Table 2.

SNPs selected in models for the regions showing evidence for multiple independent associations

						Single SNP result			Logistic regression of multiple variant models
Region	SNP name	Position	Mapped gene	Allele	Allele frequency	OR	p value	r2 with top SNP	OR	p value	R2 for melanoma risk
TERT	rs7705526	1285974	TERT	A	0.332	1.13	2.9 × 10−5	0.09	1.09	0.026	0.46
	rs2736099	1287340	TERT	A	0.374	1.12	6.6 × 10−5	0.14	1.09	0.025
	rs1801075	1317949	intergenic	C	0.172	1.23	2.7 × 10−10	0.51	1.08	0.050
	rs2447853	1333077	CLPTM1L	G	0.468	1.20	5.7 × 10−12	Top SNP	1.18	1.3 × 10−7
CDKN2A	rs869330	21804617	MTAP	G	0.513	0.81	3.9 × 10−16	Top SNP	0.81	8.0 × 10−16	0.65
	rs3088440	21968159	CDKN2A	A	0.089	1.21	2.0 × 10−5	0.03	1.13	0.014
	rs3731204	21984661	CDKN2A	C	0.148	0.81	2.2 × 10−8	0.03	0.84	8.1 × 10−6
	rs1011970	22062134	CDKN2B-AS1	T	0.166	1.17	2.3 × 10−6	0.02	1.09	0.033
CCND1	rs2290419	68919649	intergenic	G	0.057	0.78	2.1 × 10−5	0.03	0.76	7.2 × 10−6	0.37
	rs623110	69308897	intergenic	T	0.314	1.13	1.3 × 10−5	0.35	1.07	0.015
	rs12422135	69378736	intergenic	A	0.409	1.18	3.5 × 10−10	Top SNP	1.15	3.1 × 10−7
ASIP	rs74325991	32547380	intergenic	G	0.490	1.18	8.8 × 10−8	0.38	1.11	0.0025	0.31
	rs6059655	32665748	RALY	A	0.086	1.33	2.1 × 10−11	Top SNP	1.26	4.6 × 10−7

For each region the model with the greatest number of SNPs in shown after 100 iterations of Hyperlasso. Two different 2-SNP models occurred for ASIP, both include rs6059655 with either rs74325991 (presented here) or rs6088372 (not shown). The ORs (odd ratios) for the stated allele and p values are presented for the results from the single SNP analysis and when including all listed SNPs at that locus. The LD (r²) with the most significant SNP in this study (Top SNP) is estimated from the correlation coefficient. The R² for percentage of variation explained in melanoma risk is given for including all listed SNPs at that locus.