Table 3 Index SNV results from logistic regression-based genome wide analysis for joint ancestry (n = 19,861), European ancestry (n = 14,620), and African ancestry (n = 3700) samples.

From: Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection

Chr

SNV

Ref

Alt

CA

BP

Joint CAF (n = 19,861)

Logistic joint P-value

EUR CAF (n = 14,620)

Logistic EUR P-value

Logistic EUR SNV-controlled P-value

AFR CAF (n = 3700)

Logistic AFR P-value

OR (95% CI)

OR (95% CI)

OR (95% CI)

OR (95% CI)

Beta

Beta

Beta

Beta

6

rs68148149

C

A

C

32,511,725

0.17

6.83 × 10–9

0.17

8.06 × 10–14

0

0.18

7.2 × 10–1

1.36 (1.06–1.74)

1.56 (1.13–2.15)

0

0.95 (0.80–1.13)

0.13

0.2

0

-0.02

6

rs3828840

T

C

T

32,520,907

0.17

8.42 × 10–9

0.17

9.96 × 10–14

0

0.18

7.1 × 10–1

1.36 (1.06–1.74)

1.56 (1.13–2.15)

0

0.95 (0.79–1.13)

0.13

0.2

0

-0.02

6

rs35882239

A

G

A

32,522,576

0.2

1.32 × 10–8

0.21

8.18 × 10–12

9.80 × 10–1

0.2

6.7 × 10–1

1.34 (1.05–1.70)

1.49 (1.10–2.00)

1.00 (1.00–1.00)

0.94 (0.78–1.13)

0.13

0.17

0

-0.03

6

rs71534541

C

T

C

32,513,076

0.08

7.98 × 10–7

0.07

5.12 × 10–11

2.30 × 10–1

0.1

8.2 × 10–1

1.38 (1.04–1.80)

1.62 (1.12–2.33)

1.15 (0.90–1.46)

0.96 (0.81–1.14)

0.14

0.21

0.06

-0.02

6

rs35222480

A

T

A

32,522,813

0.08

8.41 × 10–7

0.08

9.88 × 10–11

2.20 × 10–1

0.1

5.0 × 10–1

1.37 (1.04–1.80)

1.59 (1.11–2.26)

1.14 (0.90–1.44)

0.89 (0.66–1.19)

0.14

0.2

0.06

-0.05

6

rs116603449

C

T

T

32,595,194

0.21

6.59 × 10–9

0.21

5.42 × 10–10

4.54 × 10–9

0.22

8.73 × 10–2

1.31 (1.05–1.62)

1.39 (1.07–1.80)

1.37 (1.06–1.77)

1.24 (0.90–1.70)

0.12

0.14

0.14

0.09

6

rs9270896

A

G

G

32,571,876

0.41

1.27 × 10–5

0.42

1.21 × 10–5

6.09 × 10–9

0.33

3.96 × 10–2

1.19 (1.01–1.40)

1.22 (1.01–1.47)

1.32 (1.05–1.65)

1.26 (0.92–1.74)

0.08

0.09

0.12

0.1

6

rs9270894

A

G

G

32,571,872

0.26

1.17 × 10–5

0.24

1.66 × 10–6

1.12 × 10–8

0.32

1.16 × 10–1

1.22 (1.01–1.47)

1.29 (1.03–1.63)

1.37 (1.06–1.77)

1.20 (1.90–1.58)

0.09

0.11

0.14

0.08

6

rs9270895

C

T

T

32,571,873

0.45

5.95 × 10–5

0.44

5.39 × 10–5

2.32 × 10–8

0.42

3.54 × 10–2

1.17 (1.00–1.37)

1.21 (1.00–1.45)

1.31 (1.05–1.64)

1.26 (0.92–1.73)

0.07

0.08

0.12

0.1

6

rs618095

G

A

A

32,574,736

0.28

5.05 × 10–7

0.25

2.69 × 10–6

3.71 × 10–8

0.36

1.19 × 10–2

1.26 (1.03–1.53)

1.29 (1.02–1.62)

1.35 (1.05–1.73)

1.32 (0.94–1.87)

0.1

0.11

0.13

0.12

  1. An additive model was used to assess the disease susceptibility impact of the minor (coded) allele at each position, while controlling for age, BMI, sex, ancestry, nursing home status, chemotherapy, diabetes, HIV, transplant medications, corticosteroids, and medium or high-risk antibiotic exposure as covariates.
  2. Chr chromosome, SNV single nucleotide variant, Ref reference allele, Alt alternate allele, CA coded allele, BP base pair, CAF coded allele frequency, OR odds ratio.
  3. Results meeting the genome-wide significance threshold (P < 5 × 10–8) are displayed in bold.
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