Table 1. SNPs with statistically significant results in EPICOLON stage 1 in the candidate-gene approach for regions 9q22 and 3q22.

SNP_ID	Gene	Location/relevance	Alleles	MAF cases	MAF controls	Test	GT counts cases	GT counts controls	OR (95% CI)	P-value
rs4149338	ABCA1	9q22/intron, triplex, mcons	C/T	0.241	0.285	Dom	201/280	248/252	0.73 (0.57–0.94)	0.0141
rs2515618	ABCA1	9q22/intron, triplex, mcons	G/A	0.255	0.278	Dom	213/287	250/260	0.77 (0.60–0.99)	0.0406
rs4149339	ABCA1	9q22/miss, ESE, mcons	C/T	0.217	0.278	Dom	183/300	247/257	0.63 (0.49–0.82)	0.00043
rs10991898	AUH	9q22/intron, triplex, mcons	C/T	0.095	0.119	Dom	87/394	117/386	0.73 (0.53–0.99)	0.0493a
rs589362	C9ORF102	9q22/3′UTR, ESE, mcons	C/G	0.320	0.358	Dom	257/223	306/198	0.75 (0.58–0.96)	0.0230
rs10123342	NOL8	9q22/promoter, mcons	T/G	0.343	0.394	Rec	52/433	86/407	0.57 (0.39–0.82)	0.0025
rs11466445	TGFBR1	9q22/3 AA deletion (GGCGGCGGC), mcons	3AA/-	0.084	0.109	Dom	77/406	105/399	0.72 (0.52–0.99)	0.0491a
rs12236219	ZNF169	9q22/miss, ESE, mcons	C/T	0.031	0.068	Allelic	30/940	69/939	0.43 (0.28–0.67)	0.00012a
rs2246945	A4GNT	3q22/miss, ESE, mcons	A/C	0.289	0.325	Rec	37/430	59/431	0.63 (0.40–0.97)	0.0340
rs2346747	A4GNT	3q22/promoter, mcons	G/A	0.317	0.352	Rec	46/434	69/417	0.64 (0.43–0.95)	0.0268
rs329387	ARMC8	3q22/intron, triplex, mcons	G/A	0.450	0.502	Dom	317/151	377/124	0.69 (0.52–0.91)	0.0095
rs939453	ARMC8	3q22/triplex, mcons	C/A	0.422	0.484	Allelic	404/554	484/516	0.78 (0.65–0.93)	0.0056
rs13088006	CDV3	3q22/intron, triplex, mcons	T/C	0.232	0.256	Rec	22/458	40/448	0.54 (0.31–0.92)	0.0217
rs1673607	CEP70	3q22/miss, ESE, ESS, mcons	A/G	0.472	0.501	Rec	108/388	140/367	0.73 (0.55–0.97)	0.0321
rs811322	FAIM	3q22/synon, ESE	A/G	0.456	0.485	Rec	98/389	128/373	0.73 (0.54–0.99)	0.0423
rs108858	IL20RB	3q22/3′UTR, ESE	A/G	0.433	0.475	Dom	313/161	362/136	0.73 (0.56–0.96)	0.0243
rs3738000	NEK11	3q22/miss, mcons	T/A	0.273	0.301	Dom	218/262	261/239	0.76 (0.59–0.98)	0.0337
rs10934954	PIK3R4	3q22/synon, ESS	C/T	0.242	0.204	Rec	33/446	19/481	1.87 (1.05–3.34)	0.0311
rs2071387	RBP1	3q22/intron, mcons	T/C	0.170	0.177	Rec	8/475	22/478	0.37 (0.16–0.83)	0.0124
rs1131597	SLCO2A1	3q22/3′UTR, mcons	G/A	0.303	0.379	Allelic	289/665	380/622	0.71 (0.59–0.86)	0.00038
rs1444601	TOPBP1	3q22/synon, mcons	A/G	0.238	0.281	Allelic	231/739	282/720	0.80 (0.65–0.98)	0.0284

Abbreviations: AA=amino acid; CI=confidence interval; Dom=dominant; ESE=exonic splicing enhancer; ESS=exonic splicing silencer; GT=genotype; MAF=minor allele frequency; mcons=conserved in mouse; miss=missense; Rec=recessive; SNP_ID=SNP identification; synon=synonymous; intron=intronic; UTR=untranslated region.

Results are shown according to the best fitting-model.

^aIf one of the genotypes had a frequency <5, then Fisher's exact test was used.