Table 2.

cASE with T2D GWAS

			COLOC		T2D GWAS					CASE
Chr	SNP	Gene	PP.H4. abf	SNP. PP.H4	EAF	EA	NEA	OR	p	Reporter variant	Ref	Alt	p	Z score
1	rs1127215	PTGFRN	0.99	0.98	0.42	T	C	0.95	2.3E-13	rs1127656	C	T	8.5E-9	14.6
4	rs10937721	WFS1	0.95	0.26	0.59	C	G	1.09	1.6E-40	rs1046320	G	A	3.2E-16	−20.9
8	rs3802177	SLC30A8	1.00	0.61	0.31	A	G	0.90	6.3E-55	rs11558471	A	G	2.9E-14	19.5
10	rs2280141	PLEKHA1	0.96	0.06	0.48	G	T	0.95	2.0E-13	rs1045216	A	G	1.7E-11	17.2
11	rs35251247	HSD17B12	0.95	0.21	0.29	A	G	1.05	8.5E-13	rs11555762	C	T	5.1E-93	52.9
11	rs35251247	RP11-613D13.5	0.93	0.07	0.29	A	G	1.05	8.5E-13	rs35251247	G	A	6.8E-12	−17.5
11	rs5215	KCNJ11	0.83	0.36	0.63	T	C	0.93	2.0E-26	rs5215	C	T	8.6E-6	−11.1
11	rs529623	FXYD2	0.95	1.00	0.52	C	T	0.97	5.8E-6	rs529623	T	C	3.4E-231	84.1
11	rs529623	RP11-728F11.3	0.91	0.81	0.52	C	T	0.97	5.8E-6	rs869789	G	A	7.2E-16	20.7
12	rs10879261	TSPAN8	0.85	0.08	0.41	G	T	1.05	3.7E-13	rs3763978	C	G	7.2E-11	−16.6
16	rs6600191	ITFG3	0.86	0.24	0.18	C	T	0.94	7.0E-13	rs7193384	C	G	1.1E-7	13.4
18	rs1788762	C18orf8	0.96	0.06	0.64	C	G	0.97	2.3E-6	rs1788820	A	G	3.2E-25	−26.7
18	rs1788762	NPC1	0.96	0.06	0.64	C	G	0.97	2.3E-6	rs1788820	A	G	3.2E-25	−26.7
19	rs3111316	CALR	0.99	0.47	0.59	A	G	1.05	1.6E-12	rs1049481	G	T	1.6E-76	−47.9

The R COLOC package reports the approximate Bayesian factor posterior probability (PP.H4.abf) that there is one common causal variant and the posterior probability (SNP.PP.H4) that the SNP is the associated causal variant. The GWAS establishes the link between the SNP and T2D; the effect alleles (EA) with a frequency (EAF) are shown with the associated effect OR and the p value. The GWAS data are as reported by the DIAGRAM Consortium (Mahajan et al., 2018). The cASE analysis provides the allelic imbalance for the allele represented by the reporter SNP with a reference allele (Ref) and an alternative allele (Alt), a p value (FDR threshold of 0.006), and a Z score. An increased Z score refers to increased expression of the reference allele.