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

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