Table 2 Posterior probabilities of systemic sclerosis fine-mapped loci

From: GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways

Chr

Credible set locus

SNPs Cred. Set

Index SNP

PP Index

SNP PP Max

PP Max

Func.refgene SNP PP Max

Func.refgene in the 95% credible set

1

IL12RB2

6

rs3790566

0.195

rs3790567

0.321

Intronic

Intronic

1

CD247

1

rs2056626

0.999

rs2056626

0.999

Intronic

-

1

TNFSF4- LOC100506023 -PRDX6

6

rs2022449

0.659

rs2022449

0.659

ncRNA Intronic

ncRNA_intronic

1

TNFSF4- LOC100506023 -PRDX6

43

rs1857066

0.046

rs11576547

0.265

ncRNA intronic

ncRNA_intronic

2

NAB1

11

rs16832798

0.191

rs716254

0.242

Intronic

Intronic; intergenic; downstream

2

STAT4-a 1

1

rs3821236

1.000

rs3821236

1.000

Intronic

-

2

STAT4-b 2

2

rs4853458

0.905

rs4853458

0.905

Intronic

Intronic

3

FLNB -DNASE1L3-PXK

6

rs7355798

0.365

rs7355798

0.365

Intronic

Intronic

3

FLNB-DNASE1L3- PXK

27

rs4076852

0.123

rs7653734

0.292

Intronic

Intronic; intergenic

3

POGLUT1-TIMMDC1-CD80- ARHGAP31

1

rs9884090

0.956

rs9884090

0.956

Intronic

-

3

IL12A

23

rs589446

0.385

rs589446

0.385

ncRNA intronic

ncRNA_intronic

4

DGKQ

2

rs11724804

0.793

rs11724804

0.793

Intronic

Intronic

4

NFKB1

6

rs230534

0.200

rs230517

0.329

Intronic

Intronic

5

TNIP1

1

rs3792783

0.999

rs3792783

0.999

Intronic

-

6

ATG5

3

rs633724

0.588

rs633724

0.588

Intronic

Intronic

8

FAM167A-BLK

1

rs2736340

1.000

rs2736340

1.000

Intergenic

-

8

RAB2A-CHD7

80

rs685985

0.003

rs6987084

0.139

Intronic

Intronic; UTR3; intergenic

11

CDHR5 -IRF7

4

rs6598008

0.760

rs6598008

0.760

Intronic

Intronic; exonic synonymous SNV; UTR3; exonic nonsynonymous

11

TSPAN32,CD81-AS1

20

rs2651804

0.184

rs2651804

0.184

Intergenic

Intergenic

11

DDX6

7

rs11217020

0.021

rs10892286

0.775

Intronic

Intronic; intergenic

15

CSK

1

rs1378942

0.993

rs1378942

0.993

Intronic

-

16

IRF8

6

rs11117420

0.202

rs11117422

0.54

Intergenic

Intergenic

17

IKZF3 -GSDMB

17

rs883770

0.032

rs9303277

0.157

Intronic

Intergenic; intronic; exonic synonymous SNV; exonic nonsynonymous

17

NUP85 -GRB2

2

rs1005714

0.940

rs1005714

0.940

Intronic

Intronic

19

IL12RB1

2

rs2305743

0.944

rs2305743

0.944

Intronic

Intronic

  1. Chr chromosome, PP posterior probability, SNP single-nucleotide polymorphism
  2. 1Name of the credible set that comprised the index SNP from STAT4 genomic region (2q32.2-q32.3)
  3. 2Name of the credible set that comprised the secondary association signal in STAT4 genomic region (2q32.2-q32.3)
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