Table 2

SNPs associated with dermatomyositis, polymyositis or IIM

PhenotypeChrSNPPosition (hg19)Locus*p ValueRisk/non-risk alleleRAF casesRAF controlsβp HeterogeneityDisease association for non-HLA SNPs3
DM 6 rs116152465 32603007 5′ HLA-DQA1 1.48542E-05 G/A 0.25667 0.20135 0.40 0.31  
DM 19 rs2304256 10475652 TYK2 0.00020 C/A 0.75478 0.7067 −0.25 0.59 T1DM
DM 6 rs114424451 32413051 3’ HLA-DRA1 0.00021 G/A 0.91272 0.86887 0.34 0.99  
DM 8 rs13277113 11349186 5’ BLK 0.00045 A/G 0.28098 0.24403 0.25 0.54 SLE
DM 8 rs2618476 11352541 BLK 0.00062 C/T 0.28903 0.25312 0.24 0.56 SLE
DM9rs70206734291747GLIS30.0023C/G0.535830.49292−0.180.64T1DM
DM5rs685921955438580ANKRD550.0023C/A0.823040.79178−0.240.80RA
DM2rs1338573133701890RASGRP30.0049T/C0.9479720.928019−0.380.67SLE
DM12rs11171739564706255’ ERBB30.0069T/C0.624210.571020.280.09T1DM
DM3rs11712165119118796ARHGAP310.0071G/T0.402450.380660.160.85Celiac
DM2rs102103022341588395’ ATG16L10.0094C/T0.512590.46989−0.170.36Crohn's
PM 6 rs116152465 32603007 5’ HLA-DQA1 0.00044 G/A 0.33252 0.20135 0.76 0.01  
PM6rs114424451324130513’ HLA-DRA10.0033G/A0.9109760.868870.350.53
PM6rs61567232574171Intergenic (HLA-DRB1)0.0035C/G0.515850.357320.520.01
PM14rs490038498498951Intergenic (c14orf64)0.0072A/G0.670730.714150.230.74T1DM
IIM 6 rs114424451 32413051 3’ HLA-DRA1 9.09513E-06 G/A 0.912097 0.86887 0.35 0.88  
IIM 6 rs116152465 32603007 5’ HLA-DQA1 1.04525E-05 G/A 0.28442 0.20135 0.51 0.06  
IIM 19 rs2304256 10475652 TYK2 0.00027 C/A 0.74672 0.7067 −0.21 0.51 T1DM
IIM12rs11171739564706255’ ERBB30.0054T/C0.627530.571020.300.02T1DM
IIM11rs6590330128311059Intergenic (ETS1)0.0064A/G0.129310.102790.220.65SLE
IIM17rs722110938770286Intergenic (SMARCE1)0.0071T/C0.378820.34209−0.150.44T1DM
IIM2rs102103022341588395’ ATG16L10.0071C/T0.505030.46989−0.140.45Crohn's
IIM8rs13277113113491865’ BLK0.0077A/G0.271010.244030.210.24SLE
IIM3rs11712165119118796ARHGAP310.0080G/T0.397230.380660.140.80Celiac
IIM8rs261847611352541BLK0.0082C/T0.2790.253120.200.27SLE
  • SNPs in bold reached Bonferroni significance.

  • *Gene is annotated where closest gene is <10 kb, otherwise annotated as intergenic with closest gene in parentheses. Chr, chromosome; DM, dermatomyositis; HLA, human leukocyte antigen; IIM, idiopathic inflammatory myopathy; PM, polymyositis; p value, p value from random-effects meta-analysis; p heterogeneity, p value of test for heterogeneity; β, effect size (META V.1.5); RA, rheumatoid arthritis; RAF, risk allele frequency; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism; T1DM, type 1 diabetes mellitus.