Table 1. Association analysis results on two datasets: the family-based data and the case-control data.

Chr.	Gene	SNP	Family-based analysis			Case-control
			FBAT	Haploview	PLINK	Haploview	PLINK	OR
			P-value	P-value	P-value	P-value	P-value
2	APIP	APIP-1-13	0.023	0.023	0.146	0.003	0.002	0.70
	ELF5	ELF5-1	0.005	0.004	0.005	3.27E-05	5.93E-05	0.54
		ELF5-3	0.018	0.016	0.037	0.325	0.241	0.63
		ELF5-5	0.002	0.002	9.23E-04	4.20E-07	1.44E-04	0.46
		ELF5-8	0.025	0.020	0.047	0.488	0.268	0.64
	CAT	CAT-E11-1	0.004	0.004	0.029	0.005	0.006	0.62
		CAT-5U-5	0.045	0.046	0.078	0.032	0.050	0.52
		CAT-5U-1	0.032	0.034	0.052	0.001	0.002	0.42
	HIPK3	HIPK3-1	0.008	0.006	0.008	0.478	0.752	0.55
	KIF18A	KIF18A-E3-3	0.001	0.001	0.004	0.006	1.47E-03	0.58
	LONP1	LONP1-2	0.020	0.031	0.094	0.060	0.043	0.67
	ADAMTS2	ADAMTS2-E2021-1	0.034	0.034	0.019	4.00E-04	3.77E-05	1.38
	COL23A1	COL23A1-E2	0.008	0.008	0.003	3.22E-07	4.76E-10	1.60
12	RAC3	RAC3-I2-4	0.020	0.020	0.108	0.951	0.381	0.71
	PYCR1	PYCR1-1	5.40E-05	8.18E-05	1.74E-04	0.181	0.186	0.30
		PYCR1-E4-E5	8.80E-05	8.77E-05	7.96E-04	0.588	0.581	0.45
	NPTX	NPTX1-4-2	9.99E-06	1.49E-05	2.23E-05	0.053	0.021	0.94
		NPTX1-3	4.03E-04	8.00E-04	5.17E-05	1.90E-08	2.95E-09	1.52
	CARD14	CARD-1-1	0.059	0.035	0.015	0.394	0.419	1.34
		CARD-4-3	0.031	0.025	0.072	0.156	0.275	1.31
	PRPSAP1	PRP-I10	0.031	0.028	0.080	9.52E-04	8.91E-04	0.63
	MIF4GD	MIF-I7	0.014	0.014	0.008	0.490	0.304	3.00
	ICT1	ICT-I6-1	0.051	0.045	0.056	0.163	0.691	0.32

Note: SNPs in bold were in haplotypes significantly associated with scrotal hernia. Four SNPs in ELF5 were found to constitute a haplotype together with the SNP EHF1 in EHF. Then after fine mapping, these four SNPs, together with three SNPs in CAT, formed another haplotype, more significantly associated with scrotal hernia (Figure 1E).