1. Supplementary Table 1

2. Supplementary Table 2 The results of screening stage analysis of colorectal cancer
SNPs were ranked according to their p Value in the screening stage of colorectal cancer. OR, Odds ratio; CI, confidence interval. ||Significance level for the departures from Hardy Weinberg equilibrium (HWE) in the control samples. †OR of minor allele from 2x2 allele frequency table. ‡p Values derived from Cochran-Armitage trend tests. Chromosomal positions are from NCBI build 36.

3. Supplementary Table 3 The results of screening stage analysis of colon cancer
SNPs were ranked according to their p Value in the screening stage of colon cancer. OR, Odds ratio; CI, confidence interval.
||Significance level for the departures from Hardy Weinberg equilibrium (HWE) in the control samples. †OR of minor allele from 2x2 allele frequency table. ‡ p Values derived from Cochran-Armitage trend tests. Chromosomal positions are from NCBI build 36.

4. Supplementary Table 4 The results of screening stage analysis of proximal colon cancer
SNPs were ranked according to their p Value in the screening stage of proximal colon cancer. OR, Odds ratio; CI, confidence interval. ||Significance level for the departures from Hardy Weinberg equilibrium (HWE) in the control samples. †OR of minor allele from 2x2 allele frequency table. ‡ p Values derived from Cochran-Armitage trend tests. Chromosomal positions are from NCBI build 36.

5. Supplementary Table 5 The results of screening stage analysis of distal colon cancer
SNPs were ranked according to their p Value in the screening stage of distal colon cancer. OR, Odds ratio; CI, confidence interval. ||Significance level for the departures from Hardy Weinberg equilibrium (HWE) in the control samples. †OR of minor allele from 2x2 allele frequency table. ‡p Values derived from Cochran-Armitage trend tests. Chromosomal positions are from NCBI build 36.

6. Supplementary Table 6 The results of screening stage analysis of rectal cancer
SNPs were ranked according to their p Value in the screening stage of rectal cancer. OR, Odds ratio; CI, confidence interval. ||Significance level for the departures from Hardy Weinberg equilibrium (HWE) in the control samples. †OR of minor allele from 2x2 allele frequency table. ‡p Values derived from Cochran-Armitage trend tests. Chromosomal positions are from NCBI build 36.

7. from Cochran-Armitage trend tests
Supplementary Table 7 SNPs mapping to SLC22A3 along with p Value obtained
from Cochran-Armitage trend tests
OR, Odds ratio; CI, confidence interval. †OR of minor allele from 2x2 allele frequency table. ‡p Values derived from Cochran-Armitage trend tests. Chromosomal positions are from NCBI build 36.

8. Supplementary Table 9 List of primers used for SNP discovery
Supplementary Table 8 The results of previously reported loci in screening stage
OR, Odds ratio; CI, confidence interval. †OR of minor allele from 2x2 allele frequency table. ‡p Values derived from Cochran-Armitage trend tests. || Minor allele frequency of control samples in the screening stage. ¶ Minor allele frequency of healthy control samples in the screening stage. Chromosomal positions are from NCBI build 36.
Supplementary Table 9 List of primers used for SNP discovery
List of optimal primer sequences as designed with Primer3.

9. Supplementary Table 10 Results of replication studies and meta-analysis for colon cancer in Japanese
OR, Odds ratio; CI, confidence interval. † OR of minor allele from 2 x 2 allele frequency table. ‡ p Values derived from Cochran-Armitage trend tests. § Result of Breslow-Day test. || Meta-analysis of all three studies. Odds ratio and p Values for independence test were calculated by Mantel-Haenzel method.
Supplementary Table 11 Results of replication studies and meta-analysis for colorectal
cancer in Japanese
OR, Odds ratio; CI, confidence interval. † OR of minor allele from 2 x 2 allele frequency table. ‡ p Values derived from Cochran-Armitage trend tests. § Result of Breslow-Day test. || Meta-analysis of all three studies. Odds ratio and p Values for independence test were calculated by Mantel-Haenzel method.