Table 2.
Summary of SLE association and functional characteristics of peak variants and functional haplotypes for 16 SLE risk loci.
| Gene | Known GWAS (tag) SNP | GWAS reference | GWAS (tag) SNP OR | Study peak SNP |
Study peak SNP OR | Peak risk- associated functional haplotype |
Risk haplotype OR | Increase in OR of haplotype versus GWAS SNP | Increase in OR of haplotype versus study peak SNP |
Related Figure in the manuscript | Strongest ENCODE effect cell line/ tissue |
eQTL data cell type/tissue |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| STAT4 | rs7574865 | Lee et al., 2012 | 1.4 | rs12612769 | 1.7 | ATTCCTTGC | 1.7 | 0.3 | 0 | Figure 4 | Mammary gland, Epithelial | Monocyte, macrophage |
| HLA-D | rs1150754 | Taylor et al., 2011 | 1.54 | rs9271593 (XL9) | 1.6910364 | CCCCTCCATC_TAGCGATGGCG AGCATCGTCA |
2.1 | 0.56 | 0.4089636 | Figure 8C-F | B-lymphocyte, lymphoblastoid | Monocyte |
| ITGAM-ITGAX | rs9888739 | Harley et al., 2008 | 1.6 | rs41476751 | 1.8696398 |
AAGCATC TAGTCTT GTCTACAA TAGTCTCTC |
1.95 | 0.35 | 0.0803602 | Figure 10.i | B-lymphocyte, lymphoblastoid | Monocyte, Peripheral blood |
| IRF5-TNPO3 | rs12531711 | Chung et al., 2011 | 1.5 | rs34350562 | 1.7593583 |
GAGTT TTCAGTCTA AGCAGT GGTCAGAAC |
1.8 | 0.3 | 0.0406417 | Figure 10.ii | Epithelial cell (Lung), B-lymphocyte | Monocyte, macrophage |
| UBE2L3 | rs5754217 | Chung et al., 2011 | 1.3 | rs181366 | 1.5217361 | TCAGTTCAC TCCTCTG |
1.4 | 0.10 | -0.1140361 | Figure 10.iii | Epithelial cell (Lung), B-lymphocyte | Monocyte |
| BANK1 | rs10516487 | Kozyrev et al., 2008 | 1.3 | rs4699260 | 1.25 | ATCTCGACGCA TGCGGA TTGGAAC |
1.3 | 0 | 0.05 | Figure 10.iv | Hela-S3, Epithelial, Fibroblast | Monocyte |
| TNIP1 | rs10036748 | Han et al., 2009; Galimberti et al., 2008 | 1.2 | rs62382335 | 1.37 | AATACGGTC | 1.3 | 0.12 | -0.05 | Figure 11.i | B-lymphocyte, lymphoblastoid | Peripheral blood |
| TNFAIP3 | rs5029939 | Graham et al., 2008 | 2.2 | rs57087937 | 1.9092441 | GGGCAATCT TTGGGGCAAAT |
2.2 | 0.04 | 0.3307559 | Figure 11.ii | B-lymphocyte, lymphoblastoid, hepatocyte | no data |
| CCL22-CX3CL1 | rs223889 | Galimberti et al., 2008 | 1.4 | rs223889 | 1.45 | TATAAAGC | 1.5 | 0.05 | 0 | Figure 11.iii | B-lymphocyte, lymphoblastoid | Monocyte |
| ZGLIP-RAVER1 | rs35186095 | Present study |
1.3 | rs35186095 | 1.3173789 | TATAGTCT GTAGGATG |
1.5 | 0.2 | 0.1826211 | Figure 11.iv | Fibroblast, K-562, HeLa-S3, B-lymphocyte | Monocyte |
| ICA1 | rs10156091 | Harley et al., 2008 | 1.3 | rs74787882 | 1.5 | GGGT | 1.5 | 0.2 | 0 | Figure 12.i | B-lymphocyte, lymphoblastoid | no data |
| BLK | rs13277113 | Hom et al., 2008 | 1.3 | rs7822109 | 1.26 | ATTTGCCCCA | 1.3 | 0 | 0.04 | Figure 12.ii | B-lymphocyte, lymphoblastoid | Monocyte, Peripheral blood |
| ETS1 | rs7932088 | Yang et al., 2010 | 1.2 | rs34516251 | 1.23 | GGGCGA | 1.4 | 0.2 | 0.17 | Figure 12.iii | B-lymphocyte, lymphoblastoid, Epithelial | Monocyte |
| TNFSF4 | rs2205960 | Han et al., 2009 | 1.3 | rs4916313 | 1.3 | TCCATCTTCGA | 1.3 | 0 | 0 | Figure 13.i | Epithelial cell (Lung), Fibroblast, HeLa-S3 | no data |
| NMNAT2-SMG7 | rs2022013 | Cunninghame Graham et al., 2011 | 1 | rs111487113 | 1.3 | TCACTAAC | 1.3 | 0.3 | 0 | Figure 13.ii | Primary Th1 T cells | no data |
| XKR6 | rs11783247 | Harley et al., 2008 | 1.2 | rs7000132 | 1.2 | TGTCGCGGCTT | 1.2 | 0.03 | 0.03 | Figure 13.iii | Neuroblastoma, Mammary gland, Fibroblast | Monocyte |