Table 2 Location and annotation of top GWAS hits after having conditioned on the most significant hit.

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

Biomarker

SNV

Conditional signal

P-value

P adj.

Effect, beta (SE)

Effect allele (ref)

MAF (effect allele)

chr:position†

Gene

Type

Location**

CCL23

rs72831705

secondary

9.52 × 10−11

1.07 × 10−05

0.44 (0.07)

T (C)

0.153

17:34321277

CCL15-CCL14

ncRNA_intronic

cis

CCL23

rs854671

tertiary

1.48 × 10−08

1.67 × 10−03

0.23 (0.05)

C (T)

0.475

17:34361300

CCL23;

CCL18

intergenic

cis

CCL4

3:51599851§*

secondary

3.53 × 10−07

2.10 × 10−02

3.09 (0.61)

A (C)

0.00098

3:51599851

RAD54L2

intronic

trans

CCL4

rs188700215*

secondary

1.01 × 10−07

5.91 × 10−03

−5.19 (0.97)

A (G)

0.00098

17:30092085

MIR365B;COPRS

intergenic

trans

CCL4

rs201079256*

tertiary

1.02 × 10−13

5.97 × 10−09

−0.36 (0.05)

T (C)

0.465

17:34522125

CCL3L1;

CCL3L3

downstream

cis

CD40

rs6063068*

secondary

7.41 × 10−08

6.27 × 10−03

3.28 (0.61)

T (A)

0.00098

20:45717496

EYA2

intronic

cis

CD40

rs182282247*

tertiary

9.99 × 10−08

8.45 × 10−03

0.82 (0.15)

A (G)

0.021

20:44730041

NCOA5;

CD40

intergenic

cis

CST-5

rs6138152

secondary

3.87 × 10−07

3.13 × 10−02

0.36 (0.07)

G (A)

0.211

20:23850130

CST2;CST5

intergenic

cis

CST-5

rs75823487

tertiary

4.56 × 10−07

3.69 × 10−02

4.25 (0.84)

T (C)

0.0015

20:29478349

MIR663AHG;

LINC01597

intergenic

trans

CXCL1

rs10938101*

secondary

7.53 × 10−07

6.54 × 10−03

−0.24 (0.05)

T (G)

0.461

4:74688772

CXCL8;CXCL6

intergenic

cis

CXCL6

rs181216093*

secondary

5.27 × 10−09

8.42 × 10−04

−1.21 (0.21)

T (C)

0.009

4:74661204

CXCL8;CXCL6

intergenic

cis

IL-15RA

rs144173272

secondary

1.49 × 10−11

1.86 × 10−06

−1.70 (0.25)

T (C)

0.013

10:6008255

IL15RA

missense

cis

IL-15RA

rs35095871

tertiary

3.06 × 10−07

3.81 × 10−02

0.41 (0.08)

G (A)

0.102

10:5700416

ASB13

intronic

cis

IL-18R1

rs12999517

secondary

4.89 × 10−19

1.31 × 10−13

−0.47 (0.05)

C (T)

0.172

2:102959260

IL1RL1

intronic

cis

MCP-2

rs74832623

secondary

6.47 × 10−32

7.79 × 10−27

−1.17 (0.10)

G (A)

0.045

17:32535173

LINC01989;CCL2

intergenic

cis

MCP-2

rs12601658

tertiary

7.15 × 10−12

8.61 × 10−07

−0.32 (0.05)

A (T)

0.244

17:32533423

LINC01989;

CCL2

intergenic

cis

MMP-1

rs470358*

secondary

9.38 × 10−09

1.56 × 10−03

0.29 (0.05)

T (C)

0.397

11:102668702

WTAPP1

ncRNA_intronic

cis

SCF

rs6104417*

secondary

2.66 × 10−07

2.53 × 10−02

0.23 (0.05)

C (T)

0.4995

20:44632542

ZNF335;MMP9

intergenic

trans

ST1A1

rs4149383

secondary

5.38 × 10−07

4.56 × 10−02

0.54 (0.11)

A (G)

0.061

16:28620320

SULT1A1

UTR5

cis

TNFB

rs746868

secondary

1.42 × 10−07

2.18 × 10−02

0.26 (0.05)

C (G)

0.061

6:31540429

TNFB

intronic

cis

TNFB

6:27190519§

tertiary

4.06 × 10−08

6.22 × 10−03

1.77 (0.32)

T (G)

0.005

6:27190519

MIR3142;

PRSS16

intergenic

trans

TNFSF14

rs2291668

secondary

4.71 × 10−07

7.36 × 10−03

0.27 (0.05)

A (G)

0.281

19:6669934

TNFSF14

synonymous

cis

TRAIL

18:21026109§*

secondary

1.01 × 10−07

1.28 × 10−02

−5.19 (0.97)

A (G)

0.00049

18:21026109

TMEM241;RIOK3

intergenic

trans

  1. The raw p-values (not adjusted for multiple testing) are shown. The adjusted p-values are based on the number of SNVs tested in each region which means that each SNV does not need to reach genome wide significance. If one biomarker had been measured twice (i.e. been measured on both INF and ONC_CVD), the SNV with the most significant p-value is presented. Additional information can be found in Supplementary Table S4.
  2. §Does not have an rs-id,
  3. †In hg19 coordinates.
  4. *Variant is from ONC_CVD. Either the p-value was lower, or no significant association was found in INF.
  5. **In cis: within 1 Mb of the gene encoding the biomarker; in trans: on another chromosome of the gene encoding the biomarker.
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