Table 2.

Associated genetic variants in the discovery sample set (n = 96 cases and n = 96 controls)

Chr	Pos (bp)	SNP rs ID	Alt	Ref	F c (%)	F p (%)	OR (95 % CI)	P value	Gene	Coding	RG score	ExAc Eur frequencya	CADD_PHREDb
1	110230569	72989301	G	A	10.0	22.1	2.5 (1.0-6.2)	0.038	GSTM1		4	0.24	NA
1	110233057	111436983	C	T	11.6	26.7	2.8 (1.2-6.2)	0.013	GSTM1		7	0.24	NA
2	216991935	12694384	A	C	29.4	17.9	0.5 (0.3-0.9)	0.04	XRCC5		5	NA	NA
2	218669225	61741262	C	T	13.6	0	NA	0.027	TNS1	p.(Asp1722Ser)	4	0.13	12.49
2	218746990	2303381	T	A	7.7	1.5	0.2 (0.0-0.9)	0.019	TNS1		6	NA	NA
3	55520778	566926	T	G	39.2	25.0	0.5 (0.3-0.9)	0.017	WNT5A		3a	NA	NA
4	106638697	72671840	G	A	2.3	11.4	5.3 (1.5-18.9)	5.8 × 10−3	GSTCD		6	NA	NA
4	106647679	72671858	T	C	3.0	10.5	3.7 (1.2-11.7)	0.026	GSTCD		7	NA	NA
4	106755996	11728716	A	G	3.4	21.0	7.4 (2.5-22.5)	6.5 × 10−5	GSTCD		1f	NA	NA
5	58284208	3805557	C	T	22.0	11.9	0.5 (0.2-0.9)	0.034	PDE4D		7	NA	NA
5	58284283	3805556	G	A	22.0	11.8	0.5 (0.2-0.9)	0.033	PDE4D		6	0.84	NA
5	58286625	1553114	C	T	22.0	11.8	0.5 (0.2-0.9)	0.033	PDE4D		7	0.84	NA
5	141993867	17223611	T	C	10.6	3.0	0.3 (0.1-0.8)	0.025	FGF1		5	NA	NA
6	142703137	2143390	T	C	2.9	19.2	7.9 (1.6-37.6)	4.5 × 10−3	GPR126	p.(Asp373=)	7	0.12	NA
6	151197501	9322290	C	T	17.4	9.0	0.5 (0.2-1.0)	0.047	MTHFD1L		5	NA	NA
6	151206894	147872265	T	C	7.6	2.2	0.3 (0.1-1.0)	0.049	MTHFD1L		7	0.002	NA
6	151263456	803451	A	G	41.8	55.7	1.8 (1.1-2.9)	0.04	MTHFD1L		7	NA	NA
6	151264132	803448	T	C	37.9	50.7	1.7 (1.0-2.7)	0.037	MTHFD1L		6	NA	NA
6	152183551	1643821	A	G	25.8	39.0	1.8 (1.1-3.1)	0.026	ESR1		6	NA	NA
8	42552530	41272375	C	G	1.5	6.9	4.8 (1.0-22.8)	0.034	CHRNB3		5	NA	NA
9	98239503	3780573	A	G	18.3	8.7	0.4 (0.2-0.9)	0.041	PTCH1		5	NA	NA
10	81706281	6413520	G	A	0.8	5.9	8.2 (1.0-66.4)	0.036	SFTPD	p.(Ser45=)	5	0.07	NA
10	123358096	41301039	G	C	25.0	2.8	0.1 (0.0-0.7)	0.017	FGFR2		4	NA	NA
11	102738499	632009	T	C	29.6	50.8	2.5 (1.5-4.1)	6.7 × 10−4	MMP12		7	NA	NA
12	23737566	11046992	A	G	21.2	33.1	1.8 (1.1-3.2)	0.039	SOX5		6	NA	NA
12	110224916	60258652	T	C	2.4	10.5	4.7 (1.0-22.9)	0.05	TRPV4		5	NA	NA
12	110224922	1861810	A	C	36.6	53.8	2.0 (1.1-3.8)	0.04	TRPV4		5	NA	NA
12	110232032	59870578	A	G	7.8	1.6	0.2 (0.0-0.9)	0.034	TRPV4		4	NA	NA
12	110232034	59940634	T	G	7.8	1.6	0.2 (0.0-0.9)	0.034	TRPV4		4	NA	NA
15	71434029	2004101	A	T	0.8	5.6	7.5 (0.9-61.6)	0.035	THSD4		7	NA	NA
15	78790189	2292115	G	A	4.8	0	NA	0.03	IREB2		7	NA	NA
15	78911181	8040868	C	T	31.8	47.8	2.0 (1.2-3.2)	8.8 × 10−3	CHRNA3	p.(Val53=)	1f	0.41	NA
16	16130514	903880	A	C	15.9	27.2	2.0 (1.1-3.6)	0.027	ABCC1		4	NA	NA
16	16205741	9673292	C	G	4.5	0	NA	0.013	ABCC1		6	NA	NA
16	16230290	212087	A	G	38.6	52.2	1.7 (1.1-2.8)	0.028	ABCC1		5	0.44	NA
16	16235366	113328089	A	G	6.9	1.5	0.2 (0.0-1.0)	0.034	ABCC1		5	NA	NA
20	15967390	41275442	T	C	9.1	17.7	2.1 (1.0-4.5)	0.049	MACROD2	p.(Thr100Met)	4	0.18	3.98

Alt, non-reference allele. Ref, reference allele, OR Odds ratio with 95 % confidence intervals, F c Frequency in controls, F p Frequency in cases (patients), RG Score, RegulomeDB score, NA Not available

^aNon-Finnish European allele frequency extracted from ExAc v.0.3.1

^bThe “PHRED-scaled” CADD score based on ranks of all SNV in the hg19 genome reference