Table 2.

SNP pairs showing evidence for interaction on the risk of melanoma

Pathway (Gene Ontology category)						MELARISK		MDACC		META-ANALYSIS		Multiple-testing corrected thresholds9
	SNP	Chr1	Genes2	Alleles3	MAF4	Interaction Effect		Interaction Effect		Interaction Effect		Tpathway	Toverall
						βint (seint)5	pint 6	βint (seint)5	pint 6	βmeta-int7 (semeta-int)7	p meta-int 8
Regulation of mitotic cell cycle	rs3863241	8	31kU TERF1	C/T	0.46	−0.27 (0.07)	2.1×10−4	−0.29 (0.08)	2.4×10−4	−0.28 (0.05)	2.0×10−7	9.8×10−7	2.0×10−7
	rs64978510	10	18kD AFAP1L2	C/G	0.48
	rs3863241	8	31kU TERF1	C/T	0.46	−0.32 (0.07)	1.3×10−5	−0.17 (0.08)	0.03	−0.25 (0.05)	3.6×10−6
	rs59737110	10	9kD AFAP1L2	G/A	0.42
Induction of programmed cell death	rs1018933911	2	PRKCE (Intron)	G/A	0.32	0.38 (0.09)	4.3×10−5	0.25 (0.095)	0.009	0.31 (0.07)	2.2×10−6	3.6×10−8	7.1×10−9
	rs17098973	10	45kU TIAL1	A/G	0.26
	rs674314411	2	PRKCE (Intron)	A/G	0.48	−0.34 (0.08)	2.8×10−5	−0.17 (0.09)	0.04	−0.26 (0.06)	1.0×10−5
	rs178295	22	15kU AIFM3	C/T	0.28
Cytokine activity	rs10912551	1	33kD TNFSF4	T/G	0.21	−0.39 (0.09)	7.7×10−6	−0.20 (0.099)	0.05	−0.31 (0.07)	3.5×10−6	1.2×10−7	2.5×10−8
	rs614004	3	CMTM7 (Intron)	G/A	0.48

¹Chr is the chromosome number where the SNP is located

²Gene symbol; k indicates distance to gene in kilobases (Build 37.1); U indicates “upstream of”; D indicates “downstream of ”. Upstream and downstream respectively refer to the 5' and 3' ends of the coding strand of each gene

³Minor allele / Major allele

⁴MAF, minor allele frequency estimated in controls

⁵β_int is the regression coefficient of interaction effect in logistic regression assuming an additive model; se_int is the standard error of β_int

⁶p_int is the p-value of the likelihood-ratio test for interaction (one degree of freedom test assuming an additive model)

⁷β_meta-int and se_meta-int are the regression coefficient and standard error of interaction effect obtained from the meta-analysis of MELARISK and MDACC results (using a fixed-effects model)

⁸β_meta-int is the p-value associated with the Wald test of meta-analyzed interaction effect

⁹T_pathway and T_overall are respectively the pathway-corrected and overall-corrected critical thresholds to take into account multiple testing (see material and methods for details)

¹⁰rs649785 and rs597371 are in moderate linkage disequilibrium (r²=0.56; D'=0.86)

¹¹rs10189339 and rs6743144 are independent (r²=0.001; D'=0.05)