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Table 3 Summary of the SNPs identified from the RNA-seq datasets in genes mapping within the GWAS regions

From: A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine

SSC

Interval

Top SNP of the GWAS interval

# SNPs called

Highest LD

SNP with highest LD

Genotypic frequency (0/0; 0/1; 1/1)

# called samples

SNP effect

Gene

Trait

1

I3

rs327733412

3

0.07

rs710447566

0.34; 0.54; 0.11

35

Low

KATNAL2

HABN

7

I2

rs336588919

2

0.4

rs330912302

0.63; 0.12; 0.25

32

Low

CHD2

NABN

13

I1

rs690794887

21

0.4

rs331304027

0.06; 0.09; 0.85

33

Moderate

ULK4

HABN

13

I2

rs327865244

11

0.2

rs323872641

0.49; 0.37; 0.14

35

Low

ABHD14A

HABN

  1. SSC, Sus scrofa chromosome; # SNPs called, number of SNPs identified in the SNP calling analysis; LD, linkage disequilibrium; Genotypic frequency: allelic frequency for each of the genotypes; # called samples, number of samples with reads in the given SNP position; HABN, head abnormalities; NABN, neck abnormalities
  2. The columns SNP effect and gene refer to the SNP with the highest LD in the region