Table 3 Top GWAS hits with WGS data in comparison to the significant genotyped/imputed associations identified by Ahsan et al.25.

From: Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Biomarker

WGS top variant

chr:pos†

MAF WGS (effect allele)

MAF imputed (effect allele)

Effect allele (ref)

Genotype quality (sd) WGS

Imputation quality for WGS variant

P present

P Ahsan25 for WGS top variant

Ahsan top variant (R2§)25

P top variant Ahsan25

CCL19

rs149941420*

6:32556454

0.160

0.125

G (T)

90.92 (13.34)

0.846

4.269 × 10−18

5.429 × 10−12

rs2395201 (0.277)

5.951 × 10−17

CCL4

rs113010081

3:46457412

0.232

0.201

C (T)

92.44 (11.21)

0.996

4.188 × 10−38

3.124 × 10−23

rs113341849 (0.992)

3.326 × 10−26

CCL4

rs4141329

17:34490448

0.472

0.483

C (A)

94.92 (10.96)

0.712

1.550 × 10−14

n.s.‡

rs113877493 (0.095)

9.181 × 10−10

CD40

rs4239702

20:44749251

0.273

0.261

T (C)

97.09 (6.08)

0.996

1.014 × 10−49

3.288 × 10−18

rs4810485 (0.911)

4.697 × 10−19

CXCL10

rs11548618

4:76943947

0.035

0.035

A (G)

92.21 (10.60)

1

5.072 × 10−47

2.132 × 10−37

rs11548618 (1)

2.132 × 10−37

CXCL5

rs425535

4:74863997

0.103

0.100

T (C)

92.63 (10.84)

0.989

1.091 × 10−34

2.081 × 10−25

rs425535 (1)

2.081 × 10−25

CXCL5

rs7088799

10:65016174

0.443

0.446

G (T)

97.22 (6.00)

0.999

7.357 × 10−16

4.598 × 10−11

rs7896910 (0.735)

2.932 × 10−11

CXCL6

rs111903579

4:74700432

0.446

NA**

T (C)

85.04 (18.31)

NA**

6.708 × 10−58

NA**

rs16850073 (1)

1.976 × 10−32

Flt3L

rs111595024

13:28768589

0.015

NA**

G (A)

50.08 (21.35)

NA**

1.008 × 10−16

NA**

rs145096717 (0.967)

3.045 × 10−14

MCP-1

rs1800024

3:46412559

0.075

0.077

T (C)

93.57 (9.38)

0.998

1.257 × 10−09

n.s. ‡

rs2888526 (0.979)

2.399 × 10−09

MMP-1

rs471994

11:102697731

0.389

0.395

A (G)

94.33 (10.16)

1

5.017 × 10−19

1.736 × 10−15

rs471994 (1)

1.736 × 10−15

MMP-10

rs17359286

11:102643718

0.081

0.058

T (G)

93.56 (9.98)

0.999

1.171 × 10−08

n.s. ‡

rs486055 (0.583)

9.246 × 10−10

SCF

rs6073958

20:44551855

0.199

0.196

C (T)

96.37 (7.18)

0.997

1.204 × 10−09

2.325 × 10−09

rs6073958 (1)

2.325 × 10−09

TRAIL

rs144242131

18:29769910

0.007

0.007

A (G)

90.74 (12.23)

0.999

1.020 × 10−12

1.387 × 10−16

rs144242131 (1)

1.387 × 10−16

  1. Results from ONC_CVD are compared*. The p-values for the top variants from the present study are shown (P present) as well as the p-values for the same variant in the imputed data (P Ahsan for WGS top variant). The most significant SNV from the previous study and corresponding p-value is also shown, and its LD (R2) with the most significant SNV from the present study. The comparisons have been filtered the same way as the present study: only biallelic variants and variants not located in a spanning deletion are compared.
  2. †In hg19 coordinates.
  3. ‡Not significant in Ahsan et al. (P > 4.2e-09).
  4. §R2 with WGS top variant.
  5. *All top variants and P-values are from the analyses of the ONC_CVD panel, except for CCL19 that is from INF.
  6. **Did not pass imputation QC or were not present in the reference panel used for the imputations.
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