Table 3.
Genotype-Immune Phenotype Correlations for Known Immune Disease Susceptibility Loci
| Chr | Pos | rsID | EA | NEA | EAF | BETA (SE) | p value | Trait | Disease | Variants | Genes |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 204690355 | rs231746 | C | G | 0.49 | 0.29 (0.06) | 4.68 × 10−6 | CD8+ IL2+ | RA (+) | rs231735∗T | CTLA4 |
| 3 | 18752031 | rs55845060 | C | T | 0.17 | 0.35 (0.08) | 8.02 × 10−5 | TNF-α | Ps (+) | rs68080462∗C | SATB1 |
| 6 | 32590924 | rs3129763 | A | G | 0.26 | 0.35 (0.08) | 2.93 × 10−5 | lymphocyte | SSc (+) | rs3129763 | HLA class II |
| 6 | 32680928 | rs7765379 | T | G | 0.11 | 0.51 (0.10) | 8.90 × 10−7 | TNF-α | RA, CD, EF (+) | rs7765379 | HLA class II |
| 6 | 33037085 | HLA-DPA1∗0103 | P | A | 0.80 | 0.32 (0.08) | 6.73 × 10−5 | memory B | hepatitis B (−) | HLA-DPA1∗0103 | HLA-DPA1 |
| 6 | 135424203 | rs6930223 | G | T | 0.54 | −0.48 (0.12) | 8.39 × 10−5 | CD8+ GM-CSF+ | HL (+) | rs7745098∗G | HBS1L-MYB |
| 10 | 94502244 | rs11187157 | C | T | 0.43 | 0.29 (0.07) | 4.30 × 10−5 | mDCs | IBD (+) | rs11187157∗C | KIF11-HHEX |
| 10 | 94436851 | rs7911264 | T | C | 0.53 | 0.31 (0.06) | 3.98 × 10−6 | mDCs | IBD (+) | rs7911264∗C | KIF11-HHEX |
| 12 | 26691549 | rs9668498 | A | G | 0.25 | 0.30 (0.08) | 6.22 × 10−5 | TNF-α | KB (+) | rs10842750∗A | ITPR2 |
| 15 | 78785944 | rs373948468 | ATT | AT | 0.31 | 0.54 (0.12) | 2.17 × 10−5 | plasmablast | COPD (+) | rs17484524∗G, rs7181486∗C | IREB2 |
| 16 | 11223454 | rs11645657 | C | G | 0.45 | 0.59 (0.12) | 4.89 × 10−6 | transitional B | AD, HF, asthma (+) | rs2041733∗T | CLEC16A |
| 16 | 50756881 | rs2076756 | G | A | 0.32 | −0.31 (0.08) | 7.63 × 10−5 | CD8+ naive | CD (+) | rs2076756∗G | NOD2 |
| 20 | 62347191 | rs62217799 | T | G | 0.69 | −0.29 (0.07) | 4.47 × 10−5 | memory B | CD (+) | rs4809330∗G | TNFRSF6B-RTEL1 |
Suggestive (p < 10−4) genotype-immune phenotype correlations in LD (r2 > 0.8) with established immune disease susceptibility SNPs (+, susceptibility; −, protection). See also Tables S4 and S6 for all non-HLA and HLA suggestive associations, respectively, and Table S5 for all suggestive associations in LD with a variant for any disease in the EBI GWAS catalog. BETA, effect; EA, effect allele (P indicates present and A absent for HLA allele); EAF, effect allele frequency; NEA, non-effect allele; Pos, position in GRCh37; rsID, reference SNP identification; SE, standard error. Traits and disease associations: AD, atopic dermatitis (Paternoster et al., 2015), asthma (Paternoster et al., 2015); CD, Crohn disease (Franke et al., 2010, Yamazaki et al., 2013); COPD, chronic obstructive pulmonary disorder obstruction (Lee et al., 2015, Lutz et al., 2015); EF, enteric fever (Dunstan et al., 2014), hepatitis B (Kamatani et al., 2009); HF, hay fever (Paternoster et al., 2015); HL, Hodgkin lymphoma (Frampton et al., 2013); IBD, inflammatory bowel disease (Jostins et al., 2012, Liu et al., 2015); KB, Kashin-Beck disease (Zhang et al., 2015a); mDCs, myeloid dendritic cells; Ps, psoriasis (Baurecht et al., 2015); RA, rheumatoid arthritis (Freudenberg et al., 2011, Gregersen et al., 2009); SSc, systemic sclerosis (Gorlova et al., 2011).