Combining omics data to identify genes associated with allergic rhinitis

Clinical Epigenetics

Table 2 Genes with cis-mQTL sites significantly associated with allergic rhinitis with or without asthma

Trait	Gene	Locus	mQTLs	GWAS analysis		EWAS analysis
Trait	Gene	Locus	p value	SNP	p value	CpGs	Δβ ^a	p value
Allergic rhinitis	*CDX1* ^b	chr5q32	6.41e−5	rs888989	0.0038	cg18424208	−5.19	0.0002
	PPAN-P2RY11	chr19p13.2	0.0245	rs3752199	0.0346	cg24118856	7.51	4.39e−5
	RNF39 ^c	chr6p22.1	0.0090	rs2844833	0.0270	cg05563515	10.11	0.0212
			0.0229	rs2844833	0.0270	cg24637044	5.85	0.0132
			0.0265	rs2844833	0.0270	cg01286685	7.78	0.0266
			0.0411	rs2523872	0.0123	cg10930308	9.50	0.0255
			0.0499	rs2523872	0.0123	cg01286685	7.78	0.0266
	SRRT	chr7q22.1	0.0412	rs6942824	0.0224	cg10426581	5.26	0.0096
Allergic rhinitis with asthma	ADORA1	chr1q32.1	0.0337	rs6661284	0.0337	cg19315653	−6.26	0.0315
	ITGB2	chr21q22.3	0.0381	rs7275203	0.0381	cg18012089	6.10	0.0068
	LINC00336	chr6p21.31	0.0073	rs9461924	0.0073	cg04329454	−7.16	0.0015
	MFSD6L	chr17p13.1	0.0120	rs9895992	0.0120	cg11685316	5.01	0.0072
	PCDH8	chr13q14.3	0.0152	rs732774	0.0295	cg14950829	7.53	0.0097
			0.0135	rs3742297	0.0480	cg14950829	7.53	0.0097
			0.0259	rs1801249	0.0296	cg14950829	7.53	0.0097
			0.0259	rs4943046	0.0298	cg14950829	7.53	0.0097
	PITX2	chr4q25	0.0257	rs2067004	0.0272	cg13385016	5.06	0.0240
	PITX2	chr4q25	0.0249	rs9992755	0.0289	cg13385016	5.06	0.0240
	RNF180	chr5q12.3	0.0130	rs7713289	0.0130	cg17370163	5.43	0.0021
	RNF39 ^c	chr6p22.1	0.0133	rs2517504	0.0047	cg03343571	9.19	0.0451
			0.0171	rs2517504	0.0047	cg01286685	8.21	0.0478
			0.0401	rs2535238	0.0248	cg01286685	8.21	0.0478
			0.0499	rs2523872	0.0299	cg01286685	8.21	0.0478
	ZFPM1	chr16q24.2	0.0304	rs750740	0.0304	cg04983687	5.53	0.0056

^aΔβ and p values for CpG sites and SNPs forming a cis-mQTL. A negative Δβ indicates a decrease in the percentage of methylation for cases compared to controls. All loci refer to the human hg19 reference genome
^bCDX1 is the only gene for which the mQTL p value survives multiple correction (p < 1e-4)
^c RNF39 is the only gene marginally associated in both traits

ISSN: 1868-7083