0.3422 |
| rs3824999 | 11q13.4 | POLD3 | Intronic variant | G | 0.53/0.49 | 1.146 | (0.92 to 1.43) | 0.2257 |
| rs3802842 | 11q23.1 | COLCA1/COLCA2 | Intronic variant | C | 0.26/0.26 | 0.9952 | (0.78 to 1.28) | 0.9696 |
| rs2238126 | 12p13.2 | ETV6 | Intronic variant | G | 0.14/0.16 | 0.8391 | (0.61 to 1.15) | 0.2764 |
| rs10849432 | 12p13.31 | CD9 | Intronic variant | T | 0.88/0.88 | 1.065 | (0.75 to 1.52) | 0.7295 |
| rs11064437 | 12p13.31 | SPSB2 | Splice acceptor variant | C | 1/0.99 | 2.453 | (0.57 to 10.48) | 0.2256 |
| rs3217901 | 12p13.32 | CCND2 | Intronic variant | G | 0.38/0.34 | 1.162 | (0.92 to 1.47) | 0.2046 |
| rs10774214 | 12p13.32 | CCND2 | Intronic variant | T | 0.37/0.35 | 1.125 | (0.89 to 1.42) | 0.3242 |
| rs3217810 | 12p13.32 | CCND2 | Intronic variant | T | 0.12/0.08 | 1.686 | (1.16 to2.45) | 0.006237 |
| rs11169552 | 12q13.12 | DIP2B/ATF1 | Intergenic variant | C | 0.76/0.76 | 0.9557 | (0.74 to 1.24) | 0.7319 |
| rs3184504 | 12q24.12 | SH2B3 | Mis-sense variant | C | 0.58/0.56 | 1.066 | (0.85 to 1.33) | 0.5737 |
| rs59336 | 12q24.21 | TBX3 | Intronic variant | T | 0.54/0.52 | 1.092 | (0.87 to 1.37) | 0.4528 |
| rs73208120 | 12q24.22 | NOS1 | Intronic variant | G | 0.06/0.05 | 1.053 | (0.64 to 1.74) | 0.8393 |
| rs4444235 | 14q22.2 | BMP4 | Intergenic variant | C | 0.56/0.55 | 1.036 | (0.83 to 1.3) | 0.7544 |
| rs1957636 | 14q22.2 | BMP4 | Intronic variant | T | 0.41/0.4 | 1.044 | (0.83 to 1.31) | 0.7078 |
| rs17094983 | 14q23.1 | RTN1 | Intergenic variant | G | 0.86/0.86 | 0.9959 | (0.72 to 1.38) | 0.9803 |
| rs4779584 | 15q13.3 | GREM1 | Intergenic variant | T | 0.25/0.17 | 1.573 | (1.21 to2.04) | 0.0006432 |
| rs9929218 | 16q22.1 | CDH1 | Intronic variant | G | 0.72/0.69 | 1.169 | (0.91 to 1.49) | 0.212 |
| rs16941835 | 16q24.1 | FOXL1 | Intergenic variant | C | 0.17/0.18 | 0.9193 | (0.68 to 1.24) | 0.5842 |
| rs12603526 | 17q13.3 | NXN | Intronic variant | C | 0.01/0.01 | 1.368 | (0.45 to 4.13) | 0.5786 |
| rs4939827 | 18q21.1 | SMAD7 | Intronic variant | T | 0.56/0.55 | 1.063 | (0.85 to 1.33) | 0.5909 |
| rs12970291 | 18q22.3 | TSHZ1 | Intergenic variant | A | 0.04/0.03 | 1.127 | (0.6 to 2.12) | 0.7105 |
| rs10411210 | 19q13.11 | RHPN2 | Intronic variant | C | 0.87/0.87 | 0.9811 | (0.71 to 1.36) | 0.9099 |
| rs2241714 | 19q13.2 | B9D2 | Mis-sense variant/2 kb upstream variant | C | 0.67/0.65 | 1.096 | (0.86 to 1.39) | 0.4517 |
| rs1800469 | 19q13.2 | TGFB1 | 2 kb upstream variant/0.5 kb downstream variant | G | 0.67/0.65 | 1.102 | (0.87 to 1.4) | 0.4215 |
| rs2423279 | 20p12.3 | HAQ1 | Intergenic variant | C | 0.28/0.31 | 0.8595 | (0.67 to 1.1) | 0.2333 |
| rs961253 | 20p12.3 | BMP2 | Intergenic variant | A | 0.34/0.32 | 1.085 | (0.86 to 1.37) | 0.4941 |
| rs4813802 | 20p12.3 | BMP2 | Regulatory region variant? | G | 0.36/0.32 | 1.216 | (0.96 to 1.54) | 0.1046 |
| rs6066825 | 20q13.13 | PREX1 | Intronic variant | A | 0.6/0.58 | 1.113 | (0.89 to 1.39) | 0.3445 |
| rs6061231 | 20q13.33 | LAMA5 | Intergenic variant | C | 0.78/0.72 | 1.412 | (1.08 to1.85) | 0.01189 |
| rs4925386 | 20q13.33 | LAMA5 | Intronic variant | C | 0.73/0.68 | 1.261 | (0.98 to 1.62) | 0.06688 |
| rs5934683 | Xp22.2 | SHROOM2 | Intronic variant | C | 0.59/0.61 | 0.9276 | (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.