Cindy Boer

Cartilage Thickness and Hip Osteoarthritis | 75 2.1 Table 3: Association of mJSW loci with other skeletal phenotypes Hip osteoarthritis SNP Locus EA Beta SE rs2862851 DOT1L A OA[1] Height[13] rs12982744 (r²=1.0) rs2523178(r²=0.1) rs2236995 TGFA T - - Rs1220662 SUPT3H-RUNX2 T OA[2], Height[13] BMD[10], OPLL[12] rs10948172(r²=0.09) rs10948222(r²=0.0) rs117755164(r²=0.04) 927485(r²=0.0) rs10948155 SUPT3H-RUNX2 A OA[2], Height[13] BMD[10], OPLL[12] rs10948172(r²=0.84) rs10948222(r²=0.0) rs117755164(r²=0.21) 927485(r²=0.0) Rs10471753 PIK3R1 C - - rs496547 TREH-DOX6 A Height[14] Metabolite levels[15] Vitiligo[16] Celiac Disease/ RS[17] SLE[18] rs494459 (r2=0.36) rs507080(r2=21) rs638893 ((r2=0.02) rs10892279(r2=0.36) rs4639966(r2=0.36) rs11880992 SLBP T Height[14] rs2247341(r²=0.6) SNP: single nucleotide polymorphism, EA: effect Allele, SE: standard Error. genes (FDR >0.05), from which three genes were also significantly prioritized in the GRAIL analysis ( Supplementary Table 5 and Supplementary Table 6 ). Next, using the Online Mendelian Inheritance in Man (OMIM) database (http://omim.org) , we iden- tified genes with mutations implicated in abnormal skeletal growth in humans; for 50% of the loci, a skeletal syndrome gene was present ( Supplementary Table 7 ). Similar- ly, we investigated if any of the genes had a known bone and cartilage development phenotype in mice. Very similar to the human phenotypes, the mice knockouts of the same genes resulted in bone and cartilage phenotypes (http://mousemutant.jax.org/ ) ( Supplementary Table 7 ). Other supporting biological evidence that we gathered con- sisted of known expression quantitative loci (eQTL) and nonsynonymous variants in LD (r 2 >0.6) with the lead SNP of a locus ( Supplementary Table 8 and Supplementary