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Chunk #1 — METHODS — UC GWAS study subjects, genotyping and analysis

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Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study.
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Data management and quality control filtering are described in the Supplementary Methods online. Case-control matching, by gender and ancestry, followed by association analyses by conditional logistic regression on gender-ancestry strata in the matched datasets (see Supplementary Table 1 online) were performed using GEM13. The GEM analysis is described in more detail in the Supplementary Methods online. The genomic control inflation factor was computed14. SNPs with nominal P values < 5×10−8 were considered to have genome-wide significant evidence for association27.