Genetic Associations

Genome-wide significant GWAS associations of the Teumer et al. (Nat Commun., 2018) dataset for the free T4 and TSH levels with the corresponding association results of additional traits added. The TPOab-positivity results are from the Medici et al. (PLoS Genetics, 2014) publication.

TSH
SNP Chr Position (hg19) Nearest Gene A1 A2 BETA SE P BETA TSH SE TSH P TSH BETA hyperthyroidism SE hyperthyroidism P hyperthyroidism BETA hypothyroidism SE hypothyroidism P hypothyroidism BETA TPOab-positivity SE TPOab-positivity P TPOab-positivity
rs12089835 1 19,771,438 CAPZB t c 0.073 0.007 1.27E-28 -0.017 0.007 1.41E-02 -0.110 0.033 7.74E-04 0.129 0.027 1.43E-06 NA NA NA
rs10917469 1 19,843,576 CAPZB a g 0.111 0.009 3.95E-39 -0.029 0.009 1.17E-03 -0.227 0.040 1.01E-08 0.234 0.037 1.90E-10 -0.002 0.047 9.74E-01
rs74804879 1 19,862,320 CAPZB t c 0.050 0.007 1.22E-14 -0.015 0.007 3.31E-02 -0.111 0.033 6.92E-04 0.095 0.027 3.71E-04 NA NA NA
rs334725 1 61,610,049 NFIA a g 0.174 0.015 2.45E-32 -0.058 0.015 1.08E-04 NA NA NA NA NA NA -0.027 0.083 7.45E-01
rs17020122 1 108,357,391 VAV3 t c 0.104 0.011 5.32E-20 -0.017 0.012 1.40E-01 -0.105 0.065 1.08E-01 0.311 0.042 6.56E-14 0.168 0.058 3.54E-03
rs16856540 2 217,580,413 IGFBP5 t c -0.055 0.008 7.81E-11 0.005 0.009 6.06E-01 0.147 0.043 6.81E-04 -0.009 0.034 8.00E-01 0.065 0.049 1.79E-01
rs13015993 2 217,625,523 IGFBP5 a g 0.082 0.007 4.52E-32 -0.016 0.008 4.41E-02 -0.171 0.034 3.48E-07 0.055 0.029 5.40E-02 -0.084 0.036 2.12E-02
rs6724073 2 218,236,786 DIRC3 t c 0.051 0.008 1.35E-10 -0.024 0.009 5.04E-03 -0.065 0.040 1.06E-01 0.061 0.033 6.34E-02 -0.222 0.065 6.06E-04
rs1663070 3 12,239,852 SYN2 t c -0.046 0.007 3.49E-11 -0.001 0.007 8.93E-01 0.055 0.036 1.32E-01 -0.083 0.028 3.14E-03 0.006 0.039 8.85E-01
rs28502438 3 149,220,109 TM4SF4 t c 0.034 0.006 3.70E-08 -0.009 0.007 1.82E-01 -0.010 0.032 7.58E-01 0.046 0.025 7.15E-02 NA NA NA
rs13100823 3 185,514,088 IGF2BP2 t c -0.041 0.007 6.76E-10 0.021 0.007 3.39E-03 0.110 0.033 8.55E-04 -0.104 0.028 1.67E-04 NA NA NA
rs59381142 3 193,916,181 HES1 a g -0.058 0.008 1.70E-14 0.007 0.008 3.49E-01 0.114 0.036 1.77E-03 -0.070 0.031 2.38E-02 NA NA NA
rs6535624 4 149,587,905 NR3C2 a g 0.042 0.006 1.60E-11 -0.006 0.007 3.87E-01 -0.093 0.032 3.39E-03 0.055 0.025 2.84E-02 0.065 0.031 3.31E-02
rs11732089 4 149,665,602 NR3C2 t c 0.115 0.008 1.73E-51 0.005 0.008 5.67E-01 -0.176 0.037 1.73E-06 0.133 0.032 2.84E-05 0.064 0.042 1.28E-01
rs62362610 5 76,439,961 ZBED3-AS1 c g 0.073 0.012 7.73E-10 -0.018 0.013 1.54E-01 -0.168 0.067 1.27E-02 0.084 0.047 7.50E-02 NA NA NA
rs1119208 5 76,488,613 PDE8B t c 0.046 0.006 6.65E-13 -0.010 0.007 1.50E-01 -0.135 0.033 4.91E-05 -0.002 0.026 9.54E-01 -0.031 0.033 3.43E-01
rs139424329 5 76,495,539 PDE8B a g -0.200 0.032 5.14E-10 0.019 0.034 5.74E-01 NA NA NA NA NA NA NA NA NA
rs2127387 5 76,532,571 PDE8B a g 0.144 0.006 1.10E-117 -0.032 0.007 2.07E-06 -0.328 0.034 4.92E-22 0.150 0.026 4.24E-09 NA NA NA
rs7702192 5 76,554,807 PDE8B a c 0.070 0.006 2.61E-30 -0.012 0.007 5.84E-02 -0.169 0.033 2.79E-07 0.075 0.026 3.65E-03 0.048 0.028 8.68E-02
rs113974964 5 76,652,403 PDE8B t c -0.124 0.015 2.06E-17 0.019 0.016 2.24E-01 NA NA NA NA NA NA NA NA NA
rs139149784 5 76,660,193 PDE8B a g 0.156 0.029 4.97E-08 0.001 0.030 9.79E-01 NA NA NA NA NA NA NA NA NA
rs182873197 5 76,773,148 WDR41 t c -0.080 0.014 1.71E-08 0.013 0.015 4.10E-01 0.086 0.074 2.45E-01 -0.079 0.061 1.93E-01 NA NA NA
rs1265091 6 31,108,129 PSORS1C1 t c 0.057 0.009 3.20E-11 -0.019 0.009 4.67E-02 -0.043 0.042 3.04E-01 0.072 0.033 3.03E-02 NA NA NA
rs744103 6 43,805,362 VEGFA a t 0.092 0.007 6.73E-41 -0.030 0.007 3.12E-05 -0.142 0.034 3.66E-05 0.116 0.029 5.71E-05 -0.015 0.049 7.67E-01
rs9381266 6 43,905,037 LOC100132354 t c 0.073 0.007 1.84E-25 -0.021 0.008 5.78E-03 -0.184 0.035 1.54E-07 0.086 0.029 3.23E-03 -0.045 0.038 2.37E-01
rs9497965 6 148,521,292 SASH1 t c 0.044 0.006 9.81E-13 -0.007 0.007 3.32E-01 -0.029 0.032 3.52E-01 0.109 0.025 1.61E-05 0.035 0.030 2.55E-01
rs73022105 6 165,973,757 PDE10A t c 0.105 0.016 1.20E-11 -0.014 0.017 4.09E-01 NA NA NA NA NA NA NA NA NA
rs1079418 6 166,047,034 PDE10A a g 0.101 0.007 8.23E-53 -0.017 0.007 1.80E-02 -0.191 0.032 3.68E-09 0.151 0.028 4.17E-08 -0.059 0.034 8.26E-02
rs56009477 8 23,356,964 SLC25A37 a g 0.052 0.008 3.72E-10 -0.016 0.009 8.50E-02 -0.107 0.041 9.09E-03 0.077 0.036 3.51E-02 NA NA NA
rs2439301 8 32,433,013 NRG1 a g -0.059 0.008 8.15E-15 0.008 0.008 3.06E-01 0.101 0.038 7.97E-03 -0.066 0.031 3.47E-02 NA NA NA
rs10957494 8 70,365,025 SULF1 a g -0.040 0.007 1.10E-09 0.009 0.007 2.20E-01 0.071 0.034 3.53E-02 -0.031 0.027 2.52E-01 NA NA NA
rs118039499 8 133,771,635 TMEM71 a c 0.184 0.024 1.99E-14 -0.021 0.025 4.02E-01 NA NA NA NA NA NA NA NA NA
rs2739067 8 133,951,991 TG a g -0.042 0.006 2.43E-11 0.015 0.007 2.72E-02 0.050 0.032 1.20E-01 -0.038 0.025 1.28E-01 NA NA NA
rs10814915 9 4,290,544 GLIS3 t c 0.042 0.006 5.06E-12 -0.027 0.007 5.94E-05 -0.115 0.032 3.14E-04 0.077 0.025 2.50E-03 NA NA NA
rs9298749 9 16,214,340 C9orf92 a c -0.039 0.006 8.80E-10 0.014 0.007 3.96E-02 -0.004 0.033 8.96E-01 -0.070 0.026 6.96E-03 -0.013 0.033 6.88E-01
rs8176645 9 136,149,098 ABO a t 0.052 0.006 3.93E-16 -0.002 0.007 8.05E-01 -0.077 0.033 2.08E-02 0.094 0.026 2.28E-04 NA NA NA
rs11255790 10 8,682,180 GATA3 t c -0.041 0.007 6.83E-10 0.007 0.007 3.53E-01 0.083 0.034 1.34E-02 -0.007 0.027 7.89E-01 -0.017 0.034 6.18E-01
rs4933466 10 89,849,519 PTEN a g 0.040 0.006 5.13E-10 -0.015 0.007 2.84E-02 -0.037 0.033 2.63E-01 0.072 0.027 6.72E-03 0.008 0.032 8.09E-01
rs200574439 10 101,283,330 NKX2-3 a c -0.047 0.006 3.69E-13 0.019 0.007 6.73E-03 0.141 0.034 3.20E-05 -0.101 0.027 1.36E-04 NA NA NA
rs12284404 11 45,228,686 PRDM11 a g -0.067 0.007 2.48E-22 0.006 0.007 4.17E-01 0.232 0.035 5.94E-11 0.002 0.029 9.53E-01 NA NA NA
rs4445669 11 115,045,237 CADM1 t c -0.040 0.006 5.76E-11 0.009 0.007 1.57E-01 0.064 0.033 5.10E-02 -0.042 0.025 9.45E-02 0.004 0.029 8.99E-01
rs7329958 13 24,782,080 SPATA13 t c -0.044 0.007 1.13E-11 0.011 0.007 1.39E-01 0.017 0.034 6.11E-01 -0.079 0.028 4.48E-03 NA NA NA
rs398745 14 36,536,181 LINC00609 a c -0.052 0.006 3.97E-17 0.025 0.007 1.72E-04 0.102 0.033 1.72E-03 -0.058 0.025 2.14E-02 0.012 0.030 6.81E-01
rs2254613 14 36,713,154 MBIP t g -0.035 0.006 3.44E-08 0.018 0.007 8.12E-03 0.073 0.032 2.40E-02 -0.021 0.026 4.18E-01 0.010 0.043 8.22E-01
rs11159482 14 81,490,842 TSHR t c 0.085 0.013 6.30E-11 -0.018 0.014 2.09E-01 -0.093 0.071 1.89E-01 0.191 0.051 1.82E-04 NA NA NA
rs59334515 14 81,594,143 TSHR t c -0.054 0.007 1.10E-13 -0.014 0.008 8.12E-02 0.095 0.038 1.37E-02 -0.093 0.031 3.06E-03 NA NA NA
rs12893151 14 81,619,945 TSHR a c -0.062 0.008 1.02E-15 -0.001 0.008 9.34E-01 0.142 0.040 3.24E-04 -0.127 0.034 1.88E-04 NA NA NA
rs8015085 14 93,585,331 ITPK1 a g 0.067 0.008 2.45E-18 -0.035 0.008 2.76E-05 -0.149 0.042 3.54E-04 0.089 0.031 4.39E-03 NA NA NA
rs17477923 15 49,711,185 FAM227B t c 0.083 0.007 2.57E-33 -0.036 0.007 1.01E-06 -0.245 0.034 6.15E-13 0.071 0.030 1.66E-02 -0.064 0.037 8.14E-02
rs11639111 15 49,749,735 FAM227B t c 0.045 0.006 3.60E-13 -0.013 0.007 4.55E-02 -0.106 0.032 9.87E-04 0.039 0.026 1.31E-01 -0.034 0.031 2.68E-01
rs13329353 15 89,113,877 DET1 t c 0.061 0.007 5.17E-21 -0.032 0.007 3.68E-06 -0.094 0.032 3.37E-03 -0.008 0.028 7.88E-01 0.021 0.035 5.50E-01
rs1045476 16 4,015,313 ADCY9 a g 0.049 0.008 2.36E-09 -0.003 0.009 7.47E-01 -0.059 0.043 1.71E-01 0.095 0.033 4.58E-03 NA NA NA
rs30227 16 14,405,428 MIR365A t c -0.047 0.006 7.59E-14 0.011 0.007 8.89E-02 0.074 0.033 2.59E-02 -0.042 0.026 1.08E-01 0.017 0.044 7.01E-01
rs17767491 16 79,745,487 MAF a g 0.088 0.007 3.35E-42 -0.013 0.007 5.56E-02 -0.164 0.033 7.25E-07 0.077 0.028 5.56E-03 -0.154 0.034 5.21E-06
rs77819282 17 44,762,589 NSF a g 0.045 0.007 1.13E-09 -0.003 0.008 7.17E-01 -0.025 0.039 5.22E-01 0.080 0.030 7.17E-03 NA NA NA
rs1157994 17 59,338,574 BCAS3 a g -0.090 0.016 5.28E-09 -0.051 0.017 2.65E-03 NA NA NA NA NA NA NA NA NA
rs1042673 17 70,121,339 SOX9 a g -0.055 0.006 3.57E-19 -0.003 0.007 6.67E-01 0.151 0.032 3.25E-06 0.004 0.026 8.74E-01 NA NA NA
rs963384 17 70,369,758 LINC00673 t c 0.035 0.006 2.77E-08 0.003 0.007 6.48E-01 -0.183 0.033 2.66E-08 -0.030 0.026 2.49E-01 NA NA NA
rs4804413 19 7,222,655 INSR t c 0.053 0.006 8.64E-18 -0.015 0.007 3.05E-02 -0.083 0.032 9.70E-03 0.080 0.026 1.88E-03 NA NA NA
rs1203944 20 22,596,879 FOXA2 t c -0.051 0.007 2.42E-12 0.011 0.008 1.44E-01 0.078 0.038 3.80E-02 -0.127 0.032 6.08E-05 0.053 0.039 1.82E-01
rs12390237 23 3,612,081 PRKX a g -0.046 0.007 1.74E-11 0.003 0.007 7.08E-01 0.093 0.036 1.00E-02 -0.014 0.032 6.61E-01 NA NA NA

free T4
SNP Chr Position (hg19) Nearest Gene A1 A2 BETA SE P BETA FT4 SE FT4 P FT4 BETA hyperthyroidism SE hyperthyroidism P hyperthyroidism BETA hypothyroidism SE hypothyroidism P hypothyroidism BETA TPOab-positivity SE TPOab-positivity P TPOab-positivity
rs145019385 1 54,252,139 TMEM48 t c 0.181 0.032 1.13E-08 -0.012 0.031 7.09E-01 NA NA NA NA NA NA NA NA NA
rs12033572 1 54,369,674 DIO1 c g 0.115 0.017 1.45E-11 -0.015 0.017 3.76E-01 NA NA NA NA NA NA 0.026 0.103 7.97E-01
rs2235544 1 54,375,570 DIO1 a c 0.139 0.007 4.20E-101 -0.012 0.006 6.33E-02 0.021 0.031 5.07E-01 -0.013 0.025 6.13E-01 -0.039 0.027 1.52E-01
rs954878 1 54,578,401 TCEANC2 a g -0.058 0.007 4.83E-19 -0.002 0.006 8.00E-01 0.015 0.031 6.22E-01 -0.030 0.025 2.30E-01 0.030 0.028 2.97E-01
rs4954192 2 135,632,981 ACMSD t c -0.041 0.007 8.38E-09 -0.006 0.006 3.33E-01 0.066 0.033 4.45E-02 -0.009 0.026 7.46E-01 0.038 0.031 2.23E-01
rs6785807 3 181,718,601 SOX2-OT a g -0.059 0.009 2.47E-10 -0.009 0.009 2.96E-01 0.085 0.043 4.81E-02 0.016 0.036 6.53E-01 -0.014 0.050 7.81E-01
rs6854291 4 170,992,760 AADAT a g 0.117 0.011 1.35E-24 0.023 0.011 3.01E-02 0.051 0.055 3.58E-01 0.024 0.043 5.85E-01 NA NA NA
rs10946313 6 19,381,386 ID4 t c 0.046 0.007 2.28E-11 0.020 0.006 1.97E-03 0.027 0.032 4.07E-01 0.028 0.026 2.82E-01 0.015 0.045 7.38E-01
rs9356988 6 25,777,481 SLC17A4 a g -0.051 0.007 3.56E-12 0.002 0.007 8.05E-01 0.028 0.034 4.10E-01 0.033 0.028 2.33E-01 -0.009 0.036 7.94E-01
rs137964359 6 26,001,742 TRIM38 t c -0.200 0.032 2.13E-10 0.030 0.031 3.35E-01 NA NA NA NA NA NA NA NA NA
rs17185536 6 100,620,931 LOC728012 t c 0.073 0.008 1.93E-19 0.003 0.008 7.09E-01 -0.029 0.038 4.43E-01 -0.028 0.031 3.66E-01 0.031 0.039 4.27E-01
rs67583169 8 61,212,179 CA8 c g 0.061 0.010 9.99E-11 -0.012 0.009 1.69E-01 -0.110 0.043 1.11E-02 -0.033 0.035 3.48E-01 NA NA NA
rs10119187 9 4,223,660 GLIS3 t c 0.050 0.009 4.11E-09 -0.037 0.008 2.34E-06 0.062 0.041 1.29E-01 -0.105 0.033 1.39E-03 NA NA NA
rs10739496 9 100,552,559 FOXE1 t c 0.078 0.007 4.20E-30 0.032 0.006 5.73E-07 0.186 0.033 1.88E-08 0.245 0.027 2.41E-19 0.032 0.033 3.37E-01
rs10984606 9 100,739,117 ANP32B t g -0.040 0.007 1.17E-09 -0.013 0.006 3.05E-02 -0.078 0.032 1.48E-02 -0.061 0.025 1.47E-02 NA NA NA
rs10818937 9 127,015,440 NEK6 t c -0.048 0.007 1.31E-11 0.022 0.007 6.02E-04 -0.017 0.035 6.25E-01 0.080 0.027 3.46E-03 0.011 0.033 7.47E-01
rs4842131 9 139,092,679 LHX3 t c -0.104 0.008 7.68E-44 -0.007 0.007 3.10E-01 0.010 0.035 7.67E-01 0.007 0.028 8.10E-01 NA NA NA
rs55679545 9 139,122,363 QSOX2 a g 0.044 0.008 8.42E-09 -0.007 0.007 3.24E-01 0.018 0.037 6.36E-01 -0.023 0.030 4.37E-01 NA NA NA
rs11039355 11 47,737,501 FNBP4 t c -0.039 0.007 3.51E-08 -0.002 0.007 7.58E-01 -0.046 0.033 1.70E-01 0.099 0.027 2.22E-04 NA NA NA
rs4149056 12 21,331,549 SLCO1B1 t c -0.051 0.009 1.34E-08 0.014 0.008 9.17E-02 -0.043 0.045 3.31E-01 -0.031 0.036 3.87E-01 -0.022 0.047 6.43E-01
rs150816132 14 80,464,293 NRXN3 a g -0.220 0.040 3.47E-08 -0.029 0.037 4.35E-01 NA NA NA NA NA NA NA NA NA
rs978055 14 80,534,869 DIO2 a t 0.038 0.007 1.06E-08 -0.003 0.006 6.45E-01 -0.029 0.032 3.71E-01 -0.004 0.026 8.88E-01 0.025 0.030 4.13E-01
rs225014 14 80,669,580 DIO2 t c 0.054 0.007 1.83E-15 0.017 0.006 6.64E-03 -0.037 0.033 2.58E-01 0.027 0.027 3.17E-01 0.028 0.032 3.79E-01
rs12323871 14 101,852,075 DIO3OS t c -0.047 0.008 1.42E-08 -0.012 0.008 1.45E-01 -0.016 0.039 6.81E-01 0.011 0.033 7.43E-01 0.005 0.065 9.44E-01
rs11626434 14 101,998,443 DIO3OS c g 0.058 0.007 4.08E-17 0.006 0.007 3.47E-01 -0.019 0.035 5.94E-01 0.042 0.028 1.27E-01 NA NA NA
rs12907106 15 63,873,658 USP3 c g -0.041 0.007 3.67E-08 0.005 0.007 4.96E-01 0.040 0.035 2.45E-01 0.008 0.029 7.85E-01 NA NA NA
rs8063103 16 12,703,395 SNX29 c g -0.052 0.009 1.61E-08 0.001 0.009 9.35E-01 -0.003 0.045 9.43E-01 0.040 0.037 2.68E-01 NA NA NA
rs11078333 17 16,049,626 NCOR1 a t 0.051 0.007 9.91E-13 -0.002 0.007 7.43E-01 -0.003 0.034 9.24E-01 -0.051 0.028 6.97E-02 NA NA NA
rs1080094 18 29,173,795 TTR a g -0.042 0.007 4.06E-10 0.007 0.006 2.73E-01 0.022 0.032 5.00E-01 -0.015 0.026 5.64E-01 NA NA NA
rs113107469 18 29,306,737 SLC25A52 t c 0.200 0.022 1.00E-19 0.013 0.020 5.09E-01 NA NA NA NA NA NA NA NA NA
rs56069042 18 57,914,644 MC4R a g 0.106 0.019 1.16E-08 0.012 0.018 4.99E-01 NA NA NA NA NA NA NA NA NA