Table 1.
Gene Loci Associated With Chronotype/Diurnal Preference in 23andme And UK Biobank Genome-wide Association Analyses.
| SNP | EAF | Chr:Pos | Nearest gene(s) | β | Cont P | OR | Bin P | Study | Known CRS function |
|---|---|---|---|---|---|---|---|---|---|
| Loci identified in all 3 GWASs | |||||||||
| rs12736689 | 0.03 | 1:182,549,729 | RGS16, RNASEL | — | — | 0.74 | 7.00E-18 | Hu | K |
| rs1144566 | 0.97 | 1:182,569,626 | RGS16 | −0.10 | 2.62E-14 | 0.74 | 1.29E-08 | Lane | K |
| rs516134 | 0.03 | 1:182,553,693 | RGS16 | 0.08 | 9.00E-13 | 1.21 | 3.00E-12 | Jones | K |
| rs55694368 | 0.93 | 2:239,317,692 | PER2 | — | — | 0.86 | 2.60E-09 | Hu | K |
| rs35333999 | 0.043 | 2:239,161,957 | PER2 | 0.06 | 8.43E-08 | 1.21 | 9.01E-06 | Lane | K |
| rs75804782 | 0.88 | 2:239,316,043 | PER2 | 0.03 | 3.00E-07 | 1.09 | 4.00E-10 | Jones | K |
| rs3972456 | 0.29 | 7:102,436,907 | FBXL13, FAM185A | — | 0.92 | 6.00E-09 | Hu | P | |
| rs372229746 | 0.45 | 7:102,158,815 | FBXL13 | 0.03 | 5.18E-10 | 1.12 | 4.29E-07 | Lane | P |
| rs372229746 | 0.55 | 7:102,158,815 | FBXL13, ORAI2, RASA4 | 0.03 | 4.00E-09 | 1.06 | 7.00E-07 | Jones | P |
| rs10493596 | 0.24 | 1:77,713,434 | AK5 | — | 1.09 | 8.00E-12 | Hu | U | |
| rs76681500 | 0.84 | 1:77,726,241 | AK5 | –0.04 | 1.50E-12 | 0.86 | 1.77E-09 | Lane | U |
| rs11162296 | 0.16 | 1:77,700,196 | AK5, PIGK | –0.04 | 2.00E-12 | 0.93 | 1.00E-12 | Jones | U |
| Loci identified in 2 GWASs | |||||||||
| rs35833281 | 0.21 | 6:55,021,561 | HCRTR2 | — | — | 0.92 | 2.60E-09 | Hu | K |
| rs76899638 | 0.22 | 6:55,147,508 | HCRTR2 | 0.03 | 4.00E-08 | 1.05 | 2.00E-07 | Jones | K |
| rs2050122 | 0.8 | 1:19,989,205 | HTR6 | 0.03 | 4.61E-08 | 1.12 | 7.94E-07 | Lane | K |
| rs2050122 | 0.2 | 1:19,989,205 | HTR6 | 0.03 | 2.00E-08 | 1.06 | 3.00E-06 | Jones | K |
| rs4821940 | 0.55 | 22:40,659,573 | TNRC6B | 0.03 | 1.05E-08 | 1.07 | 8.56E-05 | Lane | P |
| rs4821940 | 0.45 | 22:40,659,573 | TNRC6B, SGSM3 | 0.02 | 3.00E-08 | 1.05 | 4.00E-08 | Jones | P |
| rs34714364 | 0.17 | 1:150,234,657 | APH1A, CA14 | — | — | 1.12 | 2.00E-10 | Hu | P |
| rs10157197 | 0.4 | 1:150,250,636 | APH1A | 0.03 | 1.48E-09 | 1.13 | 1.27E-11 | Lane | P |
| rs12635074 | 0.65 | 3:55,982,416 | ERC2 | –0.03 | 3.08E-08 | 0.92 | 1.20E-06 | Lane | U |
| rs11708779 | 0.32 | 3:55,934,939 | ERC2 | –0.02 | 3.00E-08 | 0.96 | 2.00E-06 | Jones | U |
| Loci identified in 1 GWAS | |||||||||
| rs1015197 | 0.6 | 1:150,250,636 | PRPF3, TARS2 | 0.03 | 1.00E-09 | 1.05 | 5.00E-07 | Jones | U |
| rs11121022 | 0.42 | 1:7,836,659 | PER3, VAMP3 | — | — | 1.07 | 2.00E-08 | Hu | K |
| rs72720396 | 0.23 | 1:91,191,582 | CALB1 | –0.03 | 1.00E-07 | 0.95 | 3.00E-08 | Jones | P |
| rs12140153 | 0.9 | 1:62,579,891 | INADL | 0.04 | 7.00E-09 | 1.07 | 4.00E-06 | Jones | P |
| rs141175086 | 0.998 | 1:780,397 | LINC01128 | –0.27 | 1.42E-04 | 0.46 | 4.38E-08 | Lane | U |
| rs1075265 | 0.52 | 2:54,354,927 | PSME4, ACYP2 | –0.03 | 2.00E-10 | 0.95 | 4.00E-08 | Jones | U |
| rs70944707 | 0.23 | 2:24,257,444 | FKBP1B | 0.03 | 3.00E-08 | 1.05 | 2.00E-05 | Jones | U |
| rs11895698 | 0.14 | 2:239,338,495 | ASB1 | 0.04 | 1.15E-08 | 1.1 | 1.30E-04 | Lane | U |
| rs1595824 | 0.49 | 2:198,874,006 | PLCL1 | — | — | 1.08 | 1.20E-10 | Hu | P |
| rs148750727 | 0.995 | 4:188,022,952 | FAT1 | 0.15 | 3.61E-06 | 2.34 | 1.58E-08 | Lane | U |
| rs9479402 | 0.01 | 6:153,135,339 | VIP | — | — | 0.69 | 3.90E-11 | Hu | K |
| rs9357620* | 0.71 | 6:13,170,634 | PHACTR1 | 0.02 | 1.70E-08 | — | Hu | U | |
| rs2948276 | 0.88 | 7:96,457,119 | DLX5, SHFM1 | — | — | 0.92 | 1.10E-08 | Hu | U |
| rs2975734* | 0.43 | 8:10,030,097 | MSRA | 0.02 | 2.10E-09 | — | Hu | K | |
| rs192534763 | 0.99 | 8:36,202,946 | UNC5D | 0.1 | 3.00E-07 | 1.25 | 2.00E-08 | Jones | U |
| rs17311976 | 0.19 | 8:131,637,337 | ADCY8 | 0.19 | 1.08E-06 | 1.13 | 3.37E-08 | Lane | P |
| rs77641763 | 0.88 | 9:140,265,782 | EXD3, GRIN1, NRARP | 0.04 | 5.00E-11 | 1.07 | 7.00E-09 | Jones | U |
| rs6582618 | 0.52 | 12:38,726,137 | ALG10B | — | — | 1.07 | 1.50E-08 | Hu | U |
| rs542675489 | 0.6 | 12:120,994,888 | RNF10 | 0.03 | 3.29E-09 | 1.09 | 1.38E-05 | Lane | U |
SNP = single nucleotide polymorphism. EAF = effect allele frequency. Chr = Chromosome. Pos = position. Cont P = significance for genetic associations in GWAS on chronotype as a continuous phenotype. β = beta coefficient, i.e., effect size for genetic associations in GWAS on chronotype as a continuous phenotype. Bin P = significance for genetic associations in GWAS on chronotype as a binary (cases vs. controls) phenotype. OR = odds ratio, i.e., effect size for genetic associations in GWAS on chronotype as a binary phenotype. Known CRS function = whether gene has a previously known association with circadian rhythms or sleep. K = Known. P = Probable. U = Unknown.