Table 2 The pleiotropic loci identified by \(\mathrm{cFDR}\) and GPA method (\(\mathrm{ccFDR}\) < 0.05 and fdr11.GPA < 0.2).

From: Identification of potentially common loci between childhood obesity and coronary artery disease using pleiotropic approaches

Chr

SNP

Allel

Role

Gene

P.valueA

P.valueB

cFDR.AcB

cFDR.BcA

ccFDR

fdr11.GPA

chr16

rs9940128

G/A

Intronic

FTO

1.67E−05

9.25E−14

1.67E−05

2.45E−11

1.67E−05

0.001527

chr2

rs1866146

G/A

UTR3

EFR3B

0.000594

2.04E−06

0.003264

0.000802

0.003264

0.031703

chr11

rs7127507

T/C

ncRNA_intronic

BDNF-AS

0.000754

1.29E−05

0.005024

0.003705

0.005024

0.053765

chr2

rs11125884

A/G

ncRNA_intronic

DNAJC27-AS1

0.01177

2.73E−13

0.01177

4.88E−10

0.01177

0.109489

chr1

rs7536226

C/T

Intergenic

TSEN15, C1orf21

0.000247

5.31E−05

0.004194

0.015092

0.015092

0.064655

chr2

rs7420531

G/A

UTR3

AAK1

0.000533

8.77E−05

0.007644

0.021845

0.021845

0.088304

chr16

rs16969473

A/G

Intronic

GPR139

0.002157

8.22E−05

0.018119

0.022945

0.022945

0.126129

chr19

rs13382133

C/T

Intronic

FCHO1

7.67E−12

0.000558

1.1E−09

0.024548

0.024548

0.12562

chr13

rs12429545

G/A

Intergenic

LINC01065, LINC00558

0.02676

3.66E−11

0.02676

7.68E−08

0.02676

0.175974

chr4

rs1996023

T/G

Intergenic

GNPDA2, GABRG1

0.007574

2.73E−07

0.03787

0.00037

0.03787

0.094976

chr1

rs7531118

T/C

Intergenic

NEGR1, LINC01360

0.01305

1.29E−05

0.03915

0.007047

0.03915

0.182283

chr16

rs194546

G/A

ncRNA_intronic

LOC101927814

0.006605

8.62E−06

0.03963

0.007183

0.03963

0.123251

chr2

rs17736503

G/T

Intronic

NCOA1

0.007106

6.91E−05

0.04382

0.030049

0.04382

0.188942

  1. The SNPs are listed with their chromosomal, allele, role, annotated genes, original p-value for each phenotype, cFDR value for each phenotype, ccFDR and fdr.11.GPA values. A means CAD and B means CBMI.
  2. Chr: chromosom, ccFDR: conjunctional conditional false discovery rate, fdr.11GPA: false discovery rate of GPA when the SNP was associated with both phenotypes, GPA: genetic analysis incorporating pleiotropy and annotation.
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