Table III. cis Genes associated with 24 T1D SNPs with minimum FDR p < 0.001
IDT1D SNPs (Effect Allele)GeneEBV-B BasalEBV-B PMACD4+CD8+
6rs2165738 (C)ADCY3↓ **↓ ***↓ ****ns
7rs363609 (C)INO80Bns↓ ****nsns
9rs6543134 (C)IL18R1↓ ***↓ ****nsns
12rs3731865 (C)SLC11A1nsns↑ ***ns
17rs56297233 (T)LYRM2ns↑ ***nsns
18rs9388489 (C)C6orf173nsns↓ **↓ ***
19rs10499194 (C)IFNGR1↑ ****nsnsns
21rs7804356 (T)SKAP2↓ ***↓ ***↓ ***↓ **
22rs10272724 (T)IKZF1↑ ****↑ *↑ ****↑ **
27rs10509540 (T)C10orf59nsns↑ ***ns
29rs3764021 (T)CLEC2D↑ ****↑ ****nsns
rs10466829 (T)CLECL1nsns↓ ****↓ ****
30rs705704 (T)SUOX↓ **ns↓ ****↓ *
rs2292239 (T)ERBB3nsnsns↓ ****
32rs10877012 (C)FAM119B↓ ****↓ ****↓ ****↓ ****
TSFM↑ ****↑ *nsns
XRCC6BP1↑ **↑ ***nsns
39rs17574546 (C)RASGRP1↑ ****↑ ***nsns
40rs3825932 (C)CTSH↑ ****↑ ****nsns
41rs416603 (T)C16orf75↓ ****↓ ****↑ ****↑ **
42rs4788084 (C)LOC728734↓ ****↓ ****↓ ****↓ ****
SPNS1↓ ****nsns↓ *
TUFMnsns↓ ***ns
45rs2290400 (T)ORMDL3↑ ****↑ ****↑ ***↑ ****
GSDMB↑ ****↑ ****↑ ****↑ ****
IKZF3↓ ****↓ ****↓ **↓ ***
ZPBP2↓ ****↓ ****nsns
46rs7221109 (C)SMARCE1↓ ****↓ ****↓ ****↓ ****
48rs763361 (T)CD226↓ ****↓ ****nsns
53rs11203203 (T)UBASH3A↑ ***nsnsns
54rs5753037 (T)MTMR3↓ ****↓ ****nsns
  • For FDR, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.

  • ↓, risk (effect) allele reduces expression; ↑, risk (effect) allele increases expression (determined using β coefficient); ID, T1D loci identifiers as in Table I.