Table 2. Overlapping associations with complex diseases.
Association results from the discovery cohort immune trait analyses are reported in the first six columns. The trait ID is fully described in Table S2. The disease-associated variant, pathology, the disease-associated SNP’s best-reported P-value are indicated in the seventh-tenth columns, respectively. The risk alleles presented correlate with increased disease susceptibility and the r2 between disease SNP and immune trait, if different, are reported in parentheses after the reported SNP.
Immune trait association | Disease association | ||||||||
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Gene (Chr) | Marker | Trait ID | Trait Phenotype | Beta | P Value | Reported SNP | Disease | Best P | Reference |
FCGR2A (1) | rs1801274 | P7:110 | iMDC: %CD32+ | 0.2 | 1.6E-23 | rs1801274 (A) | IBD | 2.1E-38 | (Jostins et al., 2012) |
MFI:189 | CD27 on IgA+ B | 0.13 | 6.5E-11 | Kawasaki disease | 7.4E-11 | (Khor et al., 2011) | |||
MFI:212 | CD27 on IgG+ B | 0.14 | 5.4E-12 | Ulcerative colitis | 2.2E-20 | (Anderson et al., 2011) | |||
MFI:231 | CD161 on CD4 T | 0.13 | 2.6E-11 | Ankylosing-spondylitis | 1.4E-09 | (Cortes et al., 2013) | |||
MFI:504 | CD27 on CD4 T | 0.15 | 5.4E-14 | SLE | 6.8E-07 | (Harley et al., 2008) | |||
MFI:552 | CD27 on CD8 T | 0.19 | 1.3E-21 | HIV progression | 1.0E-04* | (Forthal et al., 2007) | |||
P7:224 | CD1c+ mDC: %CD32 | 0.12 | 4.4E-09 | Lymphoma | 0.006* | (Wang et al., 2006) | |||
Malaria | 0.013* | (Sinha et al., 2008) | |||||||
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FCGR2A (1) | rs10494359 | P7:110 | iMDC: %CD32+ | 0.34 | 2.5E-29 | rs10494360 (r2=0. 94) | Rheumatoid arthritis | 9.3E-05* | (Eyre et al., 2012) |
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ZNF804A (2) | rs6755404 | P2:3367 | Effector CD4: CD127-PD1− | 0.09 | 3.8E-04 | rs6755404 (A) | Malaria | 1.2E-06 | (Band et al., 2013) |
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MIR216B (2) | rs6751715 | P3:5372 | CD8 T: %CXCR3-R4+R6+R10− | −0.09 | 1.5E-05 | rs6751715 | HIV | 1.1E-06 | (Fellay et al., 2009) |
P3:5661 | CD8 T: %CD161+ | −0.07 | 5.1E-04 | ||||||
P6:197 | IgA+ B: %CD27-CD38− | 0.07 | 7.0E-04 | ||||||
P3:5658 | CD8 T: %CD161+PD1− | −0.07 | 7.8E-04 | ||||||
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LOC100505836 (3) | rs2593321 | Lin:19 | %NKT | 0.08 | 5.5E-04 | rs2593321 | HIV-1 control | 7.7E-06 | (Pelak et al., 2010) |
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MICA (6) | rs4418214 | P6:112 | IgE+B: %CD20-CD27-CD38+ | 0.12 | 7.6E-04 | rs4418214 (C) | HIV-1 control | 1.4E-34 | (Pereyra et al., 2010) |
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BTNL2 (6) | rs3817963 | P2:12609 | CD8 T: %CD25+CD38+45RO+ | −0.08 | 3.5E-04 | rs3817963 (A) | Hep C liver cirrhosis | 1.3E-08 | (Urabe et al., 2013) |
P2:10486 | CD8 T: %CD25+CD38+ | −0.08 | 4.1E-04 | ||||||
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HLA-DQB1 (6) | rs2856718 | P2:12609 | CD8 T: %CD25+CD38+45RO+ | −0.08 | 5.3E-04 | rs2856718 (A) | Hepatitis B | 4.0E-37 | (Mbarek et al., 2011) |
P2:10486 | CD8 T: %CD25+CD38+ | −0.07 | 7.8E-04 | ||||||
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EHMT2 (6) | rs652888 | MFI:578 | CD3 on CD8 T | −0.08 | 5.7E-04 | rs652888 | Chronic hepatitis B | 7.1E-13 | (Kim et al., 2013) |
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MTCO3P1 - HLADQA2 (62) | rs4273729 | P2:10486 | CD8 T: %CD25+CD38+ | 0.08 | 1.4E-04 | rs4273729 | Chronic Hepatitis C | 1.7E-16 | (Duggal et al., 2013) |
P2:12609 | CD8 T: %CD25+CD38+45RO+ | 0.08 | 2.3E-04 | ||||||
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ADGB (6) | rs2275606 | P1:12906 | CD8 T: %TSCM | 0.13 | 6.3E-04 | rs2275606 (A) | Leprosy | 3.9E-14 | (Zhang et al., 2011) |
ABO (9) | rs8176722 | MFI:1 | CD123 on mDC | −0.14 | 1.4E-04 | rs8176722 (A) | Malaria | 8.9E-10 | (Band et al., 2013) |
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ACTA2, FAS (10) | rs7069750 | P1:6601 | CD8 T: %TSCM | −0.14 | 4.1E-12 | rs7069750 (C) | Juv. idiopathic arthritis | 2.9E-08 | (Hinks et al., 2013) |
rs2147420 (r2=1) | CLL | 3.1E-13 | (Berndt et al., 2013) | ||||||
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KLRC4-KLRK1 (12) | rs1049172 | P4:3551 | NK: %CD314-CD158a+ | −0.13 | 8.8E-09 | rs2617170 (r2=0.922) | Behçet’s disease | 1.3E-09 | (Kirino et al., 2013) |
P4:4832 | NK: %CD314-CCR7− | −0.23 | 7.6E-22 | ||||||
P4:5538 | NK: %CD314-CD335+ | −0.27 | 1.4E-30 | ||||||
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MMP16 (8) | rs160441 | P4:3551 | NK: %CD314-CD158a+ | −0.08 | 2.3E-05 | rs160441 | Tuberculosis | 8.4E-06 | (Thye et al., 2010) |
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ARHGAP20 (11) | rs1469170 | P4:3551 | NK: %CD314-CD158a+ | −0.08 | 5.6E-04 | rs1469170 (A) | Malaria | 8.0E-08 | (Band et al., 2013) |
Disease association is significant with candidate SNP method/gene approach.