Table 1.
Genome-wide suggestive significant (p-value < 1 E-05) variants associated with RA in total study cohort and Prakriti specific RA groups. The significance status of these SNPs in other groups are also shown. Positions refer to assembly GRCh37.
| SNP | Chr | Position | Location | Gene/Nearest gene | Risk allele | PGWASTotal | OR (95% CI)* | PGWASVata | OR (95% CI)* | PGWASPitta | OR (95% CI)* | PGWASKapha | OR (95% CI)* |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total study cohort | |||||||||||||
| rs340575 (C>A) | 13 | 72876358 | intergenic | MZT1 | C | 9.707E-08 | 6.52 (2.91-14.62) | 0.21 | 2E-05 | 0.003 | |||
| rs10056189 (C>T) | 5 | 145804118 | intergenic | TCERG1 | C | 1.394E-06 | 3.41 (2.02-5.78) | 0.05 | 0.0008 | 0.01 | |||
| rs4956041 (C>T) | 4 | 109113914 | intron | LEF1-AS1 | T | 2.105E-06 | 1.92 (1.47-2.51) | 0.01 | 0.01 | 0.006 | |||
| rs4983599 (G>A) | 14 | 105011436 | intron | TMEM179 | A | 2.591E-06 | 2.13 (1.55-2.93) | 0.05 | 0.0005 | 0.06 | |||
| rs2867116 (C>A) | 2 | 682363 | upstream | TMEM18 | C | 4.734E-06 | 4.56 (2.26-9.23) | 0.0001 | 0.02 | 0.02 | |||
| rs7556762 (T>G) | 2 | 101765922 | intron | TBC1D8 | T | 6.651E-06 | 2.41 (1.63-3.55) | 0.01 | 0.002 | 0.06 | |||
| rs4548807 (G>A) | 14 | 105040988 | intron | TMEM179 | A | 7.633E-06 | 2.12 (1.53- 2.96) | 0.003 | 0.007 | 0.06 | |||
| rs3782690 (T>G) | 12 | 106464063 | intron | NUAK1 | T | 8.948E-06 | 1.84 (1.41-2.42) | 0.2 | 0.005 | 0.0008 | |||
| Vata | |||||||||||||
| rs1953175 (G>T) | 9 | 13505851 | intergenic | RP11-536O18.1 | T | 0.2 | 3.684E-06 | 6.41 (2.87-14.34) | 0.2 | 0.3 | |||
| rs4352629 (C>T) | 5 | 87756821 | intron | CTC-498M16.4 | T | 0.3 | 7.028E-06 | 5.64 (2.63-12.08) | 0.7 | 0.1 | |||
| rs7448716 (A>G) | 5 | 87752695 | intron | CTC-498M16.4 | G | 0.2 | 7.028E-06 | 5.64 (2.63-12.08) | 0.7 | 0.1 | |||
| Pitta | |||||||||||||
| rs11625685 (T>C) | 14 | 52931884 | intron | TXNDC16 | C | 5E-05 | 0.4 | 1E-06 | 4.50 (2.35-8.61) | 0.2 | |||
| rs11623917 (A>G) | 14 | 52921896 | intron | TXNDC16 | G | 0.0001 | 0.5 | 2E-06 | 4. 37 (2.28-8.38) | 0.3 | |||
| rs9527038 (A>G) | 13 | 53503775 | intergenic | PCDH8 | G | 0.003 | 0.5 | 4E-06 | 2.48 (1.69-3.64) | 0.8 | |||
| rs4620912 (C>T) | 15 | 86389516 | intergenic | KLHL25 | T | 4E-05 | 0.5 | 5E-06 | 2.80 (1.8-4.37) | 0.5 | |||
| rs10849264 (A>G) | 12 | 5531307 | intergenic | NTF3 | G | 0.0003 | 0.3 | 5E-06 | 2.35 (1.62-3.39) | 0.7 | |||
| rs1390079 (T>C) | 4 | 125523042 | intergenic | RP11-93I21.3 | C | 0.007 | 0.5 | 5E-06 | 13.32 (3.09-57.45) | 0.3 | |||
| rs7323558 (C>T) | 13 | 37250048 | intron | SERTM1 | T | 0.002 | 0.9 | 9E-06 | 2.305 (1.60-3.33) | 0.7 | |||
| Kapha | |||||||||||||
| rs3120029 (G>A) | 9 | 129649356 | downstream | ZBTB34 | A | 0.2 | 0.4 | 0.2 | 6E-06 | 4.243 (2.21-8.16) | |||
| rs9512378 (A>G) | 13 | 27363688 | intergenic | GPR12 | A | 0.01 | 0.8 | 0.7 | 7E-06 | 4.60 (3.31-9.15) | |||
| rs11762117 (C>A) | 7 | 20391383 | intron | ITGB8 | C | 0.02 | 0.3 | 0.6 | 9E-06 | 8.74 (2.93-26.03) | |||
*Odds Ratio (OR) shown for genome-wide suggestively significant SNPs.