Table 2 Results from the rheumatoid arthritis GWAS: comparison between AV and WP haplotype blocks and single-SNP analyses
From: Efficient haplotype block recognition of very long and dense genetic sequences
| Â | Â | Block | Top SNP | ||||
|---|---|---|---|---|---|---|---|
Locus | Partition method | Chr:start-end | # sign. SNPs | # SNPs | P-value | Name | P-value |
Genome-wide significant blocks that include genome-wide significant SNPs | |||||||
1 | AV & WP | 6:32,055,439-32,182,782 | 2 | 15 | 2.71 × 10 -12 | rs2239689 | 1.55 × 10 -8 |
2 | AV & WP | 6:32,204,222-32,259,421 | 1 | 14 | 1.32 × 10 -16 | rs3134943 | 5.41 × 10 -8 |
3 | AV & WP | 6:32,317,005-32,319,063 | 2 | 3 | 1.25 × 10 -8 | rs412657 | 2.17 × 10 -10 |
4 | AV | 6:32,323,166-32,328,663 | 4 | 6 | 1.99 × 10 -15 | rs9267992 | 1.14 × 10 -11 |
|  | AV | 6:32,331,236-32,390,832 | 4 | 14 | 2.34 × 10 -33 | rs6910071 | 1.92 × 10 -32 |
|  | WP | 6:32,323,166-32,331,236 | 5 | 7 | 1.32 × 10 -17 | rs3130320 | 7.50 × 10 -17 |
|  | WP | 6:32,332,366-32,390,832 | 3 | 13 | 1.38 × 10 -33 | rs6910071 | 1.92 × 10 -32 |
5 | AV & WP | 6:32,397,296-32,445,664 | 13 | 24 | 3.00 × 10 -24 | rs547077 | 2.60 × 10 -18 |
6 | AV & WP | 6:32,454,772-32,471,794 | 7 | 9 | 4.88 × 10 -27 | rs3817973 | 5.48 × 10 -26 |
7 | AV & WP | 6:32,474,399-32,476,065 | 1 | 3 | 2.00 × 10 -23 | rs3817963 | 8.55 × 10 -23 |
8 | AV & WP | 6:32,477,466-32,481,676 | 1 | 3 | 7.75 × 10 -21 | rs3806156 | 9.43 × 10 -14 |
9 | AV & WP | 6:32,483,951-32,491,086 | 5 | 8 | 7.93 × 10 -38 | rs3763312 | 7.00 × 10 -34 |
10 | AV & WP | 6:32,491,201-32,509,057 | 6 | 8 | 5.10 × 10 -41 | rs2395163 | 6.14 × 10 -37 |
11 | AV & WP | 6:32,509,195-32,514,320 | 6 | 8 | 1.80 × 10 -37 | rs2395175 | 1.83 × 10 -39 |
12 | AV & WP | 6:32,519,501-32,521,295 | 3 | 3 | 1.79 × 10 -27 | rs7192 | 2.64 × 10 -26 |
13 | WP | 6:32,522,251-32,535,767 | 2 | 2 | 1.10 × 10 -28 | rs9268832 | 4.07 × 10 -25 |
14 | AV & WP | 6:32,541,145-32,713,862 | 7 | 12 | 2.23 × 10 -47 | rs660895 | 2.60 × 10 -45 |
15 | AV | 6:32,760,295-32,766,057 | 2 | 5 | 4.99 × 10 -26 | rs9275184 | 1.49 × 10 -18 |
|  | WP | 6:32,735,692-32,762,692 | 3 | 4 | 8.33 × 10 -35 | rs9275184 | 1.49 × 10 -18 |
|  | WP | 6:32,763,196-32,766,057 | 1 | 3 | 3.33 × 10 -23 | rs7774434 | 5.43 × 10 -10 |
16 | AV & WP | 6:32,766,602-32,785,130 | 26 | 37 | 1.71 × 10 -40 | rs9275224 | 1.31 × 10 -37 |
17 | AV & WP | 6:32,786,977-32,790,115 | 6 | 10 | 9.32 × 10 -50 | rs9275595 | 1.97 × 10 -28 |
18 | AV & WP | 6:32,792,235-32,827,644 | 2 | 23 | 2.94 × 10 -19 | rs3916765 | 2.72 × 10 -9 |
19 | AV | 6:32.912,776-32,912,887 | 1 | 2 | 1.46 × 10 -8 | rs3819721 | 5.74 × 10 -9 |
|  | WP | 6:32,912,392-32,912,776 | 1 | 2 | 9.89 × 10 -10 | rs3819721 | 5.74 × 10 -9 |
|  | WP | 6:32,912,887-32,912,912 | 0 | 2 | 7.18 × 10 -11 | rs241425 | 7.53 × 10-4 |
20 | AV & WP | 9:81,662,684-81,666,969 | 1 | 2 | 2.72 × 10 -8 | rs7854383 | 3.23 × 10 -8 |
Genome-wide significant blocks with no corresponding genome-wide significant SNPs | |||||||
21 | AV & WP | 2:219,728,763-219,836,597 | 0 | 17 | 1.57 × 10 -7 | rs1052483 | 2.02 × 10-4 |
22 | AV | 6:31,723,146-31,726,740 | 0 | 3 | 3.17 × 10-7 | rs3130050 | 5.27 × 10-5 |
|  | WP | 6:31,723,146-31,726,740 | 0 | 3 | 2.98 × 10 -7 | rs3130050 | 5.27 × 10-5 |
23 | AV & WP | 6:31,728,499-31,777,475 | 0 | 10 | 4.11 × 10 -8 | rs2280800 | 1.28 × 10-4 |
24 | AV | 6:31,910,520-31,953,964 | 0 | 10 | 8.66 × 10 -8 | rs9267658 | 1.22 × 10-5 |
|  | WP | 6:31,885,925-31,945,256 | 0 | 8 | 1.08 × 10-5 | rs2075800 | 3.58 × 10-5 |
|  | WP | 6:31,946,420-31,953,964 | 0 | 5 | 1.73 × 10-6 | rs9267658 | 1.22 × 10-5 |
25 | AV | 6:31,958,311-31,959,213 | 0 | 2 | 6.00 × 10-1 | rs652888 | 1.48 × 10-2 |
|  | AV | 6:31,968,316-32,026,839 | 0 | 10 | 1.53 × 10-5 | rs1042663 | 7.47 × 10-7 |
|  | WP | 6:31,959,213-32,026,839 | 0 | 11 | 4.59 × 10 -8 | rs1042663 | 7.47 × 10-7 |
26 | AV & WP | 6:32,027,809-32,038,441 | 0 | 5 | 1.43 × 10 -9 | rs437179 | 2.20 × 10-5 |
27 | AV & WP | 6:32,262,976-32,263,559 | 0 | 2 | 8.89 × 10 -9 | rs204994 | 1.83 × 10-4 |
28 | AV & WP | 6:32,296,361-32,298,006 | 0 | 4 | 1.47 × 10 -10 | rs3132946 | 1.51 × 10-7 |
29 | AV & WP | 6:32,300,538-32,303,337 | 0 | 5 | 6.87 × 10 -10 | rs499691 | 5.62 × 10-4 |
30 | AV | 6:32,870,369-32,889,502 | 0 | 12 | 4.33 × 10 -10 | rs7767167 | 2.61 × 10-4 |
|  | WP | 6:32,871,088-32,889,502 | 0 | 11 | 3.77 × 10 -10 | rs7767167 | 2.61 × 10-4 |
31 | AV | 6:32,912,776-32,912,887 | 1 | 2 | 1.46 × 10 -8 | rs3819721 | 5.74 × 10 -9 |
|  | WP | 6:32,912,392-32,912,776 | 1 | 2 | 9.89 × 10 -10 | rs3819721 | 5.74 × 10 -9 |
|  | WP | 6:32,912,887-32,912,912 | 0 | 2 | 7.18 × 10 -11 | rs241425 | 7.53 × 10-4 |
32 | AV & WP | 6:33,012,959-33,069,082 | 0 | 21 | 8.10 × 10 -8 | rs3135034 | 5.13 × 10-5 |
Genome-wide significant SNPs with no corresponding genome-wide significant blocks | Â | Â | Â | Â | |||
33 | AV & WP | 1:18,189,820-18,200,270 | 1 | 8 | 1.81 × 10-5 | rs16861613 | 5.08 × 10 -8 |
34 | AV & WP | 6:32,307,122-32,313,088 | 2 | 5 | 2.04 × 10-6 | rs9267873 | 3.98 × 10 -8 |
35 | AV | 10:112,614,407-112,822,215 | 1 | 23 | 5.73 × 10-7 | rs3750619 | 8.29 × 10 -10 |
|  | WP | 10:112,614,407-112,749,598 | 0 | 18 | 3.37 × 10-7 | rs3750619 | 8.29 × 10 -10 |
|  | WP | 10:112,754,584-112,822,215 | 0 | 5 | 1.89 × 10-1 | rs10787298 | 1.10 × 10-1 |
36 | AV & WP | 17:34,570,514-34,575,487 | 1 | 5 | 1.40 × 10-1 | rs593772 | 5.50 × 10 -9 |
37 | AV & WP | 17:63,271,780-63,418,511 | 1 | 8 | 3.26 × 10-1 | rs7502707 | 2.02 × 10 -8 |