?Uncorrected 2 value of each separated cohort. (DOC) Click here for additional data file.(35K, doc) Table S9Independent associations found in the HLA region BMS-817378 in the ATA positive subgroup of patients in the separate four GWAS cohorts. controls. All values are GC corrected, and was 1.050.(TIF) pgen.1002178.s003.tif (385K) GUID:?92D6F1A6-F22C-4A78-9A82-DF6587FF84AA Figure S4: Manhattan plot and QQ plot showing the -log10 of the Mantel-Haenszel value of all 279,621 SNPs in the ATA positive individuals of the GWAS cohorts comprising 447 cases and 5,171 controls. All values are GC corrected, and was 1.061.(TIF) pgen.1002178.s004.tif (561K) GUID:?FAE93EE7-A54C-4954-956C-A5649A4C56B8 Figure S5: Manhattan plot showing the analysis in the GWAS cohorts imputed data. The different subphenotypes considered are represented in different colors.(TIF) pgen.1002178.s005.tif (2.5M) GUID:?34392710-0A44-459D-B09C-8888B5D4D50F Table S1: Analysis for GWAS cohorts, replication cohorts and combined analysis for all non-HLA, non-previously described associations with lcSSc subtype of the disease. ?values for GWAS cohorts are Mantel-Haenszel meta-analysis GC corrected according to the set and in the replication and combined analysis Mantel-Haenszel meta-analysis value. ?value for the totality of the SSc patients, in the case of GWAS cohorts GC corrected according to the set , and in replication and combined analysis Mantel-Haenszel meta-analysis value.(DOC) pgen.1002178.s006.doc (60K) GUID:?D90C8D0A-645A-41E6-85ED-8F3F94FE32CB Table S2: Analysis for GWAS cohorts, replication cohorts and combined analysis for all non-HLA, non-previously described associations with dcSSc subtype of the disease. ?values for GWAS cohorts are Mantel-Haenszel meta-analysis GC corrected according to the set and in the replication and combined analysis Mantel-Haenszel meta-analysis value. ?value for the totality of the SSc patients, in the case of GWAS cohorts GC corrected according to the set , and in replication and combined analysis Mantel-Haenszel meta-analysis value. *Association in rs11171747 had a significant BD value, thus making them heterogenic associations among populations.(DOC) pgen.1002178.s007.doc (50K) BMS-817378 GUID:?1FBD8705-3A60-4C48-8C90-5133DA60B6AF Table S3: Analysis for GWAS BMS-817378 cohorts, replication cohorts and combined analysis for all non-HLA, non-previously described associations with ACA positive subgroup of the disease. ?values for GWAS cohorts are Mantel-Haenszel meta-analysis GC corrected according to the set and in the replication and combined analysis Mantel-Haenszel meta-analysis value. ?value for the totality of the SSc patients, in the case of GWAS cohorts GC corrected according to the set , and in replication and combined analysis Mantel-Haenszel meta-analysis value. *Association in rs3790567 had a significant BD value, thus making them heterogeneous associations among populations.(DOC) pgen.1002178.s008.doc (40K) GUID:?363B95D8-886F-472F-8D6D-47AA9D9681FA Table S4: Analysis for GWAS cohorts, replication cohorts and combined analysis for all non-HLA, non-previously described associations with ATA positive subgroup of the disease. ?values for GWAS cohorts are Mantel-Haenszel meta-analysis GC corrected according to the set and in the replication and combined analysis Mantel-Haenszel meta-analysis value. ?value for the totality of the SSc patients, in the case of GWAS cohorts GC corrected according to the set , and in replication and combined analysis Mantel-Haenszel meta-analysis value.(DOC) pgen.1002178.s009.doc (44K) GUID:?90502D21-726B-41C5-9D7E-7D251B9ACDC7 Table S5: Power calculations and genomic inflation factors () in the whole SSc cohorts (GWAS and replication) and the lcSSc, dcSSc, ACA and ATA positive subphenotypes. 510?8 was used as significance threshold.(DOC) pgen.1002178.s010.doc (36K) GUID:?90EDCDD7-0AD7-4A33-8C58-794F8F5ABD9B Table S6: Conditional logistic regression analysis of all the independently associated SNPs in the HLA region in the ACA positive patients. ?values for Mantel-Haenszel meta-analysis GC corrected according to the set .(DOC) pgen.1002178.s011.doc (28K) GUID:?ECA87700-67CC-4621-94AE-3141E7D1FB0D Table S7: Conditional logistic regression analysis of all the independently associated SNPs in the HLA region in the ATA positive patients. ?values for Mantel-Haenszel meta-analysis GC corrected according to the set .(DOC) pgen.1002178.s012.doc (41K) GUID:?9D59AB6D-0AAB-47EB-BD09-CCC160BB72DE Table S8: Independent associations found in the HLA region in the ACA positive subgroup of patients in the separate four GWAS cohorts. ?Uncorrected 2 value MOBK1B of each separated cohort.(DOC) pgen.1002178.s013.doc (35K) GUID:?4CBDC1AB-8FC6-488E-BE2E-A2646AFB92B7 Table S9: Independent associations found in the HLA region in the ATA positive subgroup of BMS-817378 patients in the separate four GWAS cohorts. ?Uncorrected 2 value of each.