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. 2014 Oct 30;15(10):499. doi: 10.1186/s13059-014-0499-7

Table 2.

Genome-wide association study single nucleotide polymorphisms that correlate with Δphotoperiod

SNP Gene(s) a Disease Risk allele Risk allele frequency decreases with Δphotoperiod Kendall’s correlation P value b τ rank c F ST rank d lnRsb rank e Gene functional connection to circadian rhythm
Biaka-Orcadian Biaka-Maya CEPH CHB + JPT
rs1930961 LRP5L, ADRBK2 BPD C Yes 1.182 × 10−6 0.993 0.996 0.942 0.530 0.700 ADRBK2 (aka GRK3) phosphorylates melanopsin [34]
rs6746896 LMAN2L, CNNM4 BPD A Yes 8.421 × 10−7 0.995 0.550 0.350 0.780 0.790 CNNM4 is an RNAi hit (the gene does not appear in Table 1 because the SNP is non-genic)
rs8099939 GRIK5 BPD T Yes 6.538 × 10−5 0.956 0.968 0.615 0.960 0.980 -
rs2286492 FAM126A BPD G No 8.521 × 10−5 0.966 0.811 0.000 0.160 0.260 -
rs7570682 TMEM18, POU3F3 BPD A Yes 2.320 × 10−4 0.950 0.455 0.004 0.160 0.090 -
rs4075511 KCNS3, RDH14 BPD A No 7.345 × 10−9 0.999 0.797 0.156 0.720 0.730 -
rs7319311 COL4A2 BPD and SCZ A No 1.083 × 10−4 0.952 0.474 0.319 0.400 0.470 Clock-regulated in mouse cardiomyocytes [35]
rs1124376 KAT2B BPD and SCZ G Yes 3.852 × 10−4 0.950 0.860 0.076 0.880 0.150 Directly interacts with CLOCK and NPAS2 [36]
rs1605834 APOB, KLHL29 BPD and SCZ C Yes 2.857 × 10−4 0.950 0.966 0.877 0.350 0.240 -
rs17002034 MKL1 BPD and SCZ G Yes 2.322 × 10−5 0.978 0.689 0.000 0.990 0.990 RNAi hit (gene does not appear among selected hits because of heavier Bonferroni correction)
rs589249 CSF3R, GRIK3 SCZ G Yes 4.565 × 10−5 0.964 0.996 0.624 1.000 1.000 Grik3 expression is regulated by Clock in the mouse ventral tegmental area [37]
rs7004633 MMP16, RIPK2 SCZ A No 1.433 × 10−6 0.992 0.925 0.538 0.260 0.330 -
rs1009080 PTPRU, MATN1 SCZ G Yes 2.419 × 10−6 0.988 0.987 0.708 0.900 0.690 -
rs1572299 TLR4, DBC1 SCZ A Yes 3.901 × 10−4 0.951 0.950 0.321 1.000 0.200 DBC1 regulates NR1D1 stability [38]
rs892055 RASGRP4 Asperger nr na 4.268 × 10−5 0.964 0.603 0.585 0.610 0.420 -
rs9601248 NDFIP2, SPRY2 MDD C No 7.198 × 10−5 0.958 0.896 0.085 0.390 0.330 SPRY2 is a direct target of ARNTL in mouse liver [39]
rs8020095 GPHN Depression A Yes 1.273 × 10−4 0.950 0.944 0.504 0.620 0.980 GPHN shows rhythmic expression in mouse SCN [40]
rs12593813 MAP2K5 RLS A No 2.066 × 10−5 0.971 0.498 0.175 1.000 0.830 -

aOne gene is reported if the variant is genic, for intergenic SNPs the two flanking protein-coding genes are listed; bKendall’s P values for the correlation between allele frequency and Δphotoperiod; cpercentile rank in the distribution of Kendall’s correlation coefficients (τ) calculated for minor allele frequency (MAF)-matched SNPs; dFST percentile rank in the distribution of SNPs showing a similar average MAF (calculated over all populations); elnRsb percentile rank; significant values are shown in bold. BPD, bipolar disorder; 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; MDD, major depressive disorder; na, not available; nr, not reported; RLS, restless leg syndrome; SCZ, schizophrenia; SNP, single nucleotide polymorphism.