Table 2.

Candidates for core gene status

Gene symbol	Transcription site		trans-score			cis-score		T1D SNP associations within 200 kb of transcription site	Monogenic diabetes
	Chr	Start position (Mb)	Effective number of eQTLs	Log odds ratio	p value	Log odds ratio	p value
Effective number of eQTLs > 5 and$\mathbf{p}<{\mathbf{10}}^{-\mathbf{9}}$
CD1E	1	158.35	6.5	−0.12	$8\times {10}^{-10}$	−0.02	0.3	–	–
CD247	1	167.43	5.8	−0.13	$2\times {10}^{-11}$	0.02	0.4	–	–
CTLA4	2	203.87	7.6	0.21	$2\times {10}^{-28}$	−0.08	$3\times {10}^{-5}$	CTLA4	+
CD5	11	61.10	5.5	0.20	$7\times {10}^{-28}$	−0.01	0.5	SLC15A3	–
IL10RA	11	117.99	5.7	0.17	$9\times {10}^{-20}$	−0.02	0.2	–	–
MEOX1	17	43.64	5.5	−0.14	$2\times {10}^{-13}$	0.02	0.2	–	–
LGALS3BP	17	78.97	5.3	0.15	$7\times {10}^{-14}$	0.00	0.8	–	–
Monogenic cause of autoimmune diabetes and$\mathrm{p}<{10}^{-6}$
STAT1	2	190.91	5.7	0.10	$9\times {10}^{-8}$	−0.02	0.2	STAT4	+
FOXP3	X	49.25	2.9	0.23	$5\times {10}^{-35}$	–	–	–	+

Criteria for including genes based on association of T1D with trans-score for expression are shown in the header rows. The association of T1D with the cis-score for that gene is shown if a cis-score was constructed and was associated with T1D at p < 0.001. Any SNP association reported by the Type 1 Diabetes Knowledge Consortium is shown if the top SNP in the clump was within 200 kb of the transcription site of the target gene. This criterion excludes a clump of T1D-associated SNPs containing UBE4A, 263 kb downstream of IL10RA. The gene for the SNP association is that identified as the candidate or nearest gene in the original study.