Supplementary Table: Best Snps in Disease Association in the 1200KB Region Surrounding
Two missense variants in UHRF1BP1 are independently associated with systemic lupus erythematosus in Hong Kong Chinese
Yan Zhang, *Wanling Yang, Chi Chiu Mok, Tak Mao Chan, Raymond Woon Sing Wong, Mo YinMok,Ka Wing Lee, Sik Nin Wong, Alexander Moon Ho Leung, Tsz Leung Lee, Marco Hok Kung Ho, Pamela Pui Wah Lee,Wilfred Hing Sang Wong, Jing Yang, Jing Zhang,Chun-Ming Wong, Irene Oi Lin Ng , Maria-Mercè Garcia-Barceló, Stacey S. Cherny, Paul Kwong-Hang Tam, Pak Chung Sham, Chak Sing Lau, *Yu Lung Lau
Supplementary Table 1: Haplotype association results:
SNPS / HAPLOTYPE / F_A / F_U / CHISQ / DF / OR / Prs11755393|rs13205210 / OMNIBUS / NA / NA / 21.61 / 2 / NA / 2.03E-05
rs11755393|rs13205210 / GC / 0.18 / 0.1348 / 14.37 / 1 / 1.43 / 0.00015
rs11755393|rs13205210 / AT / 0.45 / 0.5181 / 16.3 / 1 / 0.768 / 5.41E-05
rs11755393|rs13205210 / GT / 0.37 / 0.3471 / 1.68 / 1 / 1.09 / 0.1949
Supplementary Table 2:Theassociation of rs13205210 is independent of HLASNPs (rs9271366, rs9275328):
CHR / SNP / BP / A1 / TEST / OR / P6 / rs9271366* / 32694832 / G / ADD / 1.549 / 3.83E-07
6 / rs9271366 / 32694832 / G / rs9275328* / 0.7345 / 0.000301
6 / rs13205210 / 34939834 / C / ADD / 1.565 / 2.86E-07
6 / rs13205210 / 34939834 / C / rs9275328 / 0.6676 / 1.18E-06
6 / rs13205210 / 34939834 / C / ADD / 1.576 / 2.01E-07
6 / rs13205210 / 34939834 / C / rs9271366 / 1.681 / 6.66E-10
SNP rs9271366 and rs9275328 are two SNPs in the HLA locus that showed the most significant association to SLE in our GWAS work.
Supplementary data: Plink result on haplotype analysis for independent contribution from each of the two SNPs.
1. Test of independent effect from rs11755393:
+++ PLINK conditional haplotype test results +++
2 SNPs, and 3 common haplotypes ( MHF >= 0.01 ) from 4 possible
CHR BP SNP A1 A2 F
6 34932614 rs11755393 A G 0.48
6 34939834 rs13205210 C T 0.162
Haplogrouping: each {set} allowed a unique effect
Alternate model
{ GC } { AT } { GT }
Null model
{ GC } { AT, GT }
HAPLO FREQ OR(A) OR(N)
------
GC 0.161 (-ref-) (-ref-)
AT 0.478 0.6523 0.7057
GT 0.359 0.7899 |
------
Model comparison test statistics:
Alternate Null
-2LL : 2.44e+003 2.45e+003
Likelihood ratio test: chi-square = 6.78
df = 1
p = 0.00921
2. Test of independent effect from rs13205210:
+++ PLINK conditional haplotype test results +++
2 SNPs, and 3 common haplotypes ( MHF >= 0.01 ) from 4 possible
CHR BP SNP A1 A2 F
6 34932614 rs11755393 A G 0.48
6 34939834 rs13205210 C T 0.162
Haplogrouping: each {set} allowed a unique effect
Alternate model
{ GC } { AT } { GT }
Null model
{ GC, GT } { AT }
HAPLO FREQ OR(A) OR(N)
------
GC 0.161 (-ref-) (-ref-)
GT 0.359 0.7899 |
AT 0.478 0.6523 0.7682
------
Model comparison test statistics:
Alternate Null
-2LL : 2.44e+003 2.45e+003
Likelihood ratio test: chi-square = 5.27
df = 1
p = 0.0217
Supplementary Figure 1
Supplementary Figure 2
