Table 2 Results of the 19 representative variants of the credible sets.

From: An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease

Varianta

Locus

AFb (FIN enrichment)

Multivariate p value

Minimum univariate p value (biomarker)

Driver traitsc

Previous biomarker associationsd

Fine-mapping posterior probabilitye

pQTL gene

pQTL p value

FinnGen disease associationsf

FinnGen association statistics

Novel disease associationg

OR

p value

chr1:g.22637683G>A (rs17887074)h

C1QA

1.48% (4.64)

1.21E−73

1.70E−23 (TNF-β)

TNF-β

IFN-γ, IL-17, TNF-β

0.975

–

–

–

–

–

–

chr1:g.169515314T>G (rs3820060)i

F5

29.60%

6.15E−20

1.07E−3 (VEGF-A)

IL-4, IL-12p70

NOVEL

0.175

–

–

–

–

–

–

chr1:g.169505159C>T (rs61808983)j

F5

4.01%

3.49E−06

4.03E−2 (VEGF-A)

–

NOVEL

0.533

EHBP1

7.1E−18

–

–

–

–

chr1:g.221344914A>G (rs151049317)

C1orf140

0.98%

1.79E−08

2.79E−2 (PDGF-BB)

PDGF-BB

NOVEL

1.000

–

–

–

–

–

–

chr2:g.224010157G>A (rs13412535)

SERPINE2

19.8%

< 1E−324

1.60E−37 (IL-10)

All 12 biomarkers

FGF2, IL-6, IL-10, IL-12p70, PDGF-BB

0.998

PDGF-BB

4.6E−13

Hypertrophic scar

1.34

7.5E−5

Yes

chr2:g.224036001del (rs58116674)

SERPINE2

71.5%

3.37E−78

6.18E−13 (IL-6)

PDGF-BB, SDF-1α, IL-4, IL-17, IL-6, IL-10, FGF2, TNF-β

FGF2, IL-6, IL-10, IL-12p70, PDGF-BB

0.067

–

–

–

–

–

–

chr2:g.224257750T>A (rs7578029)

SERPINE2

8.46%

1.02E−08

3.28E−4 (PDGF-BB)

PDGF-BB

FGF2, IL-6, IL-10, IL-12p70, PDGF-BB

0.046

–

–

Infections of the skin and subcutaneous tissue

1.12

9.7E–5

Yes

chr5:g.150128981C>G (rs2304058)

PDGFRB

37.7%

1.08E−15

2.46E−8 (SDF-1α)

SDF-1α

NOVEL

0.546

PDGFRB

2.3E−458

–

–

–

–

chr6:g.43957870G>A (rs6921438)

C6orf223 / VEGFA

48.3%

3.03E−296

3.38E−91 (VEGF-A)

VEGF-A, IL-12p70, IL-10

IL-10, IL-12p70, VEGF-A

1.000

VEGFA

7.8E−71

–

–

–

–

chr6:g.43974045A>G (rs4714726)

C6orf223 / VEGFA

45.5%

1.12E−11

6.95E−5 (VEGF-A)

VEGF-A

IL-10, IL-12p70, VEGF-A

0.055

–

–

–

–

–

–

chr9:g.2692583C>G (rs2375981)

VLDLR / KCNV2

48.0%

2.03E−17

1.29E−8 (VEGF-A)

VEGF-A, IL-12p70

IFN-γ, IL-10, IL-12p70, VEGF-A

0.748

–

–

–

–

–

–

chr9:g.2782458A>G (rs10122155)

VLDLR / KCNV2

43.3%

1.08E−04

5.43E−3 (VEGF-A)

–

IFN-γ, IL-10, IL-12p70, VEGF-A

0.162

–

–

–

–

–

–

chr9:g.133271182T>C (rs550057)

ABO

31.0%

8.49E−14

2.08E−5 (IL-4)

IL-4

FGF2

0.578

ALPI CHST15 FAM177A1 JAG1

2.8E−19 1.0E−30 9.3E−19 8.3E−14

Anemias

Other and unspecified anaemias

Other anaemias

Diseases of the blood and blood-forming organs

1.12

1.10

1.11

1.06

4.7E−8

4.9E−5

2.6E−5

2.9E−5

No

Visual field defects Diseases of the eye and adnexa

1.24 1.04

4.4E−5 9.4E−6

Yes

Diseases of the ear and mastoid process

1.04

4.8E−5

Yes

chr10:g.63288546C>A (rs7080386)

JMJD1C

38.1%

4.04E−08

1.86E−11 (VEGF-A)

VEGF-A

IFN-γ, IL-10, IL-12p70, VEGF-A

0.064

HB-EGF

1.60E−13

–

–

–

–

chr15:g.101339772G>A (rs111482836)

PCSK6

29.0%

3.42E−05

0.010 (PDGF-BB)

–

PDGF-BB

0.537

–

–

–

–

–

–

chr15:g.101345122G>A (rs12905972)

PCSK6

21.8%

0.035

0.027 (VEGF-A)

–

PDGF-BB

0.127

–

–

–

–

–

–

chr15:g.101446425G>T (rs6598475)

PCSK6

65.7%

1.27E−54

2.63E−8 (PDGF-BB)

PDGF-BB, SDF-1α, IL-4, IL-17

PDGF-BB

0.704

–

–

–

–

–

–

chr15:g.101452793C>A (rs11639051)

PCSK6

24.3%

2.71E−69

1.11E−13 (PDGF-BB)

PDGF-BB, SDF-1α, IL-4, IL-10

PDGF-BB

0.321

–

–

–

–

–

–

chr19:g.55032292G>A (rs199588110)h

GP6

0.33% (3.69)

8.54E−14

1.25E−17 (IL-17)

All 12 biomarkers

G-CSF

1.000

–

–

Benign neoplasm of meninges

6.4

4.9E−5

Yes

  1. aBolded variants are lead variants. Genomic positions are mapped to Genome Assembly GRCh38.
  2. bAF allele frequency, FIN enrichment AF in Finns compared to AF in non-Finnish, Swedish, Estonian Europeans (NFSEE) in the gnomAD genomes database; reported if it was at least 1.5-fold.
  3. cDriver traits can only be determined for those variants with a genome-wide significant association in the multivariate analysis.
  4. dPrevious associations with the 12 biomarkers were searched for in the NHGRI-EBI GWAS Catalog within a region encompassing ±500 kB around the variant. An association was regarded novel if no associations with any of the 12 biomarkers had been reported in this region.
  5. ePosterior probability of being causal, determined by FINEMAP.
  6. fOnly associations that remain significant after conditioning are reported here. Closely related disease diagnoses are represented in a shared cell.
  7. gNovelty of disease associations was assessed at gene-level.
  8. hMissense variant.
  9. iVariant was in high linkage disequilibrium (r2 = 0.997) with a missense variant (chr1:g.169529737T>C, rs6030)
  10. jVariant was in high linkage disequilibrium (r2 = 0.996) with a missense variant within its credible set (chr1:g.169515529A>G, rs9332701) predicted deleterious by SIFT and probably damaging by PolyPhen.
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