Confirmation of association of <i>HLA</i> locus, and <i>TNFSF4</i>, <i>STAT4</i>, <i>TNFAIP3</i>, <i>IRF5</i>, <i>BLK</i> with SLE.

<p>Shown are association results comparing SLE patients with controls collected in Hong Kong analyzed by Plink (−log₁₀(<i>P</i>-value) of SNPs). The best SNP in Chromosome 11 is around <i>ETS1</i> gene (rs6590330), which is in high LD with rs1128334. And the best SNP in Chromosome 10 is in <i>WDFY4</i> (rs877819).</p

Linkage disequilibrium and sequence conservation of SNPs in <i>ETS1</i>.

<p>Shown are LD for significant SNPs in and around <i>ETS1</i> detected by GWAS (A), and replicated SNPs in the 3′-UTR and downstream of the gene (B), and sequence conservation for sequences around SNP rs1128334 among different species (C).</p

Quantile-Quantile plot of expected (x-axis) and observed (y-axis) −log₁₀(<i>P</i> value) distribution in our GWAS analysis.

<p>(A) Considering all the available SNPs. (B) SNPs in and around <i>HLA locus</i>, and <i>TNFSF4</i>, <i>STAT4</i>, <i>TNFAIP3</i>, <i>IRF5</i>, <i>BLK</i>, as well as <i>BANK1</i> were excluded from analysis.</p

<i>ETS1</i> Haplotype analysis on SLE association.

<p><i>ETS1</i> Haplotype analysis on SLE association.</p

Involvement of <i>ETS1</i> in Th17 cell and B lymphocyte development and autoimmunity.

<p>Involvement of <i>ETS1</i> in Th17 cell and B lymphocyte development and autoimmunity.</p

Allelic expression of <i>ETS1</i> on SNP rs1128334 in PBMC of healthy individuals.

<p>PBMC cDNA processed from 33 healthy individuals heterozygous on rs1128334 were used for allelic expression detection of <i>ETS1</i> by pyrosequencing. (A) A case example of detection on the “A” allele and the “G” allele from both DNA and cDNA samples from the same individual. (B) The ratio of G/A allelic detection for both DNA and cDNA samples. The median G/A ratio for DNA is 1.09 (95% CI: 1.08–1.11) and the median G/A ratio for cDNA expression is 1.32 (95% CI: 1.21–1.43), <i>P</i><0.0001 by paired student's <i>t</i> test.</p

LD among <i>WDFY4</i> SNPs examined in this study (A) and sequence conservation of the three nonsynonymous variations among various species (B).

<p>LD among <i>WDFY4</i> SNPs examined in this study (A) and sequence conservation of the three nonsynonymous variations among various species (B).</p

Principal component analysis of Chinese samples collected in Hong Kong, Taiwan, and Beijing.

<p>The red dots denote SLE patient samples collected in Hong Kong used in our GWAS study and the blue dots are unaffected samples from Beijing (A), Taiwan (B), and Hong Kong (C). The data on Taiwan samples was received from deCODE Genetics; the data on Han Chinese in Beijing is available from HapMap. The data on Hong Kong controls were from other studies in the University of Hong Kong that were genotyped by the same platform. Repeat of Eigenstrat analysis for 20 times using randomly chosen 100,000 SNPs each time from all the available SNPs produced similar results.</p

SNPs showed significant association with SLE in a joint analysis of four independent Asian cohorts.

<p>SNPs showed significant association with SLE in a joint analysis of four independent Asian cohorts.</p

Replication of disease association for <i>WDFY4</i> SNPs in the Hong Kong samples.

<p>Replication of disease association for <i>WDFY4</i> SNPs in the Hong Kong samples.</p