Supplementary Table 1. Idd13 candidate interval supporting human LTC-ICs.

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1 Supplementary Table 1. Idd13 candidate interval supporting human LTC-ICs. Chr Start position Genomic marker EnsEMBL gene ID Gene symbol Primer 1 (5 3 ) Primer 2 (5 3 ) ENSMUSG Zc3h ENSMUSG Zc3h D2Ngul1725 GCCACTACCATCCGATTCTT CCTGTCTTGAAAACCCAAAA ENSMUSG Ttl ENSMUSG Rpo ENSMUSG Chchd ENSMUSG Slc20a ENSMUSG A730036I17Rik ENSMUSG Ckap2l ENSMUSG Il1a ENSMUSG Il1b ENSMUSG F830045P16Rik ENSMUSG Sirpa=Ptpns ENSMUSG Pdyn D2Jyh3941 AATGACTTGTTTGCCAAGGA TTTTATGCCCTAGGAGCCTC ENSMUSG Stk D2Ngul1849 ACTCTCTGAGTAGCCTGCCCC CCTCACCCTTACTTGGCACC The candidate interval supporting human LTC-ICs is bounded by Zc3h8 and D2Ngul1849, (see Fig. 3a) defining a 0.96 Mb interval on chromosome 2 containing 14 genes. A minimal candidate locus was defined by microsatellite markers D2Ngul1725 and D2Jyh3941 and contained 11 genes. All genomic positions and gene attributes are based on EnsEMBL version 26.33b.1. Zc3h8 primers were designed to detect a polymorphism between NOD and strains in the 5' UTR.

2 Supplementary Table 2. Expression of annotated genes in Idd13 candidate interval. Gene symbol EnsEMBL ID Genotype Cell type Mean copy number ± SD Mean copy number normalized to β-actin ± SD ( 10-3 ) Zc3h8 ENSMUSG ± ± ± ± 0.24 Rpo1-2 ENSMUSG Chchd5 ENSMUSG Slc20a1 ENSMUSG Il1a ENSMUSG Il1b ENSMUSG Stk35 ENSMUSG ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± 15 = below limit of detection = not done See Methods for description of real-time PCR. Four replicates were performed for each sample ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± 0.02

3 Supplementary Table 3. Human Samples Analyzed for SIRPΑ IgV Domain Sequence Population HapMap sample Allelic variant CEU NA12763,V2 NA07345 NA11829 NA11881 NA07056,V3 NA06994,V2 NA12154 YRI NA18504 NA18507,V6 NA18501 NA18502 V2,V5 NA18505, CHB NA18524 V2,V7 NA18526 V2 NA18532,V4 NA18555 NA18624 NA18547 NA18576 NA18608 NA18529 NA18537,V2 NA18563,V2 NA18570 V8 JPT NA18940 V2 NA NA18972 NA19005 V9 NA18959,V2 NA18964 NA18967 NA18942 NA18943 V2,V9 NA18944 NA18945,V6 NA18948,V2 NA18953 Thirty-seven unrelated individuals from Caucasian (CEU), African Yoruban (YRI), Chinese (CHB) and Japanese (JPT) populations were selected from the International HapMap phase 1 release ( Exon 3 was PCR amplified from genomic DNA from these individuals, the amplicons cloned and the resulting plasmids sequenced on both strands. Sequence analysis revealed 10 variants (-0) based upon combinatorial variation at 18 amino acids. The variant(s) observed in each sample are shown. The corresponding sequences are displayed in Fig. 5b.

4 Supplementary Table 4. Microsatellite markers used to map congenic mice. Markers used to define congenic intervals Locus Marker Chr. Position (Mb) Primer 1 (5 3 ) Primer 2 (5 3 ) IBD D1Gul GAACATAGGTGCACACTCACATA TGATGCTGGAGGTTGTCCT Idd5 D1Ngul GATGAAAGAGATAAGACAGATGTTAGATA TGGTTATTAAAGAGCTGTTTTACATG Idd5 D1Mit AAGTTGGAACTCTGCAGGACA GTGTCTTCAATGCAGCACGT Idd5 D1Mit TATTGTTTATGGAAATTGGACCC CATCTCTGAAGGAAAAAGTGCA Idd5 D1Mit GGGAGACAACAAATAATCATATTGC AGAGGTGGGTCCTGGAAACT Idd5 D1Mit CTGAAAATCGTCCCTTGACC CAGGAGCATGAAATGGGGAT Idd5 D1Mit TCCACACAAGGTGTCCTCTG GCTCAGGTGACCTCCAAAAC Idd5 Ramp ATCACCACTGTGGGCATTCTGAAC CAGTAGAGGCCAAGGGCATCAGAATC IBD D1Mit TGTCTCCCCAAAGTAGCAGG GTGATGCAGGAGTTTCTGCA IBD D2Jyh GGCAGATTTATCGCTGTGAG GTGCGCCACCAATGC Idd13 D2Jyh CTTCAGTGCTGTATCCACTGC CTCCCACTCCCATTAATTCTC Idd13 D2Mit AGGCAATTACAAGGCCTGG CACCCATCTCCCTCAGTCAT Idd13 D2Mit GTAGAGACTTGGTGGGTTTTGG ATCTCTGCTGACAAAGAACAGTG Idd13 D2Mit CATGTGCCATGGTACAAAGC TGGCTTGTTTCAGATAGCACA Idd13 D2Mit TCACCAGCCTGAAAACACTG TCTGGGTACAATCCTTAGTCCTG Idd13 D2Mit GCCAGATACAATTTTCCCTCA GTGGGACGCAATATTGGC Idd13 D2Mit TCCCACATTTCTGGCATACA CACATGTGCATTTAAGCATGC IBD D2Mit GTGAGGGGTCAATGCCAC GGCTCAGTTGTAAGCACAAGG IBD D4Mit CCTAACCCTCCCCACACC AAAGATCTGGATTCAAATCCTCC Idd9 D4Mit ACGAGTTGTCCTCTGATCAACA AGCCAGAGCAAACACCAACT Idd9 D4Mit TATGGATCCACTCTCCAGAAA CAAAGTCTCCTCCAAGGCTG Idd9 D4Mit CTGCTGCAGCGATTCTCTC TCAGGCACCTAAGTACATGTGC Idd9 D4Mit AAAAATCGTTCTTTGACTTCTACATG TTTAAAAGGGTTTCTTTATCCTGTG Idd9 D4Mit TTTTCTTAGAACATACCTTGCTTGG GGGGAAGGTGAAAATTTAAAGG Idd9 D4Mit TCTCCACGTGTGTGCCTTAG TGAAAGCACTCTGCAGACTCA Idd9 D4Mit CACTACACGGGGCTGAGATT AAGATCCAACACCCTTTTTGG IBD D4Ngul GGCAGCTTTGTGCTTTAAAA ATGGATGTTTACCTGGCGT Idd4 D11Mit ACTGGAAAATATGTTTTAAACCTCTG AAATGGGATTCTGCAAAAACC Idd4 D11Mit GTGCACTTTCCATGCCTGTA GAGTAGAAAGAGACAGAGAAAGACACA Idd4 D11Mit TCTCCAGCCCCTTCATTATG TGCCAAACACCCATGAGAC Idd4 D11Jyh TCCTTGGTGAGTCCACATCT GGCTAGGCTCTGGAAGACA IBD D11Mit ACTAGCCATATGGTTTCTGATGG GTAGCAGGGCTGTGAGCTTT Markers used to screen for background alleles in congenic mice locus marker Chr. position (cm) Primer 1 (5 3 ) Primer 2 (5 3 ) non-idd D1Mit TATTAATGTTGAAGCCAGAAGCC CTTTAATCATCTCTGTGGCAAGG non-idd D1Mit TGAAGCAAGAATTCAAGAAGAGG AGGACATACCTAGTAAGGCTTTGTC non-idd D5Mit GATCTTCCTACCTTCTTACCCAC CATGATTTTATTTGGGGGG non-idd D7Mit GTCAGACATTGGCTTAGGATCC GGTTTGTGCGCTCTCTCTCT non-idd D10Mit TTTGCCTGTAACAAGCCAGA TTGAGGCTATCAGTTTAAAATCCC non-idd D11Mit GAATAACCCATGTTTATATCGGTG CTCTGGACTTGTGTTCTATGCC non-idd D12Mit CCTCCTAATAGTGCCATTCCC CCAGCAATCACGAGTCTTCC non-idd D14Mit GACCAAAGTCATATCTATAACACC TTAATTGCAAGTAACACAATGAGTAGG non-idd D18Mit ACTGTTGCTGGGGAATGG CCAAGTTCAAAGCTGCTGG IBD = identical by descent; non-idd = regions of non-identity between NOD and outside the four Idd regions

5 Supplementary Table 5. Primers used to PCR amplify and sequence coding and untranslated regions of mouse Sirpa and human SIRPA. Forward primer Reverse primer Mouse Sirpa-1 AGTCCACCTTAAGAGGACCAAGTAGC TGTACAGAAACAGGACGCGGA Sirpa-2 TCTCCCTCCTTGCTCTGCAG TACCTCGCAGATGACCTTAGAATTAA Sirpa-3 CCTAGTGGAAAGAATGTCTCCTACAACA CATATTCTGTGTGGTTGTTAGGCTCA Sirpa-4 CCAGGTACAGTCTTTGATCCAGGA CCAGGGAGTCTCTGCTGGTCTA Sirpa-5 CATCTGTGGAAGAACTACACCAGAAGTC TACCTCAGAGAGCTGGCCGAGT Sirpa-6 CCAATGCTGACCTAATGTTGGC CATCTATACACCCGTGTGTGTATACACA Sirpa-7 AACTTGTCTTTGTCCGGGCC GGCACAGTTCATCCTCACCC Human SIRPA TAGAATACAGGCTCATGTTGCAGGT GCCTTCAGCAAATAGCATGACGT