Supplement Table 7: List of SNPs associated with thyroid functions, traits and diseases available in the database GWAS Catalog (Data downloaded from GWAS Catalog on 17/06/2015) chr Start Stop Strongest_SNPs SNPs Disease_traits Region Reported_Genes Mapped_Genes Context Extra Information about GWAS findings Plasma thyroid-stimulating 1 107814198 107814198 rs12126655-G rs12126655 hormone levels 1p13.3 VAV3 VAV3 intron 1 107823394 107823394 rs4915077-C rs4915077 Hypothyroidism 1p13.3 VAV3 VAV3 intron Thyroid peroxidase antibody 1 113630788 113630788 rs1230666-A rs1230666 levels 1p13.2 MAG13, PTPN22 MAGI3 intron rs6679677-?, Type 1 diabetes, Crohn' s disease, rs6679677-A, Rheumatoid arthritis, DCLRE1B, PTPN22, 1 113761186 113761186 rs6679677-C rs6679677 Hypothyroidism 1p13.2 RSBN1, PHTF1 PHTF1 nearGene-5 rs3761959-A, 1 157699488 157699488 rs3761959-G rs3761959 Graves disease, Multiple sclerosis 1q23.1 FCRL3 FCRL3 intron 1 160495121 160495121 rs1265883-C rs1265883 Graves disease 1q23.2 SLAMF6 SLAMF6 intron SLC4A1APP2- intergene- 1 187933850 187933850 rs655167-A rs655167 Hypothyroidism 1q31.1 LOC100129274 RPS3AP9 intergenic 1 19439024 19439024 rs12045440-T rs12045440 Thyroid volume 1p36.13 CAPZB CAPZB intron thyroid volume, goiter Serum thyroid-stimulating MINOS1, NBL1, CAPZB-intergene- 1 19501286 19501286 rs6683419-G rs6683419 hormone levels 1p36.13 CAPZB MINOS1 intergenic CAPZB-intergene- 1 19512621 19512621 rs12138950-A rs12138950 Thyroid volume 1p36.13 CAPZB MINOS1 intergenic thyroid volume CAPZB-intergene- 1 19514680 19514680 rs10799824-A rs10799824 Thyroid hormone levels 1p36.13 CAPZB MINOS1 intergenic TSH, TSH - Males, TSH - Females CAPZB-intergene- 1 19516860 19516860 rs10917468-C rs10917468 Thyroid volume 1p36.13 CAPZB MINOS1 intergenic goiter CAPZB-intergene- 1 19534612 19534612 rs10917477-A rs10917477 Thyroid function 1p36.13 CAPZB MINOS1 intergenic Plasma thyroid-stimulating 1 214501582 214501582 rs17042140-T rs17042140 hormone levels 1q41 PTPN14 PTPN14 intron 1 37814315 37814315 rs3748682-T rs3748682 Hypothyroidism 1p34.3 MTF1 MTF1 UTR-3 Multiple myeloma (hyperdiploidy), Thyroid 1 53909897 53909897 rs2235544-A rs2235544 hormone levels 1p32.3 DIO1, NR DIO1 intron FT4, FT4-Females, FT4-Males, HD vs. controls 1 61154824 61154824 rs334699-A rs334699 Thyroid hormone levels 1p31.3 NFIA NFIA intron TSH, TSH - Females, TSH - Males Thyroid peroxidase antibody RERE, 1 8429242 8429242 rs301799-C rs301799 positivity 1p36.23 NR LOC102724552 intron Thyroid peroxidase antibody levels, Thyroid peroxidase 2 1404043 1404043 rs11675434-T rs11675434 antibody positivity 2p25.3 TPO LOC101927426 nearGene-5 Thyroid peroxidase antibody TPO, 2 1413472 1413472 rs2071403-? rs2071403 positivity 2p25.3 TPO LOC101927426 UTR-5, nearGene-3 rs1024161-A, NPM1P33- 2 203857029 203857029 rs1024161-T rs1024161 Alopecia areata, Graves disease 2q33.2 ICOS, CTLA4, CD28 intergene-CTLA4 intergenic 2 203869764 203869764 rs231779-T rs231779 Hypothyroidism 2q33.2 CTLA4 CTLA4 intron IGFBP5-intergene- 2 216760800 216760800 rs13015993-A rs13015993 Thyroid hormone levels 2q35 IGFBP5 RPL31P14 intergenic TSH, TSH - Females, TSH - Males 2 217406996 217406996 rs6759952-T rs6759952 Thyroid cancer 2q35 DIRC3 DIRC3 intron 2 217445617 217445617 rs966423-C rs966423 Thyroid cancer 2q35 DIRC3 DIRC3 intron Thyroid peroxidase antibody 3 124581410 124581410 rs2010099-C rs2010099 levels 3q21.2 KALRN KALRN intron 4 112622996 112622996 rs6834538-T rs6834538 Free thyroxine concentration 4q25 C4orf21 ZGRF1 intron ATP5LP4- 4 148713873 148713873 rs10519980-C rs10519980 Hypothyroidism 4q31.23 LOC285423, ATP5LP4 intergene-DCLK2 intergenic ATP5LP4- 4 148731458 148731458 rs10028213-C rs10028213 Thyroid function 4q31.23 NR3C2 intergene-DCLK2 intergenic ATP5LP4- 4 148748354 148748354 rs10032216-T rs10032216 Thyroid hormone levels 4q31.23 NR3C2 intergene-DCLK2 intergenic TSH, TSH - Females AADAT-intergene- 4 170132368 170132368 rs11726248-A rs11726248 Thyroid hormone levels 4q33 AADAT HSP90AA6P intergenic FT4, FT4-Females 4 40301616 40301616 rs6832151-G rs6832151 Graves disease 4p14 RHOH, CHRNA9 LOC101930098 intron Thyroid stimulating hormone, 5 77222617 77222617 rs4704397-A rs4704397 Hypothyroidism 5q13.3 PDE8B PDE8B intron 5 77234524 77234524 rs6885099-A rs6885099 Thyroid hormone levels 5q13.3 PDE8B PDE8B intron TSH, TSH - Males, TSH - Females 5 77239986 77239986 rs2046045-T rs2046045 Thyroid function 5q13.3 PDE8B PDE8B intron 6 104784358 104784358 rs9322817-? rs9322817 Thyroid stimulating hormone 6q16.3 HACE1 HACE1 intron SAMD5-intergene- 6 148200156 148200156 rs9497965-T rs9497965 Thyroid hormone levels 6q24.3 SASH1 SASH1 intergenic TSH, TSH - Females 6 165632995 165632995 rs753760-C rs753760 Thyroid hormone levels 6q27 PDE10A PDE10A intron TSH, TSH - Females, TSH - Males RNASET2- intergene- 6 166969587 166969587 rs9355610-G rs9355610 Graves disease 6q27 RNASET2, FGFR1OP MIR3939 intergenic 6 29967473 29967473 rs3893464-G rs3893464 Graves disease 6p22.1 MHC TRNAI25 6 30006148 30006148 rs4313034-T rs4313034 Graves disease 6p22.1 MHC HLA-J, ZNRD1-AS1 intron 6 30569829 30569829 rs3132613-C rs3132613 Graves disease 6p21.33 MHC ABCF1 nearGene-5 6 31034839 31034839 rs4248154-C rs4248154 Graves disease 6p21.33 MHC MUC22 cds-synon

HCG22, C6orf15, HLA- B, LOC729792, 6 31050630 31050630 rs2517532-G rs2517532 Hypothyroidism 6p21.33 DHFRP2, HLA-C, HCP5 TRNAI25 rs4947296-?, HCG22, C6orf15, 6 31090401 31090401 rs4947296-C rs4947296 Behcet s disease, Graves disease 6p21.33 MUC21 TRNAI25 6 31382927 31382927 rs1521-T rs1521 Graves disease 6p21.33 HLA-B TRNAI25 Thyroid peroxidase antibody 6 31462150 31462150 rs3094228-C rs3094228 positivity 6p21.33 NR HCP5 nearGene-5 6 32369853 32369853 rs2273017-A rs2273017 Graves disease 6p21.32 MHC C6orf10 intron HLA-DRB5, HLA- DRB9, HLA-DQA1, rs3129720-C, Multiple sclerosis (OCB status), HLA-DQB1, HLA- 6 32695854 32695854 rs3129720-? rs3129720 Hypothyroidism 6p21.32 DQA2, HLA-DRB1 TRNAI25 OCB positive vs. controls HLA-DQA1, MHC, DRB1, HLA-DQB1, rs6457617-?, Systemic sclerosis, Rheumatoid DQA1, DQB1, HLA, 6 32696074 32696074 rs6457617-T rs6457617 arthritis, Graves disease 6p21.32 HLA-DQA2 TRNAI25 Thyroid peroxidase antibody 6 32819259 32819259 rs1894407-C rs1894407 positivity 6p21.32 NR TRNAI25 Thyroid peroxidase antibody 6 33087828 33087828 rs9277555-G rs9277555 levels 6p21.32 NR HLA-DPB1 UTR-3 6 33092341 33092341 rs2281388-T rs2281388 Graves disease 6p21.32 HLA, DPB1 TRNAI25 Thyroid peroxidase antibody 6 33114531 33114531 rs733208-A rs733208 positivity 6p21.32 HLA-DPB2 TRNAI25 6 33650385 33650385 rs9394159-T rs9394159 Graves disease 6p21.31 MHC ITPR3 intron 6 33850152 33850152 rs4713693-T rs4713693 Graves disease 6p21.31 MHC TRNAI25 Type 2 diabetes, Thyroid 6 43844025 43844025 rs9472138-T rs9472138 hormone levels 6p21.1 VEGFA TRNAI25 TSH, TSH - Males, TSH - Females 6 43937043 43937043 rs11755845-T rs11755845 Thyroid hormone levels 6p21.1 VEGFA LOC100132354 ncRNA TSH, TSH - Males Thyroid peroxidase antibody 6 90170674 90170674 rs10944479-A rs10944479 positivity 6q15 BACH2 BACH2 intron 6 90212021 90212021 rs370409-T rs370409 Graves disease 6q15 BACH2, MAP3K7 BACH2 intron 7 19765857 19765857 rs6977660-? rs6977660 Thyroid stimulating hormone 7p21.1 Intergenic TMEM196 intron

CDCA7L-intergene- 7 22069841 22069841 rs10499559-? rs10499559 Thyroid stimulating hormone 7p15.3 RAPGEF5 RAPGEF5 intergenic 7 28056580 28056580 rs7785730-G rs7785730 Free thyroxine concentration 7p15.1 JAZF1 JAZF1 intron 7 88852128 88852128 rs10248351-C rs10248351 Hypothyroidism 7q21.13 C7orf62, ZNF804B ZNF804B intron 8 133133268 133133268 rs2294025-T rs2294025 Graves disease 8q24.22 SLA, TG, WISP1 TG intron 8 32558756 32558756 rs7825175-A rs7825175 Thyroid hormone levels 8p12 NRG1 NRG1 intron TSH, TSH - Females 8 32574851 32574851 rs2439302-G rs2439302 Thyroid cancer 8p12 NRG1 NRG1 intron Serum thyroid-stimulating TMEM68, TGS1, LYN, 8 55445714 55445714 rs2622590-A rs2622590 hormone levels 8q12.1 SBF1P1, XKR4 XKR4 intron 8 80526185 80526185 rs1051920-T rs1051920 Hypothyroidism 8q21.13 ZBTB10, RPSAP47 ZBTB10 UTR-3 Serum alkaline phosphatase levels, Liver enzyme levels, Urinary metabolites (H-NMR rs657152-A, features), Obesity-related traits, rs657152-T, Phytosterol levels, Thyroid 9 133263862 133263862 rs657152-C rs657152 hormone levels 9q34.2 ABO ABO intron campesterol, ALP, TSH, IL6 , Unknown, TSH - Males, 1.2975 Protein quantitative trait loci, Venous thromboembolism, End- rs505922-C, stage coagulation, Pancreatic rs505922-T, cancer, Graves disease, Duodenal 9 133273813 133273813 rs505922-? rs505922 ulcer 9q34.2 ABO ABO intron Recessive, TNFA, vWF 9 136197833 136197833 rs7860634-A rs7860634 Thyroid hormone levels 9q34.3 LHX3 LHX3 intron FT4, FT4-Females, FT4-Males

ZDHHC21, TRNAH, TRNAH5-intergene- 9 14470835 14470835 rs10961534-G rs10961534 Hypothyroidism 9p22.3 GUG CDCA4P1 intergenic 9 4267209 4267209 rs1571583-A rs1571583 Thyroid hormone levels 9p24.2 GLIS3 GLIS3 intron TSH, TSH - Males

rs925489-T, Serum thyroid-stimulating KRT18P13, XPA, KRT18P13- 9 97784318 97784318 rs925489-C rs925489 hormone levels, Hypothyroidism 9q22.33 C9orf156, FOXE1 intergene-FOXE1 intergenic KRT18P13- 9 97786731 97786731 rs7850258-? rs7850258 Hypothyroidism 9q22.33 FOXE1 intergene-FOXE1 intergenic eMERGE TMOD1, HEMGN, Thyroid cancer (Papillary KRT18P13, XPA, radiation-related), Thyroid NCBP1, C9orf156, KRT18P13- 9 97793827 97793827 rs965513-A rs965513 cancer 9q22.33 C9orf97, FOXE1 intergene-FOXE1 intergenic 9 97829181 97829181 rs7045138-T rs7045138 Thyroid hormone levels 9q22.33 FOXE1 LOC101928337 intron FT4, FT4-Females, FT4-Males Plasma thyroid-stimulating 11 22083484 22083484 rs11026407-C rs11026407 hormone levels 11p14.3 ANO5 LOC102723370 intron RPL7AP56- intergene- 11 39010243 39010243 rs7951105-T rs7951105 Free thyroxine concentration 11p12 Intergenic RPL18P8 intergenic 11 45206016 45206016 rs17723470-T rs17723470 Thyroid hormone levels 11p11.2 PRDM11 PRDM11 intron TSH, TSH - Females Type 1 diabetes, Platelet counts, Blood metabolite levels, Beta-2 microglubulin plasma levels, Diastolic blood pressure, Coronary artery disease, Eosinophil counts, Systolic blood pressure, Autoimmune hepatitis type-1, Red blood cell traits, SH2B3, NAA25, Rheumatoid arthritis, Type 1 C12orf51, ATXN2, rs3184504-C, diabetes autoantibodies, BRAP, rs3184504-?, Hypothyroidism, Coronary heart LOC100101246, 12 111446804 111446804 rs3184504-T rs3184504 disease 12q24.12 PTPN11 SH2B3 missense T1D, kynurenine, Hgb, EA

Celiac disease, Thyroid peroxidase antibody levels, Peripheral artery disease, Celiac disease and Rheumatoid arthritis, Urate levels, Diastolic rs653178-T, blood pressure, Blood pressure, rs653178-G, Thyroid peroxidase antibody SH2B3, ATXN2, 12 111569952 111569952 rs653178-C rs653178 positivity, Chronic kidney disease 12q24.12 PTPN11 ATXN2 intron eGFRcys, Mean Arterial Pressure 13 23468371 23468371 rs10162002-A rs10162002 Hypothyroidism 13q12.12 TNFRSF19, SACS LINC00327 nearGene-5 14 36104812 36104812 rs1537424-T rs1537424 Thyroid hormone levels 14q13.2 MBIP LINC00609 intron TSH PTCSC3-intergene- 14 36180040 36180040 rs944289-T rs944289 Thyroid cancer 14q13.3 NKX2-1 MBIP intergenic PTCSC3-intergene- 14 36269155 36269155 rs116909374-T rs116909374 Thyroid cancer 14q13.3 MBIP MBIP intergenic 14 80984885 80984885 rs12101261-T rs12101261 Graves disease 14q31.1 TSHR TSHR intron ITPK1-AS1- intergene- 14 93129246 93129246 rs11624776-A rs11624776 Thyroid hormone levels 14q32.12 ITPK1 CYB5AP3 intergenic TSH, TSH - Males C14orf64- intergene- 14 98021670 98021670 rs1456988-? rs1456988 Graves disease 14q32.2 Intergenic C14orf177 intergenic rs4338740-T, 15 49443100 49443100 rs4338740-C rs4338740 Thyroid volume 15q21.2 FGF7, C15orf33 FGF7, FAM227B intron thyroid volume, goiter 15 49454167 49454167 rs10519227-A rs10519227 Thyroid hormone levels 15q21.2 FGF7 FGF7, FAM227B intron TSH, TSH - Males DET1-intergene- 15 88575873 88575873 rs17776563-A rs17776563 Thyroid hormone levels 15q26.1 MIR1179 MIR1179 intergenic TSH, TSH - Males 16 55570216 55570216 rs6499766-A rs6499766 Thyroid hormone levels 16q12.2 CAPNS2, LPCAT2 LPCAT2 intron FT4, FT4-Males Thyroid peroxidase antibody MAF-intergene- 16 79666550 79666550 rs4889009-G rs4889009 positivity 16q23.2 NR DYNLRB2 intergenic MAF-intergene- 16 79710651 79710651 rs17767419-T rs17767419 Thyroid volume 16q23.2 MAF DYNLRB2 intergenic thyroid volume MAF-intergene- 16 79715379 79715379 rs3813579-A rs3813579 Thyroid volume 16q23.2 MAF DYNLRB2 intergenic goiter Thyroid function, Thyroid MAF-intergene- 16 79715456 79715456 rs3813582-T rs3813582 hormone levels 16q23.2 LOC440389, MAF DYNLRB2 intergenic TSH, TSH - Males Serum thyroid-stimulating 16 79721549 79721549 rs4575545-? rs4575545 hormone levels 16q23.2 MAF LOC102467146 ncRNA LOC100131744, 17 34137135 34137135 rs9901756-A rs9901756 Hypothyroidism 17q12 CCL2 ASIC2 intron Thyrotoxic hypokalemic periodic CALM2P1- 17 70263305 70263305 rs623011-A rs623011 paralysis 17q24.3 KCNJ2 intergene-CASC17 intergenic Thyrotoxic hypokalemic periodic CALM2P1- 17 70330197 70330197 rs312691-C rs312691 paralysis 17q24.3 KCNJ2, KCNJ16 intergene-CASC17 intergenic SOX9-intergene- 17 72131395 72131395 rs9915657-T rs9915657 Thyroid hormone levels 17q24.3 SOX9 LINC00673 intergenic TSH, TSH - Females, TSH - Males MIR302F- 18 30561722 30561722 rs2729409-? rs2729409 Protein quantitative trait loci 18q12.1 DSC3 intergene-DSC3 intergenic Parathyroid hormone 18 6567183 6567183 rs948426-A rs948426 Hypothyroidism 18p11.31 LOC100130480 C18orf64 intron

MIR548AV- 18 73500517 73500517 rs7240777-A rs7240777 Thyroid hormone levels 18q22.3 NETO1, FBXO15 intergene-FBXO15 intergenic FT4-Females Thyroid peroxidase antibody MIR7-3HG, MIR7- 19 4768905 4768905 rs879564-A rs879564 positivity 19p13.3 NR 3 nearGene-5 rs4804416-G, Hypothyroidism, Thyroid INSR, 19 7223837 7223837 rs4804416-T rs4804416 hormone levels 19p13.2 INSR LOC100996405 intron, nearGene-3 TSH, TSH - Females ERP29P1- Thyroid peroxidase antibody intergene- 20 52393218 52393218 rs4811340-G rs4811340 positivity 20q13.2 NR MRPS33P4 intergenic 22 37185382 37185382 rs229526-C rs229526 Hypothyroidism 22q12.3 C1QTNF6 C1QTNF6 missense rs229527-T, 22 37185445 37185445 rs229527-? rs229527 Vitiligo, Graves disease 22q12.3 C1QTNF6, RAC2 C1QTNF6 missense GPR174-intergene- X 79241621 79241621 rs5912838-? rs5912838 Graves disease Xq21.1 ITM2A, GPR174 KIF4CP intergenic