Skip to main content

Table 1 Identified risk loci for RA with less than three credible SNPs and the cell type in which they are active

From: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability

Locus Chr Number of credible SNPs (> posterior prior 0.001) Posterior probability top SNP Total posterior probability top 3 SNPs SNP category Number of SNPs in 30% of FLS enhancers (posterior > 0.001) Number of SNPs in 30% of T cell enhancers (posterior > 0.001) Number of SNPs in 30% of B cell enhancers (posterior> 0.001) FLS, T, B, ALL, NONE (based on posteriors of SNPs in enhancers) Top posterior rs numbers
4 chr1 10 0.53 0.94 1 1 0 0 FLS rs4839319, rs4839318, rs77227025
5 chr1 2 0.91 0.99 1 0 0 0 B CELL rs6679677, rs2476601
7 chr1 10 0.25 0.62 1 0 0 0 NONE rs624988, rs771587, rs12137270, rs12405671, rs11586238
10 chr2 9 0.21 0.59 1 2 3 2 ALL rs10175798, rs10173253, rs906868, rs7579944, rs1355208
17 chr2 4 0.43 0.92 1 0 2 0 T CELL rs231724, rs231723, rs231775
20 chr3 13 0.34 0.82 1 4 2 3 ALL rs73081554, rs185407974, rs180977001, rs35677470, rs114584537
24 chr5 1 1 1 1 0 1 0 T CELL rs7731626
29 chr6 8 0.23 0.67 1 0 0 0 NONE rs17264332, rs11757201, rs6920220, rs6927172
30 chr6 15 0.42 0.86 1 2 5 3 NONE rs58721818, rs61117627
32 chr6 9 0.32 0.71 1 0 5 0 T CELL, B CELL rs1571878, rs3093017, rs10946216
40 chr9 3 0.37 0.98 1 0 0 0 NONE rs11574914, rs2812378, rs10972201
42 chr10 6 0.73 0.87 1 0 0 0 T CELL rs706778, rs10795791
44 chr10 10 0.21 0.49 1 0 10 0 T CELL rs537544, rs568727, rs570613 , rs570730, rs7897792
46 chr10 10 0.37 0.73 1 9 1 0 ALL rs12764378, rs71508903, rs77509998
60 chr15 5 0.26 0.74 1 0 0 0 NONE rs919053, rs8026898, rs7170107, rs16953656, rs8043362
62 chr16 9 0.29 0.82 1 0 0 0 B CELL rs13330176, rs2139492, rs2139493
66 chr19 2 0.6 1 1 0 0 0 NONE rs74956615, rs34536443
70 chr21 19 0.56 0.93 1 3 1 0 FLS rs8133843, rs8129030, rs9979383
73 chr22 9 0.29 0.74 1 0 0 2 B CELL rs2069235, rs909685, rs9611155
1 chr1 81 0.29 0.38 2 1 1 1 NONE rs187786174, rs60733400, rs876938
2 chr1 13 0.29 0.52 2 0 0 0 NONE rs2240336, rs12737739, rs13375202
3 chr1 36 0.43 0.51 2 1 0 0 FLS rs28411352, rs28489009, rs2306627
6 chr1 29 0.22 0.42 2 0 2 4 B CELL rs1217404, rs2476604, rs1217420
11 chr2 13 0.18 0.4 2 1 1 1 ALL rs34695944, rs56095903, rs67574266, rs13031237, rs13031721
13 chr2 17 0.27 0.63 2 0 0 1 NONE rs9653442, rs6712515, rs11676922, rs1160542, rs10865035
18 chr3 63 0.27 0.55 2 0 0 0 NONE rs4452313, rs4416363 , rs7617779
19 chr3 11 0.21 0.48 2 1 1 0 T CELL, B CELL rs9310852, rs4680838, rs9880772, rs1353286
22 chr4 49 0.2 0.29 2 0 0 0 NONE rs7660626, rs13142500, rs6831973
31 chr6 13 0.17 0.49 2 0 2 2 B CELL rs2451258, rs2485363, rs654690 , rs1994564, rs212389
33 chr7 47 0.24 0.47 2 3 1 2 ALL rs186735625, rs57585717, rs2158624
36 chr8 20 0.08 0.23 2 3 1 0 FLS, B CELL rs2736337
38 chr8 11 0.15 0.39 2 1 0 0 FLS rs678347, rs507201, rs657425
43 chr10 17 0.27 0.45 2 0 3 2 T CELL, B CELL rs947474, rs10796038, rs10796040
45 chr10 44 0.36 0.54 2 0 2 0 NONE rs12413578, rs144536148, rs186856025
47 chr11 59 0.47 0.53 2 4 2 5 NONE rs12574838, rs331463
51 chr11 17 0.12 0.36 2 2 8 0 NONE rs4936059, rs11221402, rs7106876
54 chr12 22 0.22 0.51 2 0 1 1 T CELL, B CELL rs10774624, rs3184504, rs7310615
56 chr14 12 0.13 0.37 2 3 2 0 ALL rs1950897, rs911263, rs1885013, rs2104047, rs3784099
57 chr14 21 0.22 0.45 2 7 10 6 ALL rs7146217, rs36045050, rs11158764
58 chr15 17 0.25 0.48 2 1 12 2 T CELL, B CELL rs8032939, rs8043085, rs4924273
61 chr16 18 0.08 0.23 2 0 0 0 NONE rs11075010, rs1579258, rs4584833
63 chr17 39 0.49 0.67 2 0 0 6 NONE rs7224929, rs58483057, rs2071456
67 chr20 11 0.32 0.59 2 1 1 1 ALL rs4239702, rs4810485, rs1883832
71 chr21 37 0.32 0.6 2 0 26 0 T CELL rs1893592, rs225433, rs11203203
72 chr22 103 0.24 0.26 2 9 20 22 T CELL, B CELL rs11089637, rs11089620, rs5754387