Table 2 RA-associated SNPs that are located in cell type-specific FANTOM enhancer regions.
From: Enrichment of Genetic Variants for Rheumatoid Arthritis within T-Cell and NK-Cell Enhancer Regions
Chromosome | Position/bp (NCBI37) | SNP identifier | T cell | NK cell | Dendritic cell | Basophil | Mast cell | Neutrophil | B cell | Intestinal epithelial | N cell types | Locus name/gene symbol | r2 with GWAS lead SNP, European | r2 with GWAS lead SNP, Asian |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 38291337 | rs67704103 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | MTF1/INPP5B | 0.822 | 0.941 |
2 | 30448344 | rs906868 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | LBH | 0.962 | 0.985 |
2 | 204647261 | rs749933 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | CD28 | 0.809 | 0.052 |
4 | 26090375 | rs7441808 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 15 | C4orf52 | 0.874 | 1 |
4 | 26095314 | rs35944082 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0.892 | 1 | |
5 | 55444683 | rs7731626 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | ANKRD55 | (1) | (1) |
6 | 44231479 | rs3799963 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 13 | NFKBIE | 0.969 | 1 |
6 | 138132123 | rs58905141 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | TNFAIP3 | 0.936 | NA |
6 | 138132516 | rs10499197 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 20 | 0.936 | NA | |
6 | 138168028 | rs111883038 | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 6 | 1 | 0.543 | |
6 | 138168083 | rs80126770 | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 6 | 1 | 0.566 | |
6 | 167363948 | rs3798307 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | CCR6 | 0.121 | 0.213 |
6 | 167372978 | rs2149092 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 9 | 0.375 | 0.176 | |
6 | 167411788 | rs239935 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0.373 | 0.405 | |
6 | 167504880 | rs2239826 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 4 | 0.695 | 0.435 | |
6 | 167527644 | rs9347175 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 3 | 0.683 | 0.426 | |
6 | 167527818 | rs6456157 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 3 | 0.683 | 0.426 | |
6 | 167533467 | rs1331299 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0.693 | 0.524 | |
6 | 167534290 | rs3093023 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 2 | 0.957 | 0.831 | |
8 | 11337587 | rs2409780 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | BLK | 0.979 | 0.931 |
9 | 123652898 | rs881375 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 3 | TRAF1/C5 | 0.719 | 0.388 |
9 | 123683106 | rs2109896 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 4 | 0.729 | 0.366 | |
9 | 123696871 | rs10739581 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0.968 | 0.965 | |
10 | 6102757 | rs3118471 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | IL2RA | 0.616 | 0.277 |
10 | 6114856 | rs10905718 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0.556 | 0.25 | |
10 | 6390192 | rs2387397 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 8 | PRKCQ | 0.83 | 0.968 |
10 | 6390450 | rs947474 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 8 | (1) | (1) | |
10 | 8103980 | rs374641 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | GATA3 | 0.962 | 0.888 |
10 | 8103986 | rs386680 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0.967 | 0.888 | |
10 | 8104016 | rs371668 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0.967 | 0.888 | |
11 | 118740864 | rs4936443 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 14 | CXCR5 | 0.599 | 0.473 |
11 | 118740931 | rs4938572 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 14 | 0.599 | 0.344 | |
11 | 118741157 | rs7117261 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 14 | 0.607 | 0.473 | |
11 | 118743286 | rs12365699 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0.501 | 0.184 | |
11 | 118743338 | rs4936444 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0.592 | 0.473 | |
11 | 128498760 | rs7103484 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | ETS1 | 0.152 | 0.105 |
11 | 128498762 | rs7119766 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0.18 | 0.105 | |
14 | 68749927 | rs3784099 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | RAD51B | 0.97 | 1 |
15 | 38903672 | rs16967112 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | RASGRP1 | 0.553 | 0.012 |
15 | 70011941 | rs71393457 | 1 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 7 | LOC145837 | 0.031 | 0 |
15 | 70012293 | rs71393458 | 1 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 7 | 0.031 | 0 | |
15 | 70027568 | rs36124936 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 3 | 0.031 | 0 | |
15 | 70048116 | rs10152590 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 5 | 0.031 | 0 | |
15 | 70048157 | rs10152591 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 5 | |||
16 | 86016401 | rs9927316 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 3 | IRF8 | 0.986 | 0.958 |
17 | 37912377 | rs12946510 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 4 | MED1 | 0.083 | 0.096 |
17 | 37970149 | rs9909593 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 3 | 0.076 | 0.095 | |
18 | 12777573 | rs2542148 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 7 | PTPN2 | 0.326 | 0.233 |
18 | 12777603 | rs2847274 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 7 | 0.312 | 0.233 | |
18 | 12777607 | rs11876290 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 7 | 0.097 | 0.128 |