SNP を用いた 関節リウマチ関連遺伝子解析の現況
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description
SNP を用いた 関節リウマチ関連遺伝子解析の現況. 理化学研究所 遺伝子多型研究センター 関節リウマチ関連遺伝子研究チーム 山田 亮. Large Scale SNP-based Linkage Disequilibrium Mapping ホールゲノムアプローチ RIKEN( 日本 ) 連鎖解析・標的遺伝子領域アプローチ U. of Manchester (UK) NARAC(USA). Gene. SNP. Block. Inetr-block LD. No haplotypes. No htSNPs. - PowerPoint PPT Presentation
Transcript of SNP を用いた 関節リウマチ関連遺伝子解析の現況
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SNP
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Large Scale SNP-based Linkage Disequilibrium Mapping
RIKEN()U. of Manchester (UK)NARAC(USA)
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Linkage Disequilibrium MappingChromosome 1p
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Genes associated with multiple autoimmune diseases
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RA or Crohn disease-associated SNPs in Ch5q31 Cytokine cluster
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SLC22A4RUNX1SLC22A4Crohn, Asthma(5q13)RUNX1SLETokuhiro S et al. Nat Genet 35, 341-348 (2003)
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The SNPs associated with RA, Crohn disease or Psoriatic arthritis
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3 genes with RUNX1 binding sequenceSLERAPsoriasisProkunina, L. et al.Helms, C. et al.Tokuhiro, S. et al.
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RA, SLE and Psoriasis-associated SNPs disrupt RUNX1 binding motif
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PTPN221p13110kDa tyrosine phosphataseSNP 1858C->T, R620W)Positive associationIDDM(Caucasian, Italian)Bottini N et al. RA(Caucasian)Begovich AB et al.SLE(Caucasian)Kyogoku, C. et al.
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Peptidyl citrullination by PADI4Loss of ionic NH2+ of Arg residueEffects on intra- and inter- molecular interactions
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CCP)
Sheet1
PPV
54%89%85.70%
38%98.70%97.40%
30%100%100%
Sheet2
Sheet3
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Replication study from JapanJapan 1: Suzuki et al.Japan 2: Kuwahara et al.
Sheet1
Npadi_94P
Japan 1Case8300.460.000008
Control7360.37
Japan 2Case7040.450.0035
Control9600.40
Sheet2
Sheet3
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CaucasianJapanesePDCD1MIF1CTLA4SLC22A4/A5PTPN22TNFRSF1PADI4Susceptible allelePreliminary calculation with random-effect model
Graph7
0.073
0.927
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph8
0
1
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph9
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph10
0
1
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph11
0.2160.216
0.7840.784
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph12
0.2160.216
0.7840.784
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph16
0.62
0.38
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph17
0.42
0.58
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph18
0.37
0.63
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph19
0.42
0.58
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph20
0
1
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph2
0.26
0.74
ctla4
EnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=123)(n=349)(n=781)(n=487)
G0.430.360.0280.650.620.215
0.215,1268
0.028,472
P --2
---------------------------------------------
P z
---------------------------------------------
1 0.2150000 1268 0.7891917
2 0.0280000 472 1.9110356
---------------------------------------------
z(overall) = 1.90935
p(overall) = 0.02811
= 0.62927
= 1
P = 0.42762
effect size r = 0.0457731
N fs.05 = 0.69
========================================
mif
Allele frequencyEnglishJapanese
susceptibleJIAcontrolRAcontrol
SNP No.allele(n=526)(n=259)(n=1033)(n=993)
C0.350.220.00020.230.200.013
pdcd1
Allele frequencySwedishJapanese
casecontrolcasecontrol
SNP No.Allele(n=1175)(n=3404)(n=824)(n=649)
A0.0850.0730.05300
ptpn22
Allele frequencyWhite AmericanJapanese
casecontrolcasecontrol
SNP No.Allele(n=475)(n=475)(n=822)(n=649)
T0.140.090.000700
tnfrsr1b
TNFRSF1B
Allele frequencyCaucasiansJapanese
casecontrolcasecontrol
SNP No.Allele(n=480)(n=137)(n=824)(n=648)
T0.670.260.02060.870.170.0256
0.740.8311/22
TNFRSF1B
Allele frequencyCaucasiansJapanese
casecontrolcasecontrol
SNP No.Allele(n=480)(n=137)(n=824)(n=648)
T0.670.740.02060.870.830.0256
tnfrsr1b
PADI4
PADI4
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
T0.450.420.310.460.370.00046
P --2
---------------------------------------------
P z
---------------------------------------------
1 0.3100000 1237 0.4958503
2 0.0004600 1478 3.3139134
---------------------------------------------
z(overall) = 2.69391
p(overall) = 0.00353
= 3.97074
= 1
P = 0.04630
effect size r = 0.0517009
N fs.05 = 3.36
========================================
Graph4
0.26
0.74
ctla4
EnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=123)(n=349)(n=781)(n=487)
G0.430.360.0280.650.620.215
0.215,1268
0.028,472
P --2
---------------------------------------------
P z
---------------------------------------------
1 0.2150000 1268 0.7891917
2 0.0280000 472 1.9110356
---------------------------------------------
z(overall) = 1.90935
p(overall) = 0.02811
= 0.62927
= 1
P = 0.42762
effect size r = 0.0457731
N fs.05 = 0.69
========================================
mif
Allele frequencyEnglishJapanese
susceptibleJIAcontrolRAcontrol
SNP No.allele(n=526)(n=259)(n=1033)(n=993)
C0.350.220.00020.230.200.013
pdcd1
Allele frequencySwedishJapanese
casecontrolcasecontrol
SNP No.Allele(n=1175)(n=3404)(n=824)(n=649)
A0.0850.0730.05300
ptpn22
Allele frequencyWhite AmericanJapanese
casecontrolcasecontrol
SNP No.Allele(n=475)(n=475)(n=822)(n=649)
T0.140.090.000700
tnfrsr1b
TNFRSF1B
Allele frequencyCaucasiansJapanese
casecontrolcasecontrol
SNP No.Allele(n=480)(n=137)(n=824)(n=648)
T0.670.260.02060.870.170.0256
0.740.8311/22
TNFRSF1B
Allele frequencyCaucasiansJapanese
casecontrolcasecontrol
SNP No.Allele(n=480)(n=137)(n=824)(n=648)
T0.670.740.02060.870.830.0256
tnfrsr1b
PADI4
PADI4
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
T0.450.420.310.460.370.00046
P --2
---------------------------------------------
P z
---------------------------------------------
1 0.3100000 1237 0.4958503
2 0.0004600 1478 3.3139134
---------------------------------------------
z(overall) = 2.69391
p(overall) = 0.00353
= 3.97074
= 1
P = 0.04630
effect size r = 0.0517009
N fs.05 = 3.36
========================================
MBD003A5BDA.xls
Graph16
0.62
0.38
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)P value(n=823)(n=655)P value
pdcd1_1A0.0850.0730.930.053001.00
ptpn22_1T0.140.090.910.0007001.00
mif_1C0.350.220.780.00020.230.200.800.013
tnfrsf1b_1T0.340.260.740.00590.870.870.130.7914
ctla4_1G0.430.360.640.0280.650.620.380.215
padi4_92T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
0
0
PDCD1 C
Sheet2
0
0
PDCD1 J
Sheet3
00000000
00000000
PTPN22 C
0
0
PTPN22 J
00
00
MIF11 C
00
00
MIF11 C
0
0
tnfrsf1b_1
0
0
TNFRSF1b_1
0
0
CTLA4 C
0
0
CTLA4 J
0
0
PADI4 C
0
0
PADI4 J
0
0
SLC22A4/A5
0
0
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)P value(n=823)(n=655)P value
pdcd1_1A0.0850.0730.930.053001.00
ptpn22_1T0.140.090.910.0007001.00
mif_1C0.350.220.780.00020.230.200.800.013
tnfrsf1b_1T0.340.260.740.00590.870.870.130.7914
ctla4_1G0.430.360.640.0280.650.620.380.215
padi4_92T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph15
0.36
0.64
Sheet1
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
Sheet1
PDCD1 C
Sheet2
PDCD1 J
Sheet3
PTPN22 C
PTPN22 J
MIF11 C
MIF11 C
tnfrsf1b_1
TNFRSF1b_1
CTLA4 C
CTLA4 J
PADI4 C
PADI4 J
SLC22A4/A5
SLC22A4/A5 J
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
A0.0850.0730.930.053001.00
T0.140.090.910.0007001.00
C0.350.220.780.00020.230.200.800.013
T0.340.260.740.00590.870.870.130.7914
G0.430.360.640.0280.650.620.380.215
T0.450.420.580.310.460.370.630.00046
SLC22A4/A5haplotype0.420.580.001.00
1-Pcont1-Pcont
0.073
0.927
0
1
0.090.090.090.090.090.090.090.09
0.910.910.910.910.910.910.910.91
0
1
0.2160.216
0.7840.784
0.2160.216
0.7840.784
0.26
0.74
0.87
0.13
0.36
0.64
0.62
0.38
0.42
0.58
0.37
0.63
0.42
0.58
0
1
Graph5
0.17
0.83
ctla4
EnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=123)(n=349)(n=781)(n=487)
G0.430.360.0280.650.620.215
0.215,1268
0.028,472
P --2
---------------------------------------------
P z
---------------------------------------------
1 0.2150000 1268 0.7891917
2 0.0280000 472 1.9110356
---------------------------------------------
z(overall) = 1.90935
p(overall) = 0.02811
= 0.62927
= 1
P = 0.42762
effect size r = 0.0457731
N fs.05 = 0.69
========================================
mif
Allele frequencyEnglishJapanese
susceptibleJIAcontrolRAcontrol
SNP No.allele(n=526)(n=259)(n=1033)(n=993)
C0.350.220.00020.230.200.013
pdcd1
Allele frequencySwedishJapanese
casecontrolcasecontrol
SNP No.Allele(n=1175)(n=3404)(n=824)(n=649)
A0.0850.0730.05300
ptpn22
Allele frequencyWhite AmericanJapanese
casecontrolcasecontrol
SNP No.Allele(n=475)(n=475)(n=822)(n=649)
T0.140.090.000700
tnfrsr1b
TNFRSF1B
Allele frequencyCaucasiansJapanese
casecontrolcasecontrol
SNP No.Allele(n=480)(n=137)(n=824)(n=648)
T0.670.260.02060.870.170.0256
0.740.8311/22
TNFRSF1B
Allele frequencyCaucasiansJapanese
casecontrolcasecontrol
SNP No.Allele(n=480)(n=137)(n=824)(n=648)
T0.670.740.02060.870.830.0256
tnfrsr1b
PADI4
PADI4
Allele frequencyEnglishJapanese
casecontrolcasecontrol
SNP No.Allele(n=772)(n=465)(n=823)(n=655)
T0.450.420.310.460.370.00046
P --2
---------------------------------------------
P z
---------------------------------------------
1 0.3100000 1237 0.4958503
2 0.0004600 1478 3.3139134
---------------------------------------------
z(overall) = 2.69391
p(overall) = 0.00353
= 3.97074
= 1
P = 0.04630
effect size r = 0.0517009
N fs.05 = 3.36
========================================
-
AcknowledgmentLab. Rheumatic DiseasesDr. K. Yamamoto Dr. A. SuzukiDr. X.ChangDr. Y. KochiMr. S. TokuhiroMs. R. KawaidaMs. M. MoriMs. K. KobayashiMs. M. OhtakeMs. E. KannnoMs. K. Komakine
SRC, RIKENDr. A. SekineDr. T. TsunodaDr. Y. NakamuraMr. H. KawakamiMr. T. KawaguchiClinical InstitutesDr. T. Sawada
And many other collaborators
SLC22A4SNP
