Genetic association analysis of CLEC5A and CLEC7A gene single-nucleotide polymorphisms and Crohn’s disease

Table 1 Genotype and allele frequencies of single nucleotide polymorphisms in the genes CLEC5A, CLEC7A and NOD2 in Crohn’s disease patients and controls

Gene	SNP	Genotype	Cases (n = 175)	Controls (n = 157)	Allele1	Cases (alleles)	Controls (alleles)	Genotype P value2	Dominant P value2,3	Recessive P value2,3	Allelic P value2
CLEC5A	rs1285933	GG	35	36	G, A	144, 206	155, 159	0.1093 (0.0285)	0.9727 (0.5921)	0.0523 (0.0091)	0.0900 (0.0352)
		GA	74	83
		AA	66	38
CLEC7A	rs2078178	GG	104	100	G, A	274, 76	251, 63	1.0000 (0.5713)	0.9033 (0.4320)	0.8344 (0.7618)	0.9107 (0.6335)
		AG	66	51
		AA	5	6
CLEC7A	rs16910631	CC	153	139	C, T	327, 23	294, 20	0.8078 (0.7024)	0.9056 (0.8662)	0.9269 (0.6045)	1.0000 (1.0000)
		CT	21	16
		TT	1	2
NOD2	rs2066844 (SNP8)	CC	146	148	C, T	319, 31	305, 9	0.0498 (0.0065)	0.0219 (0.0019)	0.9583 (0.5000)	0.0368 (0.0016)
		CT	27	9
		TT	2	0
NOD2	rs2066845 (SNP12)	GG	163	149	G, C	338, 12	306, 8	0.8481 (0.6453)	0.8481 (0.6453)	NA	0.7874 (0.6505)
		GC	12	8
		CC	0	0
NOD2	rs2066847 (SNP13)	C-C	147	143	C, CC	316, 34	300, 14	0.0923 (0.0321)	0.1569 (0.0682)	0.1025 (0.0312)	0.0474 (0.0103)
		C-CC	22	14
		CC-CC	6	0

¹Italic: Minor allele according to database https://www.ncbi.nlm.nih.gov/snp/.

²Numbers in brackets refer to the P value prior to Benjamini-Hochberg correction (23 tests); significant differences (P < 0.05) are indicated in bold.

³Refers to the minor allele. SNP: Single nucleotide polymorphism; NA: Not applicable (due to the absence of CC genotype).

Table 2 Odds ratios of genotypes and alleles of single nucleotide polymorphisms in the genes CLEC5A and NOD2

Gene	SNP	Genotype/allele	Odds ratio	95%CI1	P value1
CLEC5A	rs1285933	AA	1.90	1.18-3.05	0.009
		GG	0.84	0.50-1.42	0.516
		AG	0.65	0.42-1.01	0.054
		A	1.39	1.03-1.90	0.034
		G	0.72	0.53-0.97	0.034
NOD2	rs2066844 (SNP8)	TT	NA
		CC	0.31	0.14-0.67	0.003
		CT	3.00	1.36-6.60	0.006
		T	3.29	1.54-7.03	0.002
		C	0.30	0.14-0.65	0.002
NOD2	rs2066847 (SNP13)	CC-CC	NA
		C-C	0.51	0.26-1.02	0.056
		C-CC	1.47	0.72-2.98	0.287
		C	0.43	0.23-0.82	0.011
		CC	2.31	1.21-4.38	0.011

¹Unadjusted for multiple testing. SNP: Single nucleotide polymorphism; NA: Not applicable (missing in controls); CI: Confidence interval.

Table 3 Pairwise statistical interaction between single nucleotide polymorphisms in a linear model¹

SNP	CLEC5A	CLEC7A		NOD2
	rs1285933	rs2078178	rs16910631	rs2066844	rs2066845	rs2066847
rs1285933	NA	0.6490	0. 7409	0.5266	0.6875	0.2813
rs2078178	0.6490	NA	0.1036	0.8573	0.4040	0.3718
rs16910631	0.7409	0.1036	NA	0.8980	0.6698	0.9270
rs2066844	0.5266	0.8573	0.8980	NA	2.8248e-07	0.9664
rs2066845	0.6875	0.4040	0.6698	2.8248e-07	NA	0.7399
rs2066847	0.2813	0.3718	0.9270	0.9664	0.7399	NA

¹Disease—single nucleotide polymorphism (SNP) A + SNP B + SNP A: SNP B. The uncorrected P values for the last term of an ANOVA are presented in the table for all 30 interactions. The only significance was for two chromosomally neighboring SNPs within NOD2. SNP: Single nucleotide polymorphism; NA: Not applicable.