Table 4 Top GWAS hits from WGS data in comparison to the significant genotyped/imputed associations identified by Enroth et al.28.

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 of WGS top variant

P present

P Enroth28 for WGS top variant

Enroth top variant (R2§)28

P top variant Enroth28

CCL19

rs149941420

6:32556454

0.160

0.125

G (T)

90.92 (13.34)

0.846

4.269 × 10−18

n.s. ‡

rs9968904 (0.979)

5.744 × 10−13

CCL25

rs2032887

19:8121360

0.301

0.302

G (A)

92.07 (12.10)

1

1.089 × 10−37

4.368 × 10−35

rs2032887 (1)

4.368 × 10−35

CCL4

rs113010081

3:46457412

0.232

0.201

C (T)

92.44 (11.21)

0.996

4.188 × 10−38

7.834 × 10−24

rs113341849 (0.992)

7.834 × 10−24

CD40

rs1569723

20:44742064

0.256

0.257

C (A)

95.30 (8.69)

1

5.242 × 10−43

6.608 × 10−21

rs4810485 (0.997)

4.960 × 10−21

CD6

rs11230563

11:60776209

0.168

0.164

T (C)

90.08 (13.40)

1

5.235 × 10−31

1.115 × 10−18

rs11230556 (0.729)

9.259 × 10−21

CXCL10

rs11548618

4:76943947

0.035

0.035

A (G)

92.21 (10.60)

1

5.072 × 10−47

5.396 × 10−37

rs11548618 (1)

5.396 × 10−37

CXCL5

rs352045

4:74864687

0.103

0.100

T (G)

89.77 (13.54)

0.995

6.091 × 10−27

1.164 × 10−19

rs2564594 (0.974)

7.826 × 10−20

CXCL5

rs10740118

10:65101207

0.443

0.445

C (G)

96.52 (7.24)

0.999

2.927 × 10−13

5.033 × 10−10

rs12770839 (0.698)

8.833 × 10−12

CXCL6

rs111903579*

4:74700432

0.446

NA**

T (C)

85.04 (18.31)

NA**

6.708 × 10−58

NA**

rs6831029 (0.813)

1.126 × 10−26

Flt3L

rs145096717

13:28761592

0.015

0.002

A (G)

94.67 (8.47)

0.668

2.086 × 10−16

3.519 × 10−14

rs145096717 (1)

3.519 × 10−14

IL-10RB

rs8178528

21:34660980

0.425

0.423

A (G)

95.79 (8.07)

0.968

5.461 × 10−35

n.s. ‡

rs2843697 (0.951)

1.098 × 10−16

IL-12B

rs10043720

5:158767333

0.272

0.269

A (G)

91.15 (12.75)

0.998

7.988 × 10−31

1.424 × 10−17

rs10076557 (1)

4.247 × 10−18

IL-15RA

rs3136630

10:5997820

0.312

0.312

T (C)

91.43 (12.75)

1

2.644 × 10−19

1.659 × 10−11

rs3136630 (1)

1.659 × 10−11

IL-18R1

rs10190555

2:102994056

0.233

0.234

A (G)

94.92 (9.44)

0.999

2.373 × 10−72

1.155 × 10−51

rs2058660 (0.957)

5.500 × 10−51

MCP-2

rs1133763

17:32647831

0.104

0.109

C (A)

91.07 (12.04)

0.978

2.693 × 10−53

n.s. ‡

rs3138037 (1)

2.113 × 10−48

MCP-4

rs12075

1:159175354

0.474

0.473

G (A)

94.55 (10.13)

1

1.253 × 10−45

1.475 × 10−43

rs12075 (1)

1.475 × 10−43

VEGF-A

rs6921438

6:43925607

0.434

0.389

G (A)

95.10 (10.09)

0.770

8.294 × 10−40

n.s. ‡

rs7767396 (0.942)

8.048 × 10−19

  1. Results from INF 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 Enroth 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 Enroth et al. (P > 4.79e-9).
  4. §R2 with WGS top variant.
  5. *For CXCL6 the variant is from ONC_CVD since this p-value was lower.
  6. **Did not pass imputation QC or were not present in the reference panel used for the imputations.
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