Table 3. Comparision of the association of SNPs in PTPN22 region with GD in the current study with that in previous reports.
| SNP | Alleles | Case MAF(%) |
Control MAF(%) | Reported P vaule | Study population |
Study first author (reference) |
P value in our GWAS cohort | r2 with the SNP replicated in our cohort | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs3789604 | A>C | 145/828(17.5) | 109/462(23.6) | 0.0085$ | Japanese | Ichimura M (40) | 0.0012 | rs3811021:r2=0.91 | |||
| A>C | 61/352(17.3) | 115/562(20.5) | 0.24 | Japanese | Ban Y (24) | ||||||
| A>C | 181/822(22.0) | 106/624(17.0) | 0.017 | Chinese | Gu LQ (16) | ||||||
| rs3811021 | T>C | 287/1484(19.3) | 259/1396(18.6) | 0.59 | UK Caucasians | Heward JM (35) | 0.0009796 # | ||||
| C>T | 83/422(19.7) | 95/442(21.5) | 0.5 | Koreans* | Lee HS (39) | ||||||
| rs1217413 | T>C | 353/1474(23.9) | 338/1484(22.8) | 0.451 | UK Caucasians | Heward JM (35) | 0.0108 | rs1230647:r2=0.91 | |||
| rs2476599 | G>A | 43/352(12.2) | 76/562(13.5) | 0.57 | Japanese | Ban Y (24) | 0.0913 | ||||
| rs1217388 | C>T | 157/420(37.4) | 148/444(33.3) | 0.21 | Koreans* | Lee HS (39) | 0.0048 | rs1230647:r2=0.97 | |||
| rs3789607 | T>C | 61/828(7.0) | 32/462(7.0) | 0.7692 | Japanese | Ichimura M (40) | 0.1464 | ||||
| T>C | 82/850(9.7) | 64/628(10.2) | 0.729 | Chinese | Gu LQ (16) | ||||||
| rs1310182 | C>T | 663/1412(47) | 644/1422(45.3) | 0.394 | UK Caucasians | Heward JM (35) | 0.8680 | ||||
| T>C | 66/352(18.8) | 109/562(19.4) | 0.81 | Japanese | Ban Y (24) | ||||||
| T>C | 69/424(16.3) | 55/444(12.4) | 0.1 | Koreans* | Lee HS (39) | ||||||
| rs2797415§ | T>C | 140/352(39.8) | 228/562(40.6) | 0.81 | Japanese | Ban Y (24) | |||||
| rs1970559 | T>C | 33/818(4) | 28/630(4.4) | 0.7 | Chinese | Gu LQ (16) | 0.10539 | ||||
| rs2476601§ | C>T | 258/1802(14.3) | 174/1666(10.4) | 6.26×10-4 | UK Caucasians | Smyth D (21) | |||||
| C>T | 151/1098(13.8) | 67/858(7.8) | 3.40×10-5 | Caucasian | Velaga MR (20) | ||||||
| C>T | 112/580(19.3) | 76/620(12.3) | 0·0008 | Polish | Skórka A (36) | ||||||
| C>T | 0(0) | 0(0) | nonpolymorphism | Chinese | Gu LQ (16) | ||||||
| C>T | 0(0) | 0(0) | nonpolymorphism | Japanese | Ban Y (28) | ||||||
| C>T | 63/342(18.4) | 70/400(17.5) | NS | Russian | Zhebrun D (37) | ||||||
| C>T | 68/396(17.2) | 60/396(15.2) | NS | Polish | Jurecka-Lubieniecka B (38) | ||||||
| C>T | 0(0) | 0(0) | nonpolymorphism | Japanese | Ichimura M (40) | ||||||
| rs12730735 | A>G | 392/1374(28.5) | 391/1390(28.1) | 0.815 | UK Caucasians | Heward JM (35) | 0.1615 | ||||
| A>G | 39/422(9.2) | 22/444(5) | 0.01 | Koreans* | Lee HS (39) | ||||||
| rs12760457 | C>T | 23/352(6.5) | 37/562(6.6) | 0.98 | Japanese | Ban Y (24) | 0.1617 | ||||
| rs1217419 | T>G | 117/852(13.7) | 92/630(14.6) | 0.634 | Chinese | Gu LQ (16) | 0.88474 | ||||
| rs2488458 | G>A | 399/1482(26.9) | 362/1436(25.2) | 0.292 | UK Caucasians | Heward JM (35) | 0.0070 | rs1230647: r2=0.97 | |||
| A>G | 298/850(35.1) | 220/630(34.9) | 0.956 | Chinese | Gu LQ (16) | ||||||
| A>G | 163/424(38.4) | 152/444(34.2) | 0.19 | Koreans* | Lee HS (39) | ||||||
| rs2488457§ | C>G | 339/828(40.9) | 202/462(43.7) | 0.3318 | Japanese | Ichimura M (40) | |||||
| C>G | 259/796(32.5) | 222/630(35.2) | 0.284 | Chinese | Gu LQ (16) | ||||||
Note: §, The SNPs was not included in our GWAS cohort; *, The study includes 212 AITD (128 Hashimoto’s thyroiditis and 84 Graves’disease) patients, and 225 ethnically matched healthy controls; $, Corrected p-values (Pc)=0.034; #, This SNP did not showed significant difference between GD and controls in our replicaiton stage; NS: non-significant. The P value reported less than 0.05 were highlighted in bold.