Table 4. Detailed annotation information on the SLE-associated single nucleotide polymorphisms and their proxies.
| Lead SNP | Annotated gene | Proxies (r2 in ASN) | RegulomeDB score | HaploReg v4.11 |
rSNPBase |
cis-eQTL |
||||
|---|---|---|---|---|---|---|---|---|---|---|
| Promoter/Enhancer histone marks and DNAse | Proteins bound | Regulatory motifs | rSNP | Proxy/Distal regulation | seeQTL2 (q value) | Selected eQTL hit3 (P value) | ||||
| rs564799 | IL12A | rs485789 (1) | 2b | 9 | 9 | 4 | yes | yes | 4.16 × 10−2 | 2.93 × 10−12 |
| rs564799 | IL12A | rs4680536 (0.96) | 4 | 6 | 0 | 2 | no | no | 4.59 × 10−2 | 7.66 × 10−13 |
| rs564799 | IL12A | rs485499 (0.97) | 4 | 24 | 4 | 0 | no | no | — | 4.57 × 10−12 |
| rs564799 | IL12A | rs4679867 (1) | 5 | 3 | 0 | 0 | yes | yes | — | 4.57 × 10−12 |
| rs564799 | IL12A | rs564799 (1) | 5 | 2 | 0 | 0 | yes | yes | 0.18 | 2.93 × 10−12 |
| rs564799 | IL12A | rs564976 (1) | 5 | 3 | 0 | 1 | yes | yes | — | 2.69 × 10−12 |
| rs564799 | IL12A | rs589446 (1) | 6 | 0 | 0 | 4 | yes | yes | — | 3.09 × 10−12 |
| rs564799 | IL12A | rs55740284 (0.93) | no evidence | 0 | 0 | 1 | yes | yes | — | — |
| rs7726414 | TCF7 | rs4388254 (1) | 4 | 17 | 0 | 0 | no | no | — | — |
| rs7726414 | TCF7 | rs7726414 (1) | 4 | 12 | 1 | 4 | no | no | — | — |
| rs7726414 | TCF7 | rs6874758 (0.98) | 5 | 9 | 0 | 5 | no | no | — | — |
| rs7726414 | TCF7 | rs10077437 (0.98) | 6 | 1 | 0 | 2 | no | no | — | — |
| rs7726414 | TCF7 | rs10463912 (0.89) | no evidence | 0 | 0 | 5 | no | no | — | — |
(A) ASN: Asian; eQTL: expression quantitative locus; rSNP: regulatory single nucleotide polymorphism; SLE: systemic lupus erythematosus; SNP: single nucleotide polymorphism.
(B) 1The numbers indicate cell types with experimentally validated regulatory elements. 2SeeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information (http://www.bios.unc.edu/research/genomic_software/seeQTL/). 3The selected eQTL hit in this study was driven by the analysis results of mRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project (PMID: 24037378).