Table 1.

Single nucleotide polymorphisms that correlate with Δphotoperiod

SNP	Gene	Kendall's correlation P value a	τ rank b	F ST rank c		LnRsb rank d		Functional annotation e
				Biaka-Orcadian	Biaka-Maya	CEPH	CHB + JPT
Core circadian
rs11048980	ARNTL2	7.167 × 10-8	1.000	0.506	0.000	0.79	0.89	intronic
rs6811520	CLOCK	1.444 × 10-5	0.978	0.831	0.466	0.84	0.87	intronic
rs11038695	CRY2	1.626 × 10-4	0.957	0.624	0.247	0.64	0.33	intronic; in LD (r 2 = 0.93 in CEPH) with rs11038697 (within ARNTL and CLOCK binding sites)
rs4789846	CSNK1D	5.546 × 10-5	0.970	0.601	0.000	0.69	0.84	intronic
rs5995572	CSNK1E	1.053 × 10-5	0.984	0.973	0.515	0.05	0.14	intronic
rs17654772	NPAS2	2.549 × 10-7	0.998	0.615	0.377	0.84	0.43	intronic
rs4663868	PER2	9.462 × 10-5	0.962	0.286	0.219	0.97	0.90	intronic
Circadian hits (RNAi screen)
rs2583836	ABL1	3.071 × 10-7	0.995	0.936	0.311	0.97	0.63	intronic
rs12713670	ANTXR1	4.331 × 10-9	1.000	0.108	0.468	0.57	0.58	intronic
rs12193789	ASCC3	9.351 × 10-6	0.994	0.371	0.166	0.94	0.96	intronic
rs11581556	ATF6	7.326 × 10-7	0.995	0.845	0.615	0.96	0.90	intronic
rs5996513	BCR	8.368 × 10-6	0.996	0.932	0.626	0.11	0.21	intronic
rs8	CDK6	9.581 × 10-7	0.998	0.800	0.299	0.82	0.85	intronic
rs2304593	CMTM7	5.239 × 10-6	0.993	0.370	0.000	0.16	0.34	intronic
rs2279103	CTDP1	6.403 × 10-8	0.999	0.745	0.276	0.70	0.50	missense T340M
rs657801	DENND2D	9.280 × 10-6	0.983	0.797	0.352	0.94	0.94	intronic
rs2354420	EMP2	6.654 × 10-6	0.988	0.657	0.167	0.08	0.18	intronic
rs11792480	ENG	1.281 × 10-5	0.989	0.954	0.041	0.83	0.68	intronic
rs550897	FAM55D	3.670 × 10-8	0.998	0.848	0.308	0.99	0.99	missense Y398H
rs1011814	FGF10	6.501 × 10-7	0.994	0.926	0.513	0.99	1.00	intronic
rs17679400	FHIT	1.3645 × 10-7	0.998	0.742	0.255	0.26	0.20	intronic
rs1416995	GPR158	2.921 × 10-7	0.997	0.995	0.973	0.04	0.29	intronic
rs12787863	GRM5	3.597 × 10-7	0.996	0.860	0.088	0.94	0.81	intronic
rs17422	HCFC1	1.623 × 10-7	0.997	0.936	0.004	0.84	0.81	intronic
rs11586100	HNRNPR	4.271 × 10-6	0.984	0.968	0.248	1.00	1.00	intronic
rs1122821	HOMER3	8.660 × 10-6	0.980	0.479	0.013	0.46	0.61	intronic
rs2158622	JAZF1	5.810 × 10-6	0.991	0.716	0.000	0.04	0.49	intronic
rs9952025	LIPG	1.269 × 10-5	0.994	0.764	0.787	0.18	0.11	intronic
rs955816	MARCH4	1.735 × 10-6	0.991	0.910	0.186	0.85	0.37	intronic; in LD (r 2 = 0.80 in CHB + JPT) with rs11691655 (within ARNTL and CLOCK binding sites)
rs566125	MMP3	1.247 × 10-6	0.995	0.716	0.254	0.98	0.96	intronic
rs710080	MPG	1.641 × 10-7	0.998	0.989	0.840	0.44	0.54	5' UTR variant
rs1053000	PFKP	9.234 × 10-6	0.988	0.971	0.152	1.00	1.00	3' UTR variant
rs578096	PTGER3	1.272 × 10-5	0.985	0.733	0.000	0.77	0.51	intronic
rs2020945	PWP2	5.640 × 10-8	0.998	0.965	0.780	0.62	0.50	missense D25N
rs11617401	RAB20	5.288 × 10-7	0.997	0.791	0.000	0.89	0.47	intronic
rs1204897	RCC2	7.331 × 10-6	0.987	0.540	0.496	0.37	0.46	intronic
rs17682132	RCVRN	3.072 × 10-7	0.998	0.943	0.000	0.96	0.33	intronic
rs492786	SCARA3	7.034 × 10-6	0.982	0.197	0.417	0.82	0.68	intronic
rs9812406	SCHIP1	1.487 × 10-7	0.998	0.989	0.577	0.60	0.68	intronic
rs6695715	SEC16B	1.113 × 10-5	0.982	0.247	0.123	0.44	0.78	intronic
rs2224957	SH3GL2	2.399 × 10-7	0.996	0.896	0.180	0.01	0.04	intronic
rs6081636	SLC24A3	5.980 × 10-6	0.988	0.612	0.246	0.16	0.47	intronic
rs830142	SLC8A2	7.264 × 10-6	0.993	0.325	0.000	0.67	0.80	intronic
rs732611	TBC1D9	4.321 × 10-8	0.999	0.943	0.000	0.78	0.87	intronic
rs1514685	TPO	5.156 × 10-8	0.998	0.720	0.199	0.23	0.17	intronic
rs11760463	WDR86	1.279 × 10-5	0.975	0.854	0.378	1.00	0.97	intronic
rs10227271	WNT2	6.406 × 10-6	0.983	0.971	0.173	0.07	0.70	intronic
Mouse circadian/sleep disturbance
rs3753472	ADORA1	1.155 × 10-5	0.981	0.941	0.445	0.80	0.21	intronic
rs2830044	APP	5.206 × 10-6	0.985	0.833	0.311	0.53	0.71	intronic
rs228188	BTBD9	3.149 × 10-6	0.993	0.895	0.155	1.00	0.72	intronic
rs7801807	CADPS2	1.465 × 10-5	0.993	0.891	0.000	0.90	0.90	intronic
rs17818083	EBF2	2.924 × 10-6	0.992	0.939	0.000	0.11	0.24	intronic
rs809192	FYN	1.270 × 10-5	0.987	0.804	0.061	0.82	0.63	intronic
rs2134294	HCRTR2	5.923 × 10-6	0.986	0.741	0.405	1.00	0.96	intronic
rs17187747	KCNB2	6.700 × 10-7	0.994	0.652	0.349	0.33	0.54	intronic
rs12762512	KCNMA1	4.857 × 10-8	0.999	0.307	0.494	0.29	0.33	intronic
rs1943620	NCAM1	9.774 × 10-9	0.999	0.838	0.410	0.18	0.19	intronic
rs10774910	NOS1	1.693 × 10-6	0.990	0.916	0.118	1.00	1.00	intronic
rs2294678	NOX3	1.530 × 10-5	0.980	0.950	0.172	0.18	0.87	intronic
rs12043436	OMA1	2.192 × 10-6	0.991	0.840	0.129	0.99	0.95	intronic
rs595146	PHLPP1	8.637 × 10-6	0.999	0.877	0.000	0.34	0.29	intronic
rs10508958	PRKG1	4.490 × 10-7	0.996	0.873	0.193	0.99	0.69	intronic
rs3733553	PRKG2	1.212 × 10-5	0.980	0.868	0.823	0.96	0.99	intronic
rs752579	RAI1	1.023 × 10-5	0.981	0.954	0.473	1.00	0.96	intronic
rs2271733	RAX	1.464 × 10-5	0.984	0.688	0.443	0.89	0.63	missense D44E
rs10519052	RORA	3.667 × 10-6	0.991	0.448	0.234	0.68	0.68	intronic
rs968357	RORB	2.655 × 10-6	0.992	0.755	0.560	0.63	0.83	intronic
rs2236409	TNC	9.344 × 10-6	0.985	0.455	0.063	0.40	0.96	intronic
rs7300641	TPH2	1.676 × 10-5	0.975	0.827	0.400	0.01	0.02	intronic
rs4445877	UBE3A	1.849 × 10-5	0.974	0.939	0.607	0.90	0.99	intronic
Mendelian diseases causing sleep disturbance in humans
rs5909187	CDKL5	6.275 × 10-6	0.987	0.550	0.017	0.27	0.55	intronic
rs11603330	DHCR7	2.848 × 10-7	0.995	0.806	0.479	0.75	0.98	intronic
rs13414769	HDAC4	3.134 × 10-5	0.969	0.573	0.264	0.94	0.98	intronic
rs2239464	MECP2	3.189 × 10-7	0.996	0.663	0.517	0.48	0.28	intronic
rs858953	NRXN1	1.226 × 10-9	1.000	0.780	0.254	0.83	0.49	intronic
rs8137951	SHANK3	3.148 × 10-6	0.989	0.517	0.127	0.59	0.44	intronic
rs12406072	SLC2A1	2.430 × 10-5	0.980	0.952	0.518	0.56	0.52	intronic
Melanopsin signaling
rs308039	GNA11	2.387 × 10-5	0.972	0.568	0.079	0.06	0.29	intronic
rs4745672	GNAQ	4.391 × 10-6	0.986	0.790	0.610	1.00	0.92	intronic
rs2476197	INADL	1.834 × 10-7	0.998	0.943	0.252	0.92	0.96	intronic
rs2224361	PLCB4	4.222 × 10-5	0.991	0.426	0.000	0.32	0.37	intronic
rs2138004	PRKCA	3.025 × 10-5	0.971	0.974	0.708	0.24	0.33	intronic
rs10910030	PRKCZ	1.588 × 10-8	0.999	0.771	0.234	0.18	0.27	intronic
rs1392171	TRPC7	2.123 × 10-6	0.993	0.371	0.000	0.48	0.70	intronic

^aKendall’s correlation P values for the correlation between allele frequency and Δphotoperiod; ^bpercentile rank in the distribution of Kendall’s correlation coefficients (τ) calculated for minor allele frequency (MAF)-matched SNPs; ^cF_ST percentile rank in the distribution of SNPs showing a similar average MAF (calculated over all populations); ^dlnRsb percentile rank; ^einformation on ARNTL, CLOCK and CRY1 binding sites was obtained from [80]; significant values are shown in bold. CEPH, 1000 Genomes Phase I data for Utah Residents with Northern and Western European ancestry; CHB + JPT, 1000 Genomes Phase I data for Han Chinese in Beijing plus Japanese in Tokyo; RNAi, RNA interference; SNP, single nucleotide polymorphism, UTR, untranslated region.