Supplementary Figure 1 A B C D Colorectal cancer Colon cancer Proximal colon cancer Distal colon cancer

E Rectal cancer Supplementary Figure 1 A-E Manhattan plots for genome-wide association analysis of five subgroups. The title of each manhattan plot was shown on the top of each figure. Horizontal axis indicates chromosomal position. Vertical axis indicates -log10 P-values by Cochran- Armitage trend test. Blue line corresponds to the P-value of 2.5 ×10 -5.

Supplementary Figure 2 A Colorectal cancer =1.03 =1.05 =1.02 C Proximal colon cancer B Colon cancer D Distal colon cancer =1.04 E Rectal cancer =1.02 Supplementary Figure 2 A-E Quantile-quantile plots for the test statistics (Cochran-Armitage 1 d.f.  2 trend tests) for genome-wide association analysis of five subgroups. The observed P-values (y axis) are compared with the expected P-values under the null distribution (x axis). Genomic inflation factor for each analysis is shown upper left corner of each figure.

rs Supplementary Figure 3 -log 10 P Supplementary Figure 3 Regional plot of 6q26-q27 region. The top panel shows single-marker association results calculated by Cochran-Armitage trend test. Results from the screening stage and imputation analysis by MACH1.0 are indicated by black and red dots, respectively. The bottom panel shows the pairwise linkage disequilibrium for SNPs in HapMap JPT.

OR P heterogeneity = 0.79 Supplementary Figure 4 Supplementary Figure 4 Stratified analysis of each disease cohort used as controls in our study. The control samples used in our study were stratified by disease type and healthy volunteer were designated as controls. ORs and 95% CIs (per-allele) are calculated from fixed-effect models. The heterogeneity was calculated by Breslow-Day test. rs

Supplementary Figure 5 Supplementary Figure 4 Stratified analysis by age and first-degree family history for distal colon cancer. OR and 95% CIs (per-allele) are calculated from fixed-effect models. The heterogeneity was calculated by Breslow-Day test. rs