Supplemental Table 1. Forty-one genes contained within the interval between Rhbdd2 and D12Rat8 (1.7Mb)§ Gene position (bp) Gene Gene Symbol† Gene name Gene ID (NCBI) Non-synonimous Synonymous Non-synonimous SNPs SIFT PolyPhen2 intron 5' UTR 3' UTR Rat FLS RA FLS number SNPs SNPs or in/del# Prediction** Prediction** SNPs SNPs SNPs expression¶ expression 24,091,132..24,102,081 Rhbdd2 rhomboid domain containing 2 360793 1 1 V162L No effect No effect + + 24,131,529..24,152,626 1 Ccl24 chemokine (C-C motif) ligand 24 288593 + + 24,157,182..24,161,870 2 Ccl26 chemokine (C-C motif) ligand 26 685958 - 24,162,841..24,166,326 3 LOC108352436 108352436 - 24,172,840..24,173,294 LOC363903 similar to ribosomal protein S13 (pseudogene) 363903 ND 24,180,795..24,315,373 4 Hip1 huntingtin interacting protein 1 192154 1 5 A749P Affects function Affects function 1 + + 24,316,575..24,341,943 5 Pom121 nuclear pore membrane protein 121 113975 1 2 L825I No effect No effect 1 + + 24,320,708..24,320,928 D12Rat51 24,341,940..24,346,900 6 Nsun5 NOL1/NOP2/Sun domain family, member 5 288595 1 1 24,348,426..24,365,467 7 Trim50 tripartite motif-containing 50 288596 2 1 D38N, N118H No effect No effect 4 1 - + 24,365,941..24,438,088 8 Fkbp6 FK506 binding protein 6 288597 2 14 1 - 24,473,981..24,476,295 9 Fzd9 frizzled homolog 9 (Drosophila) 266608 ND 24,478,882..24,536,851 10 Baz1b bromodomain adjacent to zinc finger domain, 1B 368002 2 2 V1183M, S966N, K174 del No effect No effect 2 + + 24,543,748..24,557,093 11 Bcl7b B-cell CLL/lymphoma 7B 368001 ND 24,565,843..24,578,855 12 Tbl2 transducin beta like 2 686610 - 24,590,645..24,619,639 13 Mlxipl MLX interacting protein-like 171078 - 24,651,342..24,656,793 14 Vps37d VPS37D, ESCRT-I subunit 687208 - 24,668,398..24,669,464 15 Dnajc30 DnaJ (Hsp40) homolog, subfamily C, member 30 368190 1 3 1 - 24,669,626..24,680,833 16 Wbscr22 Williams Beuren syndrome chromosome region 22 (homolog) 365167 5 1 + 24,682,050..24,710,002 17 Stx1a syntaxin 1A (brain) 116470 3 24,722,277..24,725,760 18 Abhd11 similar to abhydrolase domain containing 11 360831 1 1 C22S No effect No effect 1 2 + 24,744,117..24,745,066 LOC686150 LOC686150 (pseudogene) 686150 ND 24,761,210..24,763,008 19 Cldn4 claudin 4 304407 1 - 24,767,351..24,775,891 20 Wbscr27 Williams Beuren syndrome chromosome region 27 688407 1 ND 24,785,637..24,786,293 21 LOC103691506 LOC103691506 103691506 - 24,803,204..24,808,287 22 Wbscr28 Williams-Beuren syndrome chromosome region 28 (homolog) 288604 2 ND 24,961,777..24,961,978 D12Arb15 24,973,679..24,980,976 23 LOC102553484 LOC102553484 102553484 - 24,978,478..25,021,864 24 Eln elastin 25043 2 4 S166G,GGLGGP695 del, L710F 9 + 25,036,630..25,070,538 25 Limk1 LIM domain kinase 1 65172 1 2 + 25,078,541..25,079,054 26 LOC108352484 LOC108352484 (pseudogene) 108352484 ND 25,093,119..25,109,805 27 Eif4h eukaryotic translation initiation factor 4H 288599 ND 25,114,099..25,128,381 28 Lat2 linker for activation of T cells family, member 2 317676 2 1 - 25,130,375..25,143,480 29 Rfc2 replication factor C (activator 1) 2 116468 1 1 + 25,148,381..25,150,352 30 LOC102553558 LOC102553558 102553558 - 25,156,737..25,157,396 LOC363906 LOC363906 (pseudogene) 363906 ND 25,161,130..25,168,182 31 Syna Syncytin a (endogenous retrovirus group FRD member 1) 288602 - 25,172,957..25,236,935 32 Clip2 CAP-GLY domain containing linker protein 2 29264 1 3 T729A No effect Affects function 1 + + 25,264,052..25,370,947 33 Gtf2ird1 GTF2I repeat domain containing 1 246770 5 3 1 + 25,372,497..25,375,302 34 LOC108352437 LOC108352437 108352437 - 25,410,804..25,487,970 35 Gtf2i general transcription factor II I 353256 3 1 - 25,487,921..25,499,152 36 LOC103691302 LOC103691302 103691302 - 25,497,104..25,506,300 37 Ncf1 neutrophil cytosolic factor 1 114553 2 V106M, Y153M Affects function Affects function + 25,509,059..25,555,554 38 Gtf2ird2 GTF2I repeat domain containing 2 288606 3 + + 25,561,871..25,592,337 39 Rcc1l Regulator of chromosome condensation 1-like repeats 360796 1 + + 25,595,800..25,638,806 40 Gatsl2 GATS protein-like 2 304410 2 - + 25,648,662..25,654,744 41 LOC102553721 LOC102553721 102553721 - 25,799,119..25,799,259 D12Rat8 § all genes were sequenced, but only the identified SNPs and insertion/deletions are shown. Blue=SSLP and SNP used in the breeding of the subcongenics; Grey=pseudogenes. # Green=non-synonimous SNPs and insertion/deletions within the new 1.7Mb critical interval; indel= insertion-deletion. ¶ FLS=fibroblast-like synoviocytes. "+" =expressed in FLS; "-"=not expressed in FLS; ND= not determined (pseudogene, not variants or no expression in synovial tissues). Only genes with amino-acid-changing SNPs or deletions/insertions were studied for FLS expression. ** SIFT and PolyPhen2 predictions of the potential consequence of the amino-acid change (yellow highlights the prediction of significant effect on protein function). §§ Expression levels in synovial tissues shown as increased in DA compared with DA.ACI(Cia25) congenics, based on a previously published microarray experiment (P<0.009).