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Table 3 Imputed lead variants in pleiotropic QTL revealed by a multi-trait meta-analyses

From: Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs

QTL

SSC

Start (bp)

Stop (bp)

Lead SNP

P-value

MAF

Ref | Alt

#traits

Candidate gene(s)

1

1

157,732,172

162,736,434

1_159637589

5.26 × 10–13

0.31

Ga | C

3

MC4R

2

1

270,331,332

272,315,496

1_270599319

2.85 × 10–36

0.14

C | CTa

6

na

3

5

65,753,637

66,210,538

5_65997650

5.40 × 10–10

0.41

G | Aa

1

CCND2

4

7

93,119,538

99,261,691

7_97636980

8.09 × 10–45

0.34

Aa | C

4

VRTN; ABCD4

5

17

10,801,927

20,928,904

17_15643342

1.19 × 10–84

0.20

Ca | T

5

BMP2

6

18

10,024,756

10,904,242

18_10678235

18_10678293

2.00 × 10–19

0.32

C | Aa

A | Ga

2

na

  1. aMinor allele in the genotyped dataset; Reference alleles were determined according to the Sscrofa11.1 genome assembly