Table 3.

Strongest CpG association per GWAS SNP

Trait	SNP	Position (hg19)	Reported genes	CpG	beta	P-value	Associated gene	Location	CpG island	Distance to SNP (kb)
Melanoma	rs401681	chr5:1322087	TERT, CLPTM1L	cg06550200	0.783	2.6 × 10−50	CLPTM1L	Body	–	−3.5
Cutaneous nevi	rs738322	chr22:38569006	PLA2G6	cg25457927	0.851	1.7 × 10−49	–	–	Shelf	−26.4
Melanoma	rs45430	chr21:42746081	MX2	cg22778903	−0.711	1.9 × 10−42	MX2	5′UTR	–	4.4
Melanoma	rs6001027	chr22:38545619	PLA2G6	cg25457927	0.843	1.3 × 10−38	–	–	Shelf	−49.8
Cutaneous nevi and Melanoma	rs2284063	chr22:38544298	PLA2G6	cg25457927	0.834	3.5 × 10−38	–	–	Shelf	−51.1
Melanoma	rs7412746	chr1:150860471	ARNT, SETDB1, LASS2, ANXA9, MCL1, CTSK	cg15448220	0.662	1.4 × 10−32	SETDB1	TSS1500	Shore	−37.4
Melanoma (2)	rs258322	chr16:89755903	MC1R	cg05714116	−0.728	5.5 × 10−14	CDK10	TSS1500	Shore	3.3
Cutaneous nevi	rs3768080	chr1:236179869	NID1	cg18765906	−0.374	6.4 × 10−14	NID1	Body	–	4.5
Melanoma	rs4785763	chr16:90066936	MC1R	cg08547343	−0.346	1.0 × 10−9	CENPBD1;AFG3L1	5′UTR; TSS200	Island	28.1
Melanoma	rs910873	chr20:33171772	CDC91L1	cg01901788	−0.441	1.8 × 10−6	MAP1LC3A	TSS1500	Shore	25.9
Melanoma	rs13097028	chr3:169464942	ACTRT3	cg27020690	−0.289	2.0 × 10−6	–	–	Island	−17.4
Melanoma	rs13016963	chr2:202162811	CASP8	cg24599065	−0.230	2.1 × 10−6	CASP10	3′UTR	–	69.0
Melanoma	rs228437	chr6:134898456	ASIP	cg24504307	−0.355	9.2 × 10−6	–	–	–	−64.7
Melanoma	rs3219090	chr1:226564691	PARP1	cg18764804	0.240	6.2 × 10−4	PARP1	TSS1500	Shore	−32.0
Melanoma	rs1031925	chr3:51379274	DOCK3	cg09456445	−0.315	8.5 × 10−4	DOCK3	3′UTR	Shore	−41.1
Melanoma	rs1722784	chr1:150961869	ANXA9	cg07479786	0.261	8.9 × 10−4	ANXA9	3′UTR	–	−6.0
Melanoma	rs16953002	chr16:54114824	FTO	cg01083598	−0.169	7.2 × 10−3	–	–	Island	−41.2
Melanoma	rs35390	chr5:33955326	SLC45A2	cg01990593	0.689	8.8 × 10−3	ADAMTS12	Body	Shore	65.0
Melanoma	rs1801516	chr11:108175462	ATM	cg08954307	−0.249	9.8 × 10−3	ATM	Body	–	−59.3
Cutaneous nevi	rs4636294	chr9:21747803	MTAP	cg03724238	−0.128	0.013	–	–	Island	51.1
Melanoma	rs4698934	chr4:106139387	TET2	cg08530497	−0.195	0.037	TET2	Body	–	−15.9
Melanoma	rs1847134	chr11:89005253	TYR	cg25941151	−0.153	0.041	TYR	TSS200	–	94.3
Melanoma (2)	rs7023329	chr9:21816528	CDKN2A	cg14548963	0.118	0.068	MTAP	Body	–	3.6
Melanoma (2)	rs1393350	chr11:89011046	TYR	cg03508346	−0.118	0.142	NOX4	3′UTR	–	−48.8
Melanoma	rs17119461	chr10:107516352	NR	cg18758405	−0.290	0.333	–	–	–	65.0
Melanoma	rs1889497	chr6:65432283	EYS	cg11999886	−0.026	0.760	EYS	Body	–	90.8

Abbreviations: GWAS, genome-wide association studies; SNP, single nucleotide polymorphism; TSS, transcription start site; UTR, untranslated region.