Appendix.
Summary of all genes and SNPs assessed
| Gene | Chromo some Location |
SNP | Region | MAF | Major/ Minor Allele |
FDR HWE Probability |
Colon Homozygote Rare OR |
Rectal Homozygote Rare OR |
|---|---|---|---|---|---|---|---|---|
| Smad1 | 4q31 | rs714195 | intronic | 0.42 | G/A | 0.73 | 0.99 (0.80, 1.21) | 1.02 (0.74, 1.39) |
| rs6537355 | 5upstream | 0.12 | A/G | 0.88 | 1.35 (0.72, 2.54) | 0.93 (0.37, 2.32) | ||
| rs2118438 | intronic | 0.19 | G/A | 0.61 | 1.11 (0.75, 1.65) | 1.29 (0.72, 2.34) | ||
| rs1016792 | intronic | 0.19 | T/C | 1.00 | 1.00 (0.69, 1.46) | 0.90 (0.51, 1.58) | ||
| rs12505085 | 3downstream | 0.23 | A/G | 0.89 | 0.88 (0.65, 1.20) | 0.91 (0.57, 1.47) | ||
| Smad2 | 18q21.1 | rs1787199 | intronic | 0.46 | A /T | 1.00 | 1.24 (1.03, 1.51) | 0.83 (0.63, 1.08) |
| rs1792658 | intronic | 0.21 | A/C | 0.96 | 1.18 (0.88, 1.58) | 1.12 (0.72, 1.74) | ||
| rs1792689 | intronic | 0.13 | C/T | 0.95 | 1.30 (0.79, 2.13) | 0.95 (0.41, 2.22) | ||
| rs4940086 | intronic | 0.33 | T/C | 1.00 | 1.33 (1.06, 1.66) | 1.05 (0.77, 1.42) | ||
| Smad3 | 15q22.33 | rs731874 | intronic | 0.28 | G/A | 1.00 | 1.06 (0.82, 1.37) | 0.94 (0.65, 1.37) |
| rs745103 | intronic | 0.45 | T/C | 0.86 | 0.96 (0.79, 1.16) | 0.98 (0.75, 1.29) | ||
| rs750766 | Unknown | 0.48 | G/A | 1.00 | 0.93 (0.77, 1.13) | 1.06 (0.81, 1.39) | ||
| rs893473 | intronic | 0.17 | C/T | 1.00 | 0.99 (0.69, 1.40) | 1.06 (0.71, 1.59) | ||
| rs991157 | intronic | 0.30 | G/A | 1.00 | 0.96 (0.75, 1.23) | 1.07 (0.75, 1.51) | ||
| rs1470003 | intronic | 0.48 | G/C | 0.96 | 0.95 (0.79, 1.15) | 1.19 (0.90, 1.57) | ||
| rs1498506 | intronic | 0.48 | A/C | 1.00 | 0.69 (0.57, 0.84) | 0.96 (0.72, 1.26) | ||
| rs1866317 | Unknown | 0.11 | C/G | 1.00 | 0.92 (0.48, 1.76) | 1.65 (0.77, 3.54) | ||
| rs1992215 | Unknown | 0.33 | T/C | 1.00 | 1.00 (0.80, 1.25) | 0.86 (0.62, 1.21) | ||
| rs2118610 | intronic | 0.45 | G/A | 0.61 | 0.94 (0.78, 1.14) | 1.02 (0.77, 1.36) | ||
| rs2118611 | intronic | 0.20 | A/G | 0.99 | 0.94 (0.66, 1.34) | 0.93 (0.62, 1.42) | ||
| rs2414937 | intronic | 0.20 | G/C | 1.00 | 0.67 (0.47, 0.97) | 1.02 (0.63, 1.67) | ||
| rs3743343 | 3utr | 0.24 | T/C | 1.00 | 1.15 (0.87, 1.52) | 1.10 (0.77, 1.58) | ||
| rs3784681 | intronic | 0.29 | G/C | 0.96 | 0.91 (0.71, 1.17) | 0.79 (0.56, 1.11) | ||
| rs3825977 | intronic | 0.19 | C/T | 1.00 | 1.01 (0.72, 1.42) | 0.76 (0.47, 1.24) | ||
| rs4147358 | intronic | 0.22 | C/A | 0.96 | 0.99 (0.73, 1.33) | 0.89 (0.60, 1.33) | ||
| rs4601989 | intronic | 0.24 | C/T | 0.68 | 0.81 (0.60, 1.08) | 0.66 (0.44, 1.00) | ||
| rs4776881 | intronic | 0.44 | T/C | 1.00 | 1.07 (0.89, 1.30) | 1.21 (0.92, 1.60) | ||
| rs4776890 | intronic | 0.40 | T/G | 0.96 | 0.97 (0.80, 1.19) | 0.96 (0.72, 1.28) | ||
| rs4776892 | intronic | 0.18 | A/T | 0.45 | 1.00 (0.67, 1.48) | 1.14 (0.69, 1.88) | ||
| rs7163381 | intronic | 0.26 | G/A | 1.00 | 0.79 (0.61, 1.03) | 1.06 (0.74, 1.51) | ||
| rs7173811 | intronic | 0.47 | C/T | 0.96 | 1.06 (0.88, 1.28) | 0.96 (0.73, 1.26) | ||
| rs7176870 | intronic | 0.43 | A/G | 1.00 | 1.06 (0.88, 1.29) | 1.19 (0.90, 1.58) | ||
| rs7181556 | intronic | 0.24 | C/T | 0.99 | 0.91 (0.69, 1.22) | 0.75 (0.50, 1.12) | ||
| rs7183244 | intronic | 0.39 | C/T | 0.84 | 1.00 (0.81, 1.23) | 1.04 (0.77, 1.41) | ||
| rs9972423 | intronic | 0.37 | T/A | 1.00 | 0.97 (0.79, 1.20) | 1.27 (0.94, 1.73) | ||
| rs11071933 | intronic | 0.33 | C/G | 1.00 | 0.94 (0.75, 1.16) | 0.92 (0.68, 1.25) | ||
| rs11637581 | intronic | 0.28 | C/T | 0.95 | 0.98 (0.76, 1.28) | 1.11 (0.77, 1.59) | ||
| rs11639295 | intronic | 0.31 | C/T | 1.00 | 0.88 (0.70, 1.12) | 0.83 (0.59, 1.16) | ||
| rs12102171 | intronic | 0.17 | C/T | 0.86 | 0.90 (0.62, 1.30) | 0.84 (0.49, 1.43) | ||
| rs12708492 | intronic | 0.48 | C/T | 1.00 | 1.02 (0.85, 1.24) | 1.10 (0.84, 1.44) | ||
| rs12901071 | intronic | 0.34 | A/G | 0.68 | 0.67 (0.53, 0.84) | 0.85 (0.60, 1.20) | ||
| rs12904944 | intronic | 0.34 | G/A | 1.00 | 0.81 (0.64, 1.01) | 1.07 (0.79, 1.47) | ||
| rs12907997 | intronic | 0.50 | C/T | 1.00 | 0.95 (0.78, 1.14) | 0.91 (0.70, 1.20) | ||
| rs12915039 | intronic | 0.24 | A/C | 1.00 | 1.01 (0.76, 1.35) | 1.08 (0.72, 1.61) | ||
| rs16950687 | intronic | 0.28 | A/G | 1.00 | 0.93 (0.72, 1.21) | 1.22 (0.85, 1.76) | ||
| rs17293443 | intronic | 0.22 | T/C | 0.92 | 0.85 (0.61, 1.19) | 1.74 (1.08, 2.82) | ||
| Smad4 | 18q21.1 | rs8096092 | intronic | 0.38 | C/A | 0.68 | 1.00 (0.81, 1.23) | 1.17 (0.87, 1.59) |
| rs10502913 | intronic | 0.24 | G/A | 0.74 | 0.81 (0.61, 1.08) | 1.09 (0.72, 1.67) | ||
| Smad7 | 18q21.1 | rs1316447 | intronic | 0.19 | C/T | 1.00 | 0.86 (0.60, 1.23) | 0.88 (0.53, 1.45) |
| rs2337106 | intronic | 0.47 | C/G | 1.00 | 0.88 (0.72, 1.06) | 1.11 (0.85, 1.45) | ||
| rs2337107 | intronic | 0.41 | G/A | 0.99 | 1.12 (0.92, 1.36) | 0.97 (0.74, 1.28) | ||
| rs3736242 | intronic | 0.22 | G/A | 1.00 | 0.94 (0.69, 1.28) | 1.33 (0.84, 2.09) | ||
| rs3764482 | intronic | 0.19 | C/T | 1.00 | 1.25 (0.86, 1.81) | 0.60 (0.34, 1.07) | ||
| rs4464148 | intronic | 0.31 | T/C | 1.00 | 1.06 (0.83, 1.35) | 0.76 (0.54, 1.09) | ||
| rs4939827 | intronic | 0.49 | T/C | 1.00 | 0.79 (0.66, 0.95) | 0.95 (0.73, 1.23) | ||
| rs4939832 | intronic | 0.24 | A/G | 1.00 | 1.00 (0.76, 1.32) | 1.29 (0.87, 1.92) | ||
| rs7238442 | intronic | 0.46 | T/C | 0.82 | 1.12 (0.93, 1.35) | 0.92 (0.71, 1.20) | ||
| rs12456328 | intronic | 0.13 | C/T | 1.00 | 0.81 (0.49, 1.33) | 1.16 (0.51, 2.66) | ||
| rs12953717 | intronic | 0.42 | C/T | 1.00 | 1.36 (1.12, 1.65) | 0.90 (0.68, 1.19) | ||
| TGFβ1 | 19q13.1 | rs1800469 | 5upstream | 0.31 | G/A | 1.00 | 0.65 (0.51, 0.84) | 0.98 (0.71, 1.38) |
| rs4803455 | intronic | 0.48 | C/A | 0.92 | 1.43 (1.18, 1.73) | 1.04 (0.79, 1.35) | ||
| TGFβR1 | 9q22 | rs1571590 | intronic | 0.20 | A/G | 0.67 | 1.39 (0.98, 1.96) | 1.42 (0.85, 2.39) |
| rs6478974 | intronic | 0.49 | T/A | 1.00 | 0.86 (0.71, 1.04) | 0.84 (0.63, 1.10) | ||
| rs10733710 | intronic | 0.20 | G/A | 0.96 | 1.06 (0.77, 1.46) | 1.22 (0.78, 1.91) |
Minor Allele Frequency (MAF) and FDR-adjusted Hardy-Weinberg Equilibrium (FDR HWE) based on white control population.
ORs are adjusted for age, center, race, and sex.
*
Indicates dominant model used due to MAF < 0.1