Top Associations with Additional SNPs.

<p>Associations with pvalues <5×10⁻⁵ are listed here. Of the ∼115,000 SNPs tested for this table, ∼20,000 SNPs are not in linkage disequilibrium. Since 3 phenotypes were tested, the Bonferroni correction for multiple comparisons is 0.05/(20,000×3) = 8×10⁻⁷.</p><p>Top Associations with Additional SNPs.</p

Description of study subjects.

<p>Description of study subjects.</p

Association of known IBD SNPs.

<p>“Previously reported SNPs” are those IBD snps added to the design of the ImmunoChip; one per locus is shown here. Since 2 phenotypes were tested for this table (CD and UC) and 100 of the SNPs were not in linkage disequilibrium in Puerto Rico controls, the Bonferroni correction for multiple comparisons is 0.05/(2*100) = 0.00025.</p><p>Association of known IBD SNPs.</p

“Global” continental ancestry in Puerto Rican subjects.

<p>A. Principal components analysis of the combined Puerto Rican and HGDP subjects. B. “Global” continental ancestry was estimated using Admixture 1.2 in an analysis supervised by data from HGDP populations as described in Methods (AFR, sub-Saharan African continent, dark blue; EUR, European continent, red; and AMR, Mexico, Central and South America continents, green). HGDP subjects not originating from these three continents are black. Puerto Rican subjects were sorted left-to-right based on ancestry from the African continent.</p

NOD2 haplotypes.

<p>Haplotypes were determined using Phase v2.3; SNPs are, in order, rs2066842 (SNP5), rs2066843 (SNP6), rs2066844 (SNP8), rs2066845 (SNP12), and rs5743293 (SNP13). The association of each haplotype was tested by permutation.</p><p>Footnotes:</p><p>1) IBD susceptibility haplotype in Europeans.</p><p>NOD2 haplotypes.</p