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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

   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     
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