Appendix Table A1.

Details of Single Nucleotide Polymorphisms Selected for This Study

SNP	Chromosomal position (GRCh38.p12)	Gene: consequence	Allelesa	MAFb	MAF in controls (current study)	HWE in controls (current study)	References
rs4898c	chrX:47585586	TIMP1: Synonymous Variant	T/C	0.46	0.39	0.09	Indelicato et al. (2006), Skarmoutsou et al. (2012)
		SYN1: Intron Variant
		MIR4769: 2KB Upstream Variant
rs344781	chr19:43670636	PLAUR: 2KB Upstream Variant	A/G	0.25	0.25	1.00	Manetti et al. (2011)
rs1126579	chr2:218136011	CXCR2: 3 Prime UTR Variant	C/T	0.49	0.37	0.66	Renzoni et al. (2000), Salim et al. (2012)
rs1341239	chr6:22303975	PRL: 2KB Upstream Variant	G/T	0.35	0.35	0.46	Fojtíková et al. (2010)
rs1799724	chr6:31574705	TNF: 2KB Upstream Variant	C/T	0.09	0.18	0.79	Sato et al. (2004), Otieno et al. (2007)
		LTA: 500B Downstream Variant
rs1799964	chr6:31574531	TNF: 2KB Upstream Variant	T/C	0.21	0.22	0.39	Sato et al. (2004), Otieno et al. (2007)
		LTA: 500B Downstream Variant
		LOC100287329: 2KB Upstream Variant
rs1800890	chr1:206776020	IL19: Intron Variant	T/A	0.37	0.25	0.35	Hudson et al. (2005), Peng et al. (2012b)
rs1800896	chr1:206773552	IL19: Intron Variant	A/G	0.45	0.38	0.79	Ates et al. (2008), Salim et al. (2013)
		IL10: 2KB Upstream Variant
rs2430561	chr12:68158742	IFNG: Intron Variant	T/A	0.46	0.49	0.12	Wastowski et al. (2009)
rs3117230	chr6:33107858	HLA-DPB1: Downstream Variant	A/G	0.23	0.14	0.55	Zhou et al. (2009)
rs3128930	chr6:33107889	HLA-DPB1: Downstream Variant	G/A	0.26	0.16	0.12	Zhou et al. (2009)
rs3128965	chr6:33088122	HLA-DPB1: 3 Prime UTR Variant	G/A	0.19	0.14	0.55	Zhou et al. (2009)
rs6918698	chr6:131952117	CCN2: 2KB Upstream Variant	G/C	0.49	0.47	0.68	Fonseca et al. (2007), Kawaguchi et al. (2009)
rs7574865	chr2:191099907	STAT4: Intron Variant	G/T	0.23	0.32	0.76	Dieude et al. (2009), Gourh et al. (2009), Rueda et al. (2009), Tsuchiya et al. (2009), Allanore et al. (2011), Liang et al. (2012), Peng et al. (2012a), Yi et al. (2013), Zheng et al. (2013), Zochling et al. (2014), Xu et al. (2016)
rs9399005	chr6:131947824	CCN2: 500B Downstream Variant	C/T	0.30	0.27	0.80	Granel et al. (2010)
rs12528892	chr6:32725729	HLA-DQA2:Upstream variant	C/T	0.07	0.02	0.84	Mayes et al. (2014)
rs131654	chr22:21562901	UBE2L3: Intron Variant	T/G	0.33	0.24	0.52	Hasebe et al. (2012)
rs2298428	chr22:21628603	YDJC: Missense Variant	C/T	0.18	0.27	0.00	Hasebe et al. (2012)

^aMajor/Minor allele based on the current and published studies.

^bMAF of European population submitted in 1000 Genome Project (dbSNP).

^cCalculations for this SNP in the current study were performed using only the female patient genotypes since it is located on the X-chromosome.

HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; SNP, single nucleotide polymorphism.