Table 1.

Variants selected from circadian clock genes and Li response association results. Gene and SNP information including the minor allele frequency (MAF) for the rare allele is indicated. Additive, dominant and recessive genetic transmission models were used, the nominal p-values (P) and odds ratios (OR) are shown for each (Add, Dom, Rec). Uncorrected p<0.05 was considered nominally statistically significant with one degree of freedom for each analysis. In some cases, exclusions for quality control slightly reduced total sample size.

Gene	SNP	Chr	Position	Location	N=	Minor allele	Major allele	MAF	Wald Stat	OR Add	P Add	OR Dom	P Dom	OR Rec	P Rec
ARNTL	rs2279287	11	13298485	Enhancer	281	A	G	0.27	0.56	1.11	0.57	1.10	0.68	1.30	0.57
ARNTL	rs1982350	11	13350131	Enhancer	281	T	C	0.35	−0.18	0.97	0.86	1.04	0.89	0.80	0.56
ARNTL	rs2278749	11	13397878	Promoter	282	A	G	0.19	0.72	1.18	0.47	1.11	0.69	2.67	0.24
CLOCK	rs1801260	4	56301369	Exon	281	C	T	0.26	0.32	1.07	0.75	1.32	0.26	0.45	0.13
CLOCK	rs3736544	4	56309992	Exon	279	A	G	0.36	−1.64	0.75	0.10	0.68	0.12	0.68	0.27
CLOCK	rs34897046	4	56325365	Exon	282	C	G	0.05	0.75	1.34	0.45	1.52	0.31	NA	NA
CRY1	rs8192440	12	107395106	Exon	278	A	G	0.41	−2.50	0.64	0.01	0.54	0.02	0.59	0.11
GSK3B	rs6438552	3	119631814	Enhancer	281	C	T	0.42	1.38	1.28	0.17	1.17	0.54	1.82	0.08
NR1D1	rs2071427	17	38254492	Promoter	282	A	G	0.28	1.95	1.45	0.05	1.90	0.01	0.91	0.83
PER2	rs2304672	2	239186589	Exon	281	G	C	0.09	−1.65	0.59	0.10	0.60	0.12	NA	NA
PER3	rs228729	1	7845695	Intron	282	A	G	0.31	0.69	1.14	0.49	1.25	0.36	0.97	0.95
PER3	rs228642	1	7863293	Intron	282	C	T	0.43	0.56	1.11	0.58	1.06	0.83	1.27	0.46
PER3	rs228666	1	7868725	Intron	282	C	T	0.37	−0.51	0.92	0.61	0.95	0.84	0.78	0.46
PER3	rs228697	1	7887579	Exon	281	G	C	0.11	0.44	1.12	0.66	1.10	0.75	1.58	0.61
PER3	rs2859388	1	7888215	Promoter	282	G	A	0.36	0.26	1.05	0.79	0.99	0.97	1.26	0.55
PER3	rs2640909	1	7890117	Exon	277	C	T	0.33	−0.72	0.88	0.47	0.83	0.45	0.87	0.73