Disease associated variation - ClinVar Allele ID Type Name RS#dbSNP Phenotype IDs Chromosome Start Stop Reference Alternate 20108 insertion HDAC4, 1-BP INS, 2399C -1 MedGen:C1838126,OMIM:600430 na -1 -1 na na 20109 deletion HDAC4, 65-BP DEL, NT490+56 -1 MedGen:C1838126,OMIM:600430 na -1 -1 na na 191236 single nucleotide variant NM_006037.3(HDAC4):c.1419C>T (p.Asn473=) 754530774 MedGen:CN169374 2 240048251 240048251 G A 191236 single nucleotide variant NM_006037.3(HDAC4):c.1419C>T (p.Asn473=) 754530774 MedGen:CN169374 2 239126555 239126555 G A 191687 single nucleotide variant NM_006037.3(HDAC4):c.2037C>T (p.Ala679=) 754442298 MedGen:CN169374 2 240029806 240029806 G A 191687 single nucleotide variant NM_006037.3(HDAC4):c.2037C>T (p.Ala679=) 754442298 MedGen:CN169374 2 239108110 239108110 G A 191915 duplication NM_006037.3(HDAC4):c.2219-5dupC 775488590 MedGen:CN169374 2 240016757 240016757 G GG 191915 duplication NM_006037.3(HDAC4):c.2219-5dupC 775488590 MedGen:CN169374 2 239095061 239095061 G GG 193135 single nucleotide variant NM_006037.3(HDAC4):c.3159C>T (p.Ala1053=) 142279745 MedGen:CN169374 2 239975212 239975212 G A 193135 single nucleotide variant NM_006037.3(HDAC4):c.3159C>T (p.Ala1053=) 142279745 MedGen:CN169374 2 239053516 239053516 G A 195699 single nucleotide variant NM_006037.3(HDAC4):c.681C>T (p.His227=) 148880349 MedGen:CN169374 2 240078400 240078400 G A 195699 single nucleotide variant NM_006037.3(HDAC4):c.681C>T (p.His227=) 148880349 MedGen:CN169374 2 239156704 239156704 G A 265637 single nucleotide variant NM_006037.3(HDAC4):c.1794G>A (p.Glu598=) 148813865 MedGen:CN169374 2 240033391 240033391 C T 265637 single nucleotide variant NM_006037.3(HDAC4):c.1794G>A (p.Glu598=) 148813865 MedGen:CN169374 2 239111695 239111695 C T 265793 single nucleotide variant NM_006037.3(HDAC4):c.2646A>G (p.Thr882=) 140526832 MedGen:CN169374 2 240002880 240002880 T C 265793 single nucleotide variant NM_006037.3(HDAC4):c.2646A>G (p.Thr882=) 140526832 MedGen:CN169374 2 239081184 239081184 T C 266143 single nucleotide variant NM_006037.3(HDAC4):c.1938C>T (p.Pro646=) 146056747 MedGen:CN169374 2 240033247 240033247 G A 266143 single nucleotide variant NM_006037.3(HDAC4):c.1938C>T (p.Pro646=) 146056747 MedGen:CN169374 2 239111551 239111551 G A 267176 single nucleotide variant NM_006037.3(HDAC4):c.567G>A (p.Arg189=) 141942329 MedGen:CN169374 2 240085543 240085543 C T 267176 single nucleotide variant NM_006037.3(HDAC4):c.567G>A (p.Arg189=) 141942329 MedGen:CN169374 2 239163847 239163847 C T 267433 single nucleotide variant NM_006037.3(HDAC4):c.2148G>A (p.Ser716=) 61735030 MedGen:CN169374 2 240024542 240024542 C T 267433 single nucleotide variant NM_006037.3(HDAC4):c.2148G>A (p.Ser716=) 61735030 MedGen:CN169374 2 239102846 239102846 C T 267757 single nucleotide variant NM_006037.3(HDAC4):c.2356G>A (p.Ala786Thr) 61754648 MedGen:CN169374 2 240011722 240011722 C T 267757 single nucleotide variant NM_006037.3(HDAC4):c.2356G>A (p.Ala786Thr) 61754648 MedGen:CN169374 2 239090026 239090026 C T 268168 single nucleotide variant NM_006037.3(HDAC4):c.955G>A (p.Ala319Thr) 76224543 MedGen:CN169374 2 240061403 240061403 C T 268168 single nucleotide variant NM_006037.3(HDAC4):c.955G>A (p.Ala319Thr) 76224543 MedGen:CN169374 2 239139707 239139707 C T 268451 single nucleotide variant NM_006037.3(HDAC4):c.2136G>A (p.Gln712=) 138137158 MedGen:CN169374 2 240024554 240024554 C T 268451 single nucleotide variant NM_006037.3(HDAC4):c.2136G>A (p.Gln712=) 138137158 MedGen:CN169374 2 239102858 239102858 C T 268455 single nucleotide variant NM_006037.3(HDAC4):c.684G>A (p.Pro228=) 144387989 MedGen:CN169374 2 240078397 240078397 C T 268455 single nucleotide variant NM_006037.3(HDAC4):c.684G>A (p.Pro228=) 144387989 MedGen:CN169374 2 239156701 239156701 C T 268957 single nucleotide variant NM_006037.3(HDAC4):c.958G>A (p.Val320Ile) 73000144 MedGen:CN169374 2 240061400 240061400 C T 268957 single nucleotide variant NM_006037.3(HDAC4):c.958G>A (p.Val320Ile) 73000144 MedGen:CN169374 2 239139704 239139704 C T 268967 single nucleotide variant NM_006037.3(HDAC4):c.1677G>A (p.Lys559=) 114495208 MedGen:CN169374 2 240036848 240036848 C T 268967 single nucleotide variant NM_006037.3(HDAC4):c.1677G>A (p.Lys559=) 114495208 MedGen:CN169374 2 239115152 239115152 C T 269095 single nucleotide variant NM_006037.3(HDAC4):c.1963+8G>A 200120991 MedGen:CN169374 2 239111518 239111518 C T 269095 single nucleotide variant NM_006037.3(HDAC4):c.1963+8G>A 200120991 MedGen:CN169374 2 240033214 240033214 C T 269188 single nucleotide variant NM_006037.3(HDAC4):c.1095+10C>G 11896634 MedGen:CN169374 2 240056213 240056213 G C 269188 single nucleotide variant NM_006037.3(HDAC4):c.1095+10C>G 11896634 MedGen:CN169374 2 239134517 239134517 G C 270321 single nucleotide variant NM_006037.3(HDAC4):c.2175G>A (p.Thr725=) 149067286 MedGen:CN169374 2 240024515 240024515 C T 270321 single nucleotide variant NM_006037.3(HDAC4):c.2175G>A (p.Thr725=) 149067286 MedGen:CN169374 2 239102819 239102819 C T 270795 single nucleotide variant NM_006037.3(HDAC4):c.952C>T (p.Pro318Ser) 886043422 MedGen:CN169374 2 240061406 240061406 G A 270795 single nucleotide variant NM_006037.3(HDAC4):c.952C>T (p.Pro318Ser) 886043422 MedGen:CN169374 2 239139710 239139710 G A 271179 single nucleotide variant NM_006037.3(HDAC4):c.1991A>G (p.Lys664Arg) 886043528 MedGen:CN169374 2 240029852 240029852 T C 271179 single nucleotide variant NM_006037.3(HDAC4):c.1991A>G (p.Lys664Arg) 886043528 MedGen:CN169374 2 239108156 239108156 T C 271249 single nucleotide variant NM_006037.3(HDAC4):c.1100C>T (p.Thr367Met) 886043549 MedGen:CN169374 2 240056135 240056135 G A 271249 single nucleotide variant NM_006037.3(HDAC4):c.1100C>T (p.Thr367Met) 886043549 MedGen:CN169374 2 239134439 239134439 G A 272204 single nucleotide variant NM_006037.3(HDAC4):c.222G>A (p.Glu74=) 145137674 MedGen:CN169374 2 240111646 240111646 C T 272204 single nucleotide variant NM_006037.3(HDAC4):c.222G>A (p.Glu74=) 145137674 MedGen:CN169374 2 239189950 239189950 C T 272373 single nucleotide variant NM_006037.3(HDAC4):c.2331C>T (p.Cys777=) 144099208 MedGen:CN169374 2 240011747 240011747 G A 272373 single nucleotide variant NM_006037.3(HDAC4):c.2331C>T (p.Cys777=) 144099208 MedGen:CN169374 2 239090051 239090051 G A 273144 single nucleotide variant NM_006037.3(HDAC4):c.571C>T (p.Leu191=) 886044037 MedGen:CN169374 2 240085539 240085539 G A 273144 single nucleotide variant NM_006037.3(HDAC4):c.571C>T (p.Leu191=) 886044037 MedGen:CN169374 2 239163843 239163843 G A 273620 single nucleotide variant NM_006037.3(HDAC4):c.339+10G>A 199918439 MedGen:CN169374 2 240111519 240111519 C T 273620 single nucleotide variant NM_006037.3(HDAC4):c.339+10G>A 199918439 MedGen:CN169374 2 239189823 239189823 C T 275032 single nucleotide variant NM_006037.3(HDAC4):c.2419A>G (p.Ser807Gly) 886044559 MedGen:CN169374 2 240009265 240009265 T C 275032 single nucleotide variant NM_006037.3(HDAC4):c.2419A>G (p.Ser807Gly) 886044559 MedGen:CN169374 2 239087569 239087569 T C 361540 single nucleotide variant NM_006037.3(HDAC4):c.3205G>A (p.Ala1069Thr) 115552422 MedGen:CN221809 2 239053470 239053470 C T 361540 single nucleotide variant NM_006037.3(HDAC4):c.3205G>A (p.Ala1069Thr) 115552422 MedGen:CN221809 2 239975166 239975166 C T 361541 single nucleotide variant NM_006037.3(HDAC4):c.1554G>A (p.Pro518=) 201334158 MedGen:CN221809 2 239115275 239115275 C T 361541 single nucleotide variant NM_006037.3(HDAC4):c.1554G>A (p.Pro518=) 201334158 MedGen:CN221809 2 240036971 240036971 C T

Disease associated variation - GWASdb Chr Pos SNP ID(dbSNP 142) Ref Alt Ori SNP ID P-value Drug Name Drug Anno GWAS Trait HPO ID DO ID AA Type Trait or Drug 2 240039401 rs3791426 A G rs3791426 0.000506 METHIONINE CASPASE 1|CASPASE 9|CASP9 PROTEIN, HUMAN|5'-METHYLTHIOADENOSINE|APIP PROTEIN, HUMAN|DEOXYADENOSINES|THIONUCLEOSIDES|APOPTOSIS REGULATORY PROTEINS Salmonella-induced pyroptosis NA NA A intron GWASdb_drug 2 240045350 rs3791446 T C rs3791446 3.47E-04 ALDOSTERONE BIOLOGICAL MARKERS|NATRIURETIC PEPTIDE, BRAIN|RENIN Blood pressure, CVD RF and other traits (body mass index (BMI), waist:hip ratio, renin activity in plasma, aldosterone concentration in plasma, BNP levels in plasma, alcohol consumption) HPOID:0011025 DOID:10763 C intron GWASdb_drug 2 240055553 rs2121980 T C rs2121980 0.0000346 INFLIXIMAB|ADALIMUMAB|IMMUNOGLOBULIN G TUMOR NECROSIS FACTOR-ALPHA|ANTIRHEUMATIC AGENTS|ANTIBODIES, MONOCLONAL, HUMANIZED|TNFR-FC FUSION PROTEIN|ANTIBODIES, MONOCLONAL|RECEPTORS, TUMOR NECROSIS FACTOR Anti-TNF treatment response in rheumatoid arthritis (by DAS-28 score change at 3 months) HPOID:0001370 DOID:7148 T intron GWASdb_drug 2 240055553 rs2121980 T C rs2121980 3.46E-05 LEUCOVORIN|METHOTREXATE SLCO1B1 PROTEIN, HUMAN|ORGANIC ANION TRANSPORTERS Methotrexate clearance (acute lymphoblastic leukemia) HPOID:0006721 DOID:9952|DOID:12603 T intron GWASdb_drug 2 240115818 rs6735945 G C rs6735945 6.28E-05 CISPLATIN|CARBOPLATIN NAG PROTEIN, HUMAN|ORGANOPLATINUM COMPOUNDS|NEOPLASM PROTEINS Cisplatin and carboplatin cytotoxicity, in blood cell lines HPOID:0100526|HPOID:0012288|HPOID:0010788 DOID:9256|DOID:11934|DOID:2998|DOID:1324 G intron GWASdb_drug 2 240216021 rs6737742 G A rs6737742 5.53E-05 ACETAMINOPHEN|GLUTATHIONE N-ACETYL-4-BENZOQUINONEIMINE|RNA, MESSENGER|IMINES|BENZOQUINONES Response to acetaminophen (hepatotoxicity) HPOID:0001392 DOID:409 G intron GWASdb_drug 2 240217522 rs908262 C A rs908262 3.71E-05 ACETAMINOPHEN|GLUTATHIONE N-ACETYL-4-BENZOQUINONEIMINE|RNA, MESSENGER|IMINES|BENZOQUINONES Response to acetaminophen (hepatotoxicity) HPOID:0001392 DOID:409 G intron GWASdb_drug 2 240290494 rs11124194 C T rs11124194 5.22E-05 GEMCITABINE|CYTARABINE MANNOSYLTRANSFERASES|PIGB PROTEIN, HUMAN|RNA, SMALL INTERFERING|DEOXYCYTIDINE Response to cytadine analogues (cytosine arabinoside) HPOID:0002664 DOID:162 T intron GWASdb_drug 2 240290494 rs11124194 C T rs11124194 6.62E-04 GEMCITABINE|CYTARABINE MANNOSYLTRANSFERASES|PIGB PROTEIN, HUMAN|RNA, SMALL INTERFERING|DEOXYCYTIDINE Response to cytidine analogues (gemcitabine) HPOID:0002664 DOID:162 T intron GWASdb_drug 2 240004245 rs3752755 C T rs3752755 5.40E-04 Coronary heart disease HPOID:0001677 DOID:3393 G intron GWASdb_trait 2 240025666 rs3791398 G A rs3791398 1.80E-05 Carotid intima media thickness HPOID:0005344 DOID:1936 G intron GWASdb_trait 2 240025761 rs3791399 G A rs3791399 3.70E-06 Urinary metabolites HPOID:0000079 DOID:557 A intron GWASdb_trait 2 240032319 rs747787 G A rs747787 4.80E-04 Myocardial infarction HPOID:0001658 DOID:5844 G,A intron GWASdb_trait 2 240039401 rs3791426 A G rs3791426 0.000506 Salmonella-induced pyroptosis NA NA A intron GWASdb_trait 2 240045350 rs3791446 T C rs3791446 3.47E-04 Blood pressure, CVD RF and other traits (body mass index (BMI), waist:hip ratio, renin activity in plasma, aldosterone concentration in plasma, BNP levels in plasma, alcohol consumption) HPOID:0011025 DOID:10763 C intron GWASdb_trait 2 240051965 rs3791461 G A rs3791461 3.78E-04 Multiple complex diseases HPOID:0000118 NA G intron GWASdb_trait 2 240051965 rs3791461 G A rs3791461 1.40E-05 Urinary metabolites HPOID:0000079 DOID:557 G intron GWASdb_trait 2 240053966 rs12469994 G A rs12469994 5.41E-04 Alzheimer's disease HPOID:0002511 DOID:10652 G intron GWASdb_trait 2 240055553 rs2121980 T C rs2121980 7.10E-05 Dental caries HPOID:0000670 DOID:216 T intron GWASdb_trait 2 240055553 rs2121980 T C rs2121980 0.0000346 Anti-TNF treatment response in rheumatoid arthritis (by DAS-28 score change at 3 months) HPOID:0001370 DOID:7148 T intron GWASdb_trait 2 240055553 rs2121980 T C rs2121980 3.46E-05 Methotrexate clearance (acute lymphoblastic leukemia) HPOID:0006721 DOID:9952|DOID:12603 T intron GWASdb_trait 2 240080540 rs3791511 G A rs3791511 6.43E-05 Melanoma HPOID:0002861 DOID:8923 G intron GWASdb_trait 2 240086580 rs7599555 C T rs7599555 5.15E-04 Multiple complex diseases HPOID:0000118 NA C intron GWASdb_trait 2 240092739 rs1448430 G A rs1448430 8.10E-05 Bipolar disorder HPOID:0007302 DOID:3312 A intron GWASdb_trait 2 240099456 rs489806 C A rs489806 3.06E-04 Hemoglobin concentration HPOID:0011902 DOID:2860 C intron GWASdb_trait 2 240109024 rs3791549 G A rs3791549 4.17E-05 Multiple complex diseases HPOID:0000118 NA G intron GWASdb_trait 2 240109568 rs3828222 C T rs3828222 4.55E-05 Multiple complex diseases HPOID:0000118 NA C intron GWASdb_trait 2 240112972 rs3791556 G A rs3791556 2.80E-05 Diabetic retinopathy HPOID:0000819|HPOID:0000488 DOID:8947 G intron GWASdb_trait 2 240112972 rs3791556 G A rs3791556 8.00E-06 Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) HPOID:0000729|HPOID:0007018|HPOID:0007302|HPOID:0100753 DOID:0060041|DOID:1094|DOID:3312|DOID:1470|DOID:5419 G intron GWASdb_trait 2 240114137 rs753302 A G rs753302 7.04E-04 Amyotrophic Lateral Sclerosis HPOID:0007354 DOID:332 T intron GWASdb_trait 2 240115818 rs6735945 G C rs6735945 6.28E-05 Cisplatin and carboplatin cytotoxicity, in blood cell lines HPOID:0100526|HPOID:0012288|HPOID:0010788 DOID:9256|DOID:11934|DOID:2998|DOID:1324 G intron GWASdb_trait 2 240155231 rs496316 T C rs496316 1.80E-05 Urinary metabolites HPOID:0000079 DOID:557 A intron GWASdb_trait 2 240176736 rs12151485 G A rs12151485 1.62E-04 IgE levels HPOID:0010701 DOID:6024 A intron GWASdb_trait 2 240180336 rs7595357 C A rs7595357 1.29E-05 IgE levels HPOID:0010701 DOID:6024 A intron GWASdb_trait 2 240180336 rs7595357 C A rs7595357 7.04E-05 Weight HPOID:0004323 DOID:9970 A intron GWASdb_trait 2 240181872 rs1403608 G A rs1403608 5.86E-04 Type 2 diabetes HPOID:0005978 DOID:9352 G,A intron GWASdb_trait 2 240186518 rs7587786 G A rs7587786 6.73E-06 Body mass index HPOID:0001507 DOID:9970 G intron GWASdb_trait 2 240187632 rs6742576 G A rs6742576 6.56E-06 Body mass index HPOID:0001507 DOID:9970 G intron GWASdb_trait 2 240188918 rs10208713 C T rs10208713 4.94E-04 Hemoglobin concentration HPOID:0011902 DOID:2860 C intron GWASdb_trait 2 240193575 rs6745266 G A rs6745266 6.15E-06 Body mass index HPOID:0001507 DOID:9970 G intron GWASdb_trait 2 240216021 rs6737742 G A rs6737742 8.58E-05 Hemoglobin concentration HPOID:0011902 DOID:2860 G intron GWASdb_trait 2 240216021 rs6737742 G A rs6737742 5.53E-05 Response to acetaminophen (hepatotoxicity) HPOID:0001392 DOID:409 G intron GWASdb_trait 2 240217522 rs908262 C A rs908262 8.58E-05 Hemoglobin concentration HPOID:0011902 DOID:2860 G intron GWASdb_trait 2 240217522 rs908262 C A rs908262 3.71E-05 Response to acetaminophen (hepatotoxicity) HPOID:0001392 DOID:409 G intron GWASdb_trait 2 240241255 rs925738 C T rs925738 4.76E-04 Hemoglobin concentration HPOID:0011902 DOID:2860 G intron GWASdb_trait 2 240258244 rs950225 C T rs950225 7.90E-04 Myocardial infarction HPOID:0001658 DOID:5844 G intron GWASdb_trait 2 240262287 rs908265 T C rs908265 9.27E-05 Triglycerides HPOID:0003119 DOID:3393|DOID:3146|DOID:2349 G intron GWASdb_trait 2 240286146 rs11686104 G A rs11686104 1.03E-04 Hemoglobin concentration HPOID:0011902 DOID:2860 G,A intron GWASdb_trait 2 240290494 rs11124194 C T rs11124194 5.22E-05 Response to cytadine analogues (cytosine arabinoside) HPOID:0002664 DOID:162 T intron GWASdb_trait 2 240290494 rs11124194 C T rs11124194 6.62E-04 Response to cytidine analogues (gemcitabine) HPOID:0002664 DOID:162 T intron GWASdb_trait 2 240294969 rs2411843 A C rs2411843 5.47E-05 Bladder cancer (smoking interaction) HPOID:0002862 DOID:4007 C intron GWASdb_trait

Disease associated variation - GWAS Central Study Name Source Marker Accession Chromosome Marker Start Marker Stop Alleles Gene Section P-value -log(p-value) GWAS of prostate cancer rs3791601 2 240133710 240133710 intronic 0.979552 0.0089725043209802 GWAS of prostate cancer rs3791529 2 240092523 240092523 intronic 0.975815 0.0106325102992196 GWAS of prostate cancer rs2291188 2 240016177 240016177 intronic 0.965393 0.0152958545461179 GWAS of prostate cancer rs10208713 2 240188918 240188918 intronic 0.866831 0.062065565639945905 GWAS of prostate cancer rs2898716 2 240048911 240048911 intronic 0.848587 0.0713036257293256 GWAS of prostate cancer rs1399629 2 240257958 240257958 intronic 0.798849 0.0975353041206293 GWAS of prostate cancer rs3791406 2 240030484 240030484 intronic 0.775377 0.11048708561051 GWAS of prostate cancer rs6706275 2 240265617 240265617 intronic 0.77485 0.11078236262578499 GWAS of prostate cancer rs9308908 2 239996179 239996179 intronic 0.741458 0.12991344461516 GWAS of prostate cancer rs7590833 2 240283334 240283334 intronic 0.736953 0.13256020887301 GWAS of prostate cancer rs3791471 2 240059625 240059625 intronic 0.731297 0.13590620817853902 GWAS of prostate cancer rs3791370 2 240001331 240001331 intronic 0.679929 0.167536435114485 GWAS of prostate cancer rs3791507 2 240078905 240078905 intronic 0.649791 0.18722630819172198 GWAS of prostate cancer rs2176046 2 240295613 240295613 intronic 0.624861 0.20421658049077698

Disease associated variation - OMIM Ensembl_gene_ID Approved Gene Symbol MIM Number ENSG00000068024.16 HDAC4 605314