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. Author manuscript; available in PMC: 2016 Apr 9.
Published in final edited form as: Cell. 2015 Mar 12;161(2):387–403. doi: 10.1016/j.cell.2015.02.046

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

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)

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)

ZNF804A (2) rs6755404 P2:3367 Effector CD4: CD127-PD1− 0.09 3.8E-04 rs6755404 (A) Malaria 1.2E-06 (Band et al., 2013)

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

LOC100505836 (3) rs2593321 Lin:19 %NKT 0.08 5.5E-04 rs2593321 HIV-1 control 7.7E-06 (Pelak et al., 2010)

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)

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

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

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)

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

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)

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)

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

MMP16 (8) rs160441 P4:3551 NK: %CD314-CD158a+ −0.08 2.3E-05 rs160441 Tuberculosis 8.4E-06 (Thye et al., 2010)

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.