These summary statistics represent Colorectal cancer case-control analyses in the Japanese population as represented in the BioBank Japan. DNA samples of 7,090 CRC patients in the screening and 3,713 CRC patients and 7,333 noncancer controls in the replication analysis were obtained from BioBank Japan. The 33,887 noncancer controls were from three population-based cohorts, including the JPHC (Japan Public Health Center)-based prospective study, the J-MICC (Japan Multi-Institutional Collaborative Cohort) study and ToMMo (Tohoku Medical Megabank Organization). After initial quality check, 6,692 cases and 27,178 controls were used for screening. Imputation of the ungenotyped SNPs was conducted by MaCH and minimac using the data from the JPT/CHS/CHD subjects and using the 1000 Genome Project Phase 1 (release 16 March 2012) as a reference. We excluded SNP with a large allele frequency difference between the reference panel and the GWAS (>0.16) as described previously. We also excluded SNPs with low imputation quality score (Rsq < 0.3) and insertion/deletion polymorphisms. The association of SNPs with CRC risk was investigated using logistic regression analysis using PC1 and PC2 as covariates. If you use these statistics please cite the following publication: Tanikawa C et al. GWAS identifies two novel colorectal cancer loci at 16q24.1 and 20q13.12. Carcinogenesis. 2018 May 3;39(5):652-660. doi: 10.1093/carcin/bgy026. The file is comma-separated (csv) and the column headings in the results file are as follows: #MARKER,CHR,POS,EffectAllele,NonEffectAllele,FREQ1,CASE_FREQ1,CTRL_FREQ1,RSQR,EFFECT1,OR,STDERR,WALDCHISQ,PVALUE,LRCHISQ,LRPVAL,contig,contigloc,num_of_gene,gene,relativeloc