Tumour site* | Locus | Nearby gene(s) | rsID lead variant | Chr. | Position (build 37) | Alleles (risk/ other) | RAF (%) | OR | 95% CI | P value | r2 | I2 | Phet | N cases | N controls |
Colon | 1p31.1 | PTGER3 | rs3124454 | 1 | 71 040 166 | G/T | 58.1 | 1.07 | 1.04 to 1.09 | 1.4E-08 | 0.926 | 6.1 | 0.38 | 32 002 | 64 159 |
Left-sided | 2q21.3 | LCT | rs1446585 | 2 | 136 407 479 | G/A | 39.9 | 1.07 | 1.04 to 1.10 | 3.3E-08 | 1.121 | 43.7 | 0.11 | 30 588 | 64 159 |
Proximal colon | 3p22.2 | MLH1 | rs1800734† | 3 | 37 034 946 | A/G | 24.7 | 1.15 | 1.11 to 1.19 | 3.8E-18 | 1.008 | 43.8 | 0.11 | 15 706 | 64 159 |
Colon | 3p21.2 |
STAB1; TLR9;
NISCH | rs353548 | 3 | 52 269 491 | G/A | 95.3 | 1.15 | 1.10 to 1.21 | 1.3E-08 | 0.975 | 0 | 0.48 | 32 002 | 64 159 |
Left-sided | 5q32 | CDX1 | rs2302274† | 5 | 149 546 426 | G/A | 47.8 | 1.07 | 1.04 to 1.09 | 4.9E-09 | 1.008 | 3.8 | 0.39 | 30 588 | 64 159 |
Left-sided | 7q32.3 |
KLF14;
LINC00513 | rs73161913† | 7 | 130 607 779 | G/A | 94.3 | 1.16 | 1.10 to 1.22 | 1.3E-09 | 0.975 | 0 | 0.79 | 30 588 | 64 159 |
Left-sided | 10q23.31 | PANK1; KIF20B | rs7071258† | 10 | 91 574 624 | A/G | 21.6 | 1.08 | 1.05 to 1.11 | 8.4E-09 | 0.993 | 0 | 0.71 | 30 588 | 64 159 |
Rectal | 14q22.1 |
PYGL;
NIN; ABHD12B | rs28611105† | 14 | 51 359 658 | G/T | 21.5 | 1.11 | 1.07 to 1.15 | 4.7E-09 | 0.983 | 50.5 | 0.07 | 16 212 | 64 159 |
Proximal colon | 14q32.12 | RIN3 | rs61975764 | 14 | 93 014 929 | G/A | 55.3 | 1.08 | 1.05 to 1.11 | 2.8E-08 | 0.987 | 0 | 0.71 | 15 706 | 64 159 |
Proximal colon | 14q32.2 | BCL11B | rs80158569† | 14 | 99 782 937 | A/G | 7.5 | 1.18 | 1.12 to 1.24 | 8.6E-11 | 0.899 | 29.9 | 0.21 | 15 706 | 64 159 |
Left-sided | 19p13.3 | STK11; SBNO2 | rs62131228 | 19 | 1 157 642 | G/A | 98.1 | 1.28 | 1.17 to 1.40 | 2.4E-08 | 0.788 | 0 | 0.95 | 29 632 | 63 385 |
Left-sided | 20q13.31 | BMP7 | rs6014965† | 20 | 55 831 203 | A/G | 55.4 | 1.07 | 1.04 to 1.09 | 4.5E-09 | 0.995 | 10.5 | 0.35 | 30 588 | 64 159 |
Colon | 22q13.31 | FAM118A; FBLN1 | rs736037 | 22 | 45 724 999 | A/G | 28.6 | 1.07 | 1.04 to 1.09 | 2.8E-08 | 1.015 | 0 | 0.74 | 32 002 | 64 159 |
Lead variant is the most significant variant at the locus. Reference single nucleotide polymorphism (SNP) cluster ID (rsID) based on NCBI dbSNP Build 152. Alleles are on the + strand. All p values reported in this table are from a sample size-weighted fixed-effects meta-analysis of logistic regression-based likelihood-ratio test results. Reported imputation qualities r2 are effective sample size (Neff)-weighted means across the six data sets, where Neff=4/(1/Ncases+1/Ncontrols). The I2 statistic measures heterogeneity on a scale of 0–100%. Phet is the p value from Cochran’s Q test for heterogeneity.
*Colon: proximal colon+distal colon+colon, unspecified site; left-sided: distal colon+rectal. Details of tumour site definitions including ICD-9 codes are given in the Methods section and online supplemental materials.
†Variant attained Bonferroni-adjusted genome-wide significance (5E-08/5=1E-08), corrected for the number of CRC case subgroups analysed.
Chr., chromosome; CRC, colorectal cancer; RAF, risk allele frequency.