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. Author manuscript; available in PMC: 2021 Oct 15.
Published in final edited form as: Nat Genet. 2020 Sep 14;52(10):1036–1045. doi: 10.1038/s41588-020-0684-4

Table 1 |.

Multiple coincident associations between immune traits and diseases

Immune trait association Disease association Correlation bw trait and disease
Gene Trait name Trait rsID Derived/ancestral allele Derived allele effect s.e. P value Disease Disease rsID Effect/other allele OR P value Reference r 2 Derived allele/corresponding allele in disease Effects of derived allele/corresponding allele in disease
FCGR2A CD27 on IgD−CD38dim rs1801274 G/A −0.204 0.03 1.14 × 10−14 CRO rs1801274 G/A 0.93 1.53 × 10−7 Ref. 17 1.00 G/G −/−
IBD 0.89 2.00 × 10−38
CD40 rs1883832 T/C 0.640 0.03 6.21 × 10−147 CRO rs6074022 C/T 1.10 3.00 × 10−12 Ref. 33 0.98 T/C +/+
IBD 1.08 8.00 × 10−11
FCGR2A CD27 on sw mem rs1801274 G/A −0.293 0.03 2.48 × 10−28 CRO rs1801274 G/A 0.93 1.53 × 10−7 Ref. 17 1.00 G/G −/−
IBD 0.89 2.00 × 10−38
CD40 rs1883832 T/C 0.585 0.03 2.53 × 10−118 CRO rs6074022 C/T 1.10 3.00 × 10−12 Ref. 33 0.98 T/C +/+
IBD 1.08 8.00 × 10−11
CD28, CTLA4 CD28 on CD4+ rs1973872 T/G −0.386 0.03 2.24 × 10−42 MS rs6435203 G/A 0.93 1.00 × 10−7 Ref. 16 0.83 T/G −/−
BACH2 rs72928038 A/G 0.247 0.03 4.43 × 10−13 rs72928038 A/G 1.14 1.50 × 10−15 1.00 A/A +/+
BACH2 CD28 on CD28+CD45RA+CD8br rs619192 C/T −0.199 0.03 2.97 × 10−10 T1D rs597325 A/G 0.85 3.38 × 10−10 Ref. 37 0.98 C/A −/−
rs72928038 A/G 0.589 0.03 5.13 × 10−67 rs72928038 A/G 1.20 6.40 × 10−14 Ref. 23 1.00 A/A +/+
FCGR2A CD64 on CD14+CD16+ monocyte rs1801274 G/A 0.383 0.03 1.86 × 10−48 SLE rs1801274 G/A 1.16 1.04 × 10−12 Ref. 52 1.00 G/G +/+
ATXN2, BRAP rs11065979 T/C 0.150 0.03 6.46 × 10−9 rs653178 C/T 1.14 7.00 × 10−9 Ref. 15 0.97 T/C +/+
TNFSF15, TNFSF8 HLA DR+ T cell %T cell rs7032773 T/C −0.147 0.03 1.46 × 10−9 UC rs726657 T/C 0.89 2.26 × 10−14 Ref. 22 0.91 T/T −/−
CIITA rs3087456 A/G −0.461 0.03 3.08 × 10−70 rs4781011 G/T 0.87 3.00 × 10−6 Ref. 53 0.94 A/G −/−
LCT-AS1 pDC AC rs2164210 C/T 0.194 0.03 2.12 × 10−13 SLE rs12615624 A/G 1.11 4.00 × 10−7 Ref. 15 0.76 C/A +/+
SPATA48, IKZF1 rs876039 C/G −0.197 0.03 9.51 × 10−13 rs4917014 G/T 0.72 3.00 × 10−23 Ref. 12 0.99 C/G −/−
TNFSF13B Unsw mem %lymphocyte rs200748895 A/GCTGT 0.209 0.03 1.49 × 10−14 MS rs200748895 A/GCTGT 1.27 1.23 × 10−9 Ref. 11 1.00 A/A +/+
SLE 1.44 6.74 × 10−10
NCOA5, CD40 rs6032660 G/A 0.153 0.03 7.20 × 10−9 MS rs4810485 T/G 1.11 7.70 × 10−16 Ref. 16 0.98 G/T +/+
SLE 1.43 1.00 × 10−8 Ref. 15

Columns indicate: annotated gene name(s) (column 1); association statistics (obtained using a linear mixed model accounting for population structure and hidden relatedness) for the immune traits including trait name, its associated marker, corresponding derived and ancestral alleles, effect size for the derived allele expressed in standard deviation units, its standard error (s.e.) and P value (columns 2–6). Association statistics for pathologies obtained from published papers and comprising disease name, its associated marker, corresponding effect and non-effect alleles, OR for the effect allele and P value (columns 7–11); disease association reference papers (column 12). Correlation between trait-associated and disease-associated markers including LD (r2) between immune trait variant and disease associated variant (column 13), derived immune trait allele and corresponding allele of associated disease variant (column 14), and their corresponding direction of effect. Specifically, ‘+’ indicates increased trait levels or predisposition for the disease, whereas ‘−’ indicates decreased trait levels or protection for disease (column 15). AC, cell absolute count; other acronyms are as in Fig. 3.