Table 1.

Independent association signals uncovered at known CRC risk loci in conditional analyses (conditional P < 1 × 10⁻⁶)

Fine-mapping region	SNP	Chr	Position	Nearby gene	Alleles	AF	Single-SNP analysis		Joint analysis		Group
							OR (95% CI)	P valuea	OR (95% CI)	P valueb
region_1	rs11579545	1	22249333	HSPG2	T/C	0.445	0.96 (0.95–0.98)	4.34E−07	0.96 (0.95–0.98)	5.63E−07	Trans-ancestry
region_1	rs112191583	1	22554378	MIR4418	T/C	0.974	0.88 (0.83–0.92)	1.19E−07	0.87 (0.83–0.92)	5.29E−08	Trans-ancestry
region_1	rs12137525	1	22584118	MIR4418	T/C	0.107	1.07 (1.04–1.09)	2.90E−08	1.08 (1.06–1.11)	1.14E−11	European
region_9	rs12122827	1	202172769	LGR6	T/G	0.715	1.04 (1.02–1.06)	9.44E−07	1.05 (1.03–1.06)	7.94E−08	European
region_22	rs2554878	3	41200064	RP11-372H2.1	T/G	0.036	1.12 (1.08–1.16)	5.85E−09	1.12 (1.08–1.16)	3.75E−09	Trans-ancestry
region_27	rs9283588	3	133874566	RYK	A/G	0.715	1.06 (1.04–1.07)	3.43E−10	1.04 (1.03–1.06)	7.32E−07	Trans-ancestry
region_30	rs902443	4	105888417	RP11-556I14.1	A/T	0.536	1.04 (1.03–1.06)	1.49E−11	1.04 (1.03–1.06)	1.26E−11	Trans-ancestry
region_36	rs582489	5	39908712	GCSHP1	T/C	0.570	0.97 (0.96–0.99)	8.23E−05	0.96 (0.94–0.97)	7.29E−09	European
region_36	rs77781678	5	40626064	SNORA63	T/C	0.020	0.84 (0.79–0.89)	2.09E−09	0.84 (0.79–0.89)	1.75E−09	European
region_43	rs4714081	6	11977905	RP11-456H18.1	A/G	0.451	0.96 (0.95–0.97)	2.50E−09	0.96 (0.95–0.97)	1.21E−09	Trans-ancestry
region_43	rs4714350	6	12270290	EDN1	A/T	0.283	0.96 (0.94–0.97)	8.60E−09	0.96 (0.95–0.98)	4.43E−07	Trans-ancestry
region_43	rs17615624	6	12376025	RN7SKP293	C/G	0.975	0.87 (0.83–0.91)	7.29E−09	0.88 (0.84–0.92)	2.28E−07	European
region_44	rs3094576	6	29516242	OR2I1P	A/C	0.131	0.94 (0.92–0.96)	1.83E−07	0.94 (0.92–0.96)	2.26E−08	European
region_44	rs2517671	6	29937977	MICD	A/G	0.591	0.96 (0.95–0.98)	2.35E−08	0.96 (0.95–0.97)	2.87E−09	Trans-ancestry
region_45	rs6920820	6	30969938	MUC22	C/G	0.980	0.84 (0.79–0.9)	6.87E−08	0.8 (0.75–0.85)	1.89E−12	European
region_45	rs9264180	6	31219902	HLA-C	A/C	0.570	1.03 (1.02–1.05)	1.71E−06	1.04 (1.02–1.05)	5.62E−07	Trans-ancestry
region_45	rs9265501	6	31297568	XXbac-BPG248L24.10	A/G	0.678	0.88 (0.85–0.92)	3.05E−10	0.88 (0.84–0.91)	5.21E−11	European
region_45	rs116000952	6	32541270	HLA-DRB1	T/G	0.843	0.92 (0.89–0.96)	5.74E−06	0.9 (0.87–0.94)	1.50E−08	European
region_45	rs2858331	6	32681277	XXbac-BPG254F23.7	A/G	0.601	1.03 (1.02–1.05)	1.18E−05	1.05 (1.04–1.07)	2.67E−13	Trans-ancestry
region_50	rs13204733	6	55566108	RP11-228O6.2	A/G	0.858	0.94 (0.92–0.96)	4.20E−08	0.93 (0.91–0.95)	1.17E−12	European
region_60	rs10089517	8	60178721	SNORA51	A/C	0.380	1.03 (1.02–1.05)	7.44E−07	1.03 (1.02–1.05)	2.81E−07	Trans-ancestry
region_61	rs117310502	8	117593052	EIF3H	A/G	0.048	0.92 (0.89–0.96)	9.36E−05	0.88 (0.85–0.92)	4.03E−10	European
region_61	rs72681666	8	117641754	EIF3H	T/C	0.043	1.09 (1.05–1.13)	1.57E−05	1.12 (1.08–1.17)	6.99E−10	European
region_61	rs1793717	8	118278575	SNORA31	A/C	0.629	1.03 (1.02–1.05)	6.90E−05	1.04 (1.03–1.06)	1.55E−07	European
region_62	rs79122086	8	128397907	CASC8	T/G	0.840	0.92 (0.9–0.93)	5.46E−20	0.94 (0.93–0.96)	9.34E−10	Trans-ancestry
region_62	rs77569096	8	128468955	CASC8	A/G	0.763	0.92 (0.9–0.94)	2.06E−15	0.93 (0.91–0.95)	2.67E−12	European
region_68	rs4994332	9	137117194	RP11-145E17.2	T/C	0.423	0.97 (0.96–0.98)	4.05E−05	0.96 (0.95–0.97)	9.08E−08	European
region_74	rs117746067	10	101222300	RP11-441O15.3	A/G	0.101	1.06 (1.03–1.08)	3.64E−06	1.08 (1.05–1.1)	1.74E−09	European
region_80	rs9795065	11	74376844	POLD3	T/C	0.981	1.19 (1.13–1.25)	5.37E−13	1.17 (1.12–1.23)	6.06E−11	Trans-ancestry
region_85	rs1003563	12	6424577	PLEKHG6	A/G	0.433	0.95 (0.94–0.97)	1.67E−12	0.95 (0.94–0.96)	1.23E−14	Trans-ancestry
region_106	rs68097734	14	92717447	RP11-472N19.3	T/C	0.496	1.06 (1.03–1.09)	7.71E−06	NA	−	Asian
region_108	rs28630996	15	32993860	SCG5	A/T	0.713	0.9 (0.89–0.92)	1.25E−32	0.93 (0.91–0.94)	3.02E−17	Trans-ancestry
region_108	rs144674978	15	33149751	FMN1	T/C	0.013	1.34 (1.25–1.43)	1.11E−18	1.23 (1.15–1.31)	3.82E−10	European
region_109	rs3784710	15	68072458	MAP2K5	T/C	0.763	1.05 (1.03–1.07)	1.32E−07	1.05 (1.03–1.07)	1.34E−08	European
region_111	rs12913420	15	90797010	RP11-697E2.6	C/G	0.376	1.04 (1.03–1.06)	2.29E−09	NA	−	Trans-ancestry
region_114	rs11117455	16	86179919	RP11-805I24.4	T/C	0.181	1.04 (1.02–1.06)	7.52E−06	1.05 (1.03–1.07)	6.97E−07	European
region_115	rs73975588	17	816741	NXN	A/C	0.874	1.09 (1.07–1.12)	6.62E−16	1.07 (1.04–1.09)	6.08E−09	European
region_117	rs112592783	17	70633625	LINC00511	T/C	0.175	1.05 (1.03–1.07)	5.87E−09	1.05 (1.03–1.07)	5.95E−09	Trans-ancestry
region_120	rs4939821	18	46371993	CTIF	T/C	0.304	0.91 (0.89–0.92)	4.12E−32	0.96 (0.94–0.97)	1.89E−07	European
region_121	rs72971616	19	987366	WDR18	T/G	0.063	0.92 (0.89–0.95)	4.89E−06	NA	−	European
region_126	rs12460535	19	49098750	SULT2B1	A/G	0.349	0.96 (0.95–0.98)	5.76E−07	NA	−	European
region_127	rs8099852	19	58895221	RPS5	T/C	0.546	1.03 (1.02–1.05)	5.15E−07	NA	−	Trans-ancestry
region_133	rs1971480	20	48897080	RP11-290F20.3	T/G	0.672	0.96 (0.95–0.98)	8.61E−07	0.96 (0.94–0.97)	6.50E−09	European
region_133	rs149942633	20	48983073	RP11-290F20.2	T/C	0.153	1.12 (1.08–1.16)	1.93E−08	1.1 (1.05–1.14)	3.94E−06	European
region_133	rs6126008	20	49075315	COX6CP2	A/T	0.660	0.96 (0.94–0.97)	1.07E−08	0.96 (0.94–0.97)	3.74E−09	European
region_134	rs34161672	20	56020599	RBM38	A/G	0.321	1.04 (1.02–1.05)	2.40E−06	1.04 (1.03–1.06)	1.64E−07	European
region_142	rs78106213	22	46121230	ATXN10	T/G	0.693	1.04 (1.03–1.06)	2.41E−07	1.05 (1.03–1.06)	8.20E−09	European

All independent association signals presented in this table are those not previously reported.

Chr and Position GRCh37, Alleles risk allele/Reference allele, AF Allele frequency, OR odds ratio, CI confidence interval.

^aP value derived from trans-ancestry or ancestry-specific meta-analysis under the fixed-effects inverse variance weighted model.

^bP value derived from conditional analysis conditioning on all other independent association signals in each fine-mapping region. “NA”—Only a single association signal was detected in the fine-mapping region in the analysis group.