Table 2 AS-WAS novel genes presented in novel and known GWAS loci

From: Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility

Locusa

Gene

Zb

ACAT_Pc

Nearest lead variant

Distance (Mb)d

Cond_ACAT_Pe

Novel loci

      

1p31.3

MIER1

− 5.40

1.32 × 10−07

rs3124454

3.62

4.20 × 10−08

17p11.2

MPRIP

− 5.02

5.12 × 10−07

rs1078643

6.34

1.06 × 10−05

17q12

FBXL20

5.47

4.56 × 10−08

rs1078643

28.54

9.27 × 10−08

19q13.2

ACTN4

− 5.15

7.08 × 10−07

rs1800469

2.64

1.18 × 10−07

Known loci

      

10q24.2

SLC25A28

− 5.39

7.21 × 10−08

rs35564340

0.03

1.47 × 10−05

11q23.1

PPP2R1B

− 5.32

1.03 × 10−07

rs3087967

0.45

4.00 × 10−02

11q12.2

DAGLA

6.56

5.46 × 10−11

rs174537

0.05

6.61 × 10−01

11q13.4

MRPL48

6.65

2.88 × 10−11

rs11236187

0.83

6.00 × 10−03

1q25.3

NPL

− 5.42

6.09 × 10−08

rs8179460

0.26

1.87 × 10−01

12q24.13

TMEM116

− 5.11

3.15 × 10−07

rs653178

0.43

2.98 × 10−01

12p11.21

DDX11

– 5.47

8.97 × 10−08

rs77969132

0.34

2.58 × 10−06

12p13.32

PARP11

− 4.93

8.12 × 10–07

rs10774214

0.39

4.00 × 10−03

12q13.12

MCRS1

6.42

2.74 × 10−10

rs11169572

1.26

4.46 × 10−01

12q15

KCNMB4

5.33

9.79 × 10−08

rs11178634

0.69

8.91 × 10−01

13q13.3

EXOSC8

7.21

1.10 × 10−12

rs12427846

0.08

5.72 × 10−01

15q13.3

RP11-1000B6.3

6.69

4.50 × 10−11

rs1554865

0.13

1.81 × 10−04

19q13.43

MZF1

− 6.31

5.73 × 10−10

rs11670192

0.06

9.40 × 10−01

20q11.22

GSS

− 5.19

2.12 × 10−07

rs6059938

0.33

1.10 × 10−02

20q13.11

SRSF6

6.19

6.02 × 10−10

rs6017248

0.57

9.90 × 10−02

20q13.13

FAM65C

5.19

2.15 × 10−07

rs6091189

0.04

6.44 × 10−05

20q13.2

NFATC2

− 5.44

5.23 × 10−08

rs6091189

0.75

2.27 × 10−08

20q13.33

ARFGAP1

8.26

1.40 × 10−16

rs2738783

0.40

4.59 × 10−17

2q35

AAMP

6.10

1.08 × 10−09

rs3731861

0.06

3.94 × 10−01

3p21.2

ACY1

− 5.34

9.22 × 10−08

rs2001732

0.86

3.40 × 10−02

3p21.1

STAB1

– 6.36

2.02 × 10−10

rs2001732

0.34

8.51 × 10−04

5p13.1

RICTOR

5.05

4.32 × 10−07

rs55810369

1.14

8.75 × 10−04

6p22.1

TRIM26

− 5.38

7.27 × 10−08

rs1476570

0.36

5.78 × 10-08

6p21.33

FLOT1

− 5.97

2.43 × 10−09

rs116353863

0.30

9.63 × 10−09

6p24.3

SSR1

5.83

5.43 × 10−09

rs9379084

0.07

7.00 × 10−03

  1. a For locus with multiple identified genes, only the gene with the most significant association with CRC risk is presented. Additional genes for loci include: 11q13.4 (PAAF1, ARRB1); 12q13.12 (SPATS2); 20q13.13 (ZNFX1, SLC9A8, RTEL1); 3p21.1 (DNAH1); 6p21.33 (BAG6); 6p21.33 (SKIV2L, TNXB).
  2. b For each gene, the Z score of the most significant association is presented.
  3. c P-value was calculated through ATAC using the Cauchy combination test statistics through joint analysis of multi-ancestry AS-WAS associations.
  4. d Distance between a gene with the closest risk variant identified from previous GWAS in CRC.
  5. e P-value was calculated through ATAC using the Cauchy combination test statistics through joint analysis of multi-ancestry AS-WAS associations conditioned on the closest risk variant.
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