Table 2 Independent TWAS risk genes of cardiovascular disease identified by OTTERS

From: OTTERS: a powerful TWAS framework leveraging summary-level reference data

CHROM

ID

OTTERS

P+T (0.001)

P+T (0.05)

lassosum

SDPR

PRS-CS

1

CLCN6a

5.75E–15

4.94E–09

5.40E–08

8.77E–09

1.19E–15

1.43E–09

1

NPPAb

4.32E–08

1.55E–08

2.14E–07

–

–

6.71E–06

1

PSRC1a

8.37E–20

5.68E–08

8.46E–07

6.26E–11

1.67E–20

1.41E–12

2

RP11-378A13.1a

9.78E–09

3.97E–02

4.98E–02

1.62E–05

1.96E–09

1.15E–04

4

LINC01093c

2.57E–09

9.85E–02

5.31E–02

5.13E–10

1.08E–02

2.41E–02

5

CPEB4b

3.05E–14

1.26E–02

2.05E–02

2.70E–05

6.05E–15

1.60E–07

6

SERPINB6c

1.47E–07

2.12E–01

2.24E–01

7.56E–03

2.95E–08

7.53E–04

6

CARMIL1c

9.23E–09

5.34E–03

3.41E–03

4.15E–03

1.85E–09

1.72E–03

6

ZSCAN12P1c

1.84E–08

6.00E–01

5.75E–01

4.62E–01

3.67E–09

3.10E–01

6

HCG4P7c

8.93E–50

3.70E–01

3.69E–01

2.30E–01

1.79E–50

7.26E–01

6

HCG4P3c

5.33E–20

4.20E–01

4.05E–01

5.03E–04

1.07E–20

2.42E–03

6

HLA-Sc

4.57E–07

7.13E–01

7.31E–01

3.02E–01

9.14E–08

2.33E–01

7

PSPHP1c

1.21E–09

2.17E–01

2.26E–01

9.65E–03

2.43E–10

1.10E–01

8

LPLc

5.73E–07

1.78E–03

3.26E–03

4.44E–02

1.15E–07

1.05E–04

8

PTP4A3c

1.28E–06

8.13E–02

8.33E–02

6.23E–05

2.58E–07

1.67E–03

10

CAMK1Da

2.51E–09

3.83E–02

4.97E–02

1.23E–03

5.03E–10

4.97E–05

10

NT5C2b

1.21E–07

1.69E–06

2.92E–06

1.64E–05

3.15E–07

2.69E–08

11

TNNT3b

1.67E–10

1.09E–06

3.33E–06

2.03E–09

3.40E–11

4.01E–07

11

C11orf49b

2.28E–06

8.55E–07

1.78E–06

5.44E–05

–

2.93E–04

11

SIDT2a

7.26E–09

6.14E–05

1.33E–04

3.66E–05

1.46E–09

3.81E–07

15

CSKb

2.30E–09

1.70E–07

2.15E–06

7.41E–10

2.80E–09

2.17E–09

15

FESb

2.87E–32

4.78E–08

1.23E–06

9.13E–24

5.75E–33

1.94E–15

15

SLCO3A1c

3.78E–08

1.85E–02

3.15E–02

4.65E–05

7.57E–09

1.14E–03

16

MBTPS1b

5.80E–08

2.62E–01

3.05E–01

9.15E–04

1.16E–08

2.34E–03

16

MTHFSDa

4.65E–07

5.16E–02

5.94E–02

1.65E–02

9.30E–08

3.20E–03

17

ACEb

9.42E–07

4.93E–06

1.03E–05

4.23E–06

9.66E–07

2.68E–07

18

RALBP1c

1.40E–06

1.48E–01

1.54E–01

2.12E–04

2.81E–07

5.55E–03

19

MRI1b

8.38E–09

8.34E–03

1.60E–02

7.79E–03

1.68E–09

2.65E–03

19

HAUS8b

1.60E–07

4.41E–08

1.38E–07

1.67E–06

1.42E–06

3.29E–05

19

SULT2B1c

2.32E–06

7.73E–07

–

–

2.97E–02

1.10E–02

19

NTN5a

9.03E–10

2.75E–08

1.16E–07

6.23E–06

1.85E–10

9.73E–09

19

RPL28b

3.76E–07

7.33E–02

1.16E–01

6.64E–03

7.52E–08

4.23E–03

20

CTSZb

3.32E–09

2.57E–02

1.99E–02

3.40E–09

8.25E–10

1.04E–01

20

EDN3c

1.29E–07

3.61E–08

9.15E–08

8.60E–06

5.90E–03

1.58E–02

20

ZBTB46c

1.07E–06

2.83E–07

8.35E–06

–

1.81E–03

1.27E–05

20

OPRL1a

5.84E–07

3.44E–07

2.69E–06

1.85E–03

5.51E–05

1.90E–07

21

FAM3Bc

1.08E–10

2.28E–02

2.58E–02

8.07E–06

2.17E–11

1.04E–05

21

MX1c

6.04E–22

4.36E–01

3.83E–01

3.16E–07

1.21E–22

1.24E–03

  1. Reference eQTL summary data from eQTLGen consortium and GWAS summary data from UKBB were used. The corresponding TWAS p values by 5 individual PRS methods and OTTERS are shown in the table with significant p values < \(2.998\times {10}^{-6}\) (Bonferroni corrected significance level) in bold, and those for genes with test GReX \({R}^{2}\) ≤ 0.01 are shown as a dash. p values were the genomic-control corrected p values from the Z-score test from TWAS (two-sided).
  2. aRisk gene of UKBB cardiovascular disease in TWAS-hub identified using GTEx whole blood tissue.
  3. bRisk genes of UKBB cardiovascular disease in TWAS-hub identified using other GTEx tissue types.
  4. cRisk gene of UKBB cardiovascular disease not in TWAS-hub.
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