Analysis of association of <i>PTPN22</i> ‘haplotype 6–10’ group (<i>rs12144309</i>: C&gt;T) with rheumatoid arthritis.

<p>1. Cases top line, controls bottom line. The NZ controls deviated mildly from HWE (<i>P</i> = 0.02).</p><p>2. Imputed genotypes were taken from <a href="http://www.wtccc.org.uk" target="_blank">www.wtccc.org.uk</a>.</p><p>3. The Mantel-Haenszel combined OR = 0.90 [0.82–0.98], <i>P</i> = 0.021. The Breslow-Day test for heterogeneity <i>P</i> = 0.90.</p

Haplotype structure of structure of a portion of the <i>PTPN22</i> haplotype block.

<p>The figure was generated by Haploview using Phase 2 CEPH CEU HapMap data downloaded from <a href="http://www.hapmap.org" target="_blank">www.hapmap.org</a>, with the boundaries being <i>rs4145859</i> (114.312 Mb) and <i>rs10745340</i> (114.437 Mb).</p

Analysis of association of <i>PTPN22</i> ‘haplotype 5’ (<i>rs3789607</i>: T&gt;C) with rheumatoid arthritis.

<p>1 Cases top line, controls bottom line. The Carlton Set 2 cases and controls, the combined other cases and total cases deviated mildly from HWE (<i>P</i> = 0.02, 0.03, 0.05 and 0.02, respectively).</p><p>2 Allele 2; number of chromosomes (frequency).</p><p>3 Genotype data from <i>rs17274634</i> were used (r² = 1 with <i>rs3789607</i> in CEPH CEU (<a href="http://www.hapmap.org" target="_blank">www.hapmap.org</a>)).</p><p>4 The Mantel-Haenszel pooled OR = 0.87 [0.82–0.93], <i>P</i> = 7.5×10⁻⁶; Breslow-Day test for heterogeneity <i>P</i> = 0.083. The Mantel-Haenszel pooled OR excluding Carlton et al data was 0.91 [0.85–0.98], <i>P</i> = 0.016; Breslow-Day <i>P</i> = 0.50.</p

Analysis of association of <i>PTPN22</i> ‘haplotype 4’ (<i>rs3811021</i>: A&gt;G) with rheumatoid arthritis.

<p>1 Cases top line, controls bottom line.</p><p>2 Imputed genotypes were taken from <a href="http://www.wtccc.org.uk" target="_blank">www.wtccc.org.uk</a>.</p><p>3 The Mantel-Haenszel combined OR  = 0.85 [0.72–1.01], <i>P</i> = 0.071. The Breslow-Day test for heterogeneity <i>P</i>&lt;0.001.</p

<i>Rs2476601-rs12566340</i> haplotypic analysis.

<p>1. Within each cell in the RA half, NZ data are top, WTCCC data middle and combined bottom.</p