. 2015 May 28;11(5):e1005202. doi: 10.1371/journal.pgen.1005202

Table 5. Analysis of linkage disequilibrium between SNPs in GWAS loci of select phenotypes and TCF21 peak regions for chosen phenotypes.

Traits	Average LD Values	GWAS SNPs	GWAS SNPs having R2 with TCF21 SNPs	TCF21 SNPs before LD pruning	TCF21 SNPs with LD pruning	P-value with 10000 permutations
Inflammatory bowel disease	0.474119347	117	79	535	169	P<10e-4
Height	0.410534747	321	218	1143	432	P<10e-4
Schizophrenia	0.45038231	120	83	450	167	0.0004
Ulcerative colitis	0.446449065	82	55	401	115	0.0041
^* CAD extended nolipid	0.406510724	223	150	718	296	0.0052
^* CAD extended	0.402737992	229	152	735	305	0.0086
Insulin resistance	0.461195794	51	31	132	58	0.0104
CAD nolipid	0.41715869	122	76	316	150	0.0197
CAD	0.416045058	126	78	328	155	0.0209
Blood pressure	0.419870421	111	65	322	123	0.0263
Platelets	0.426035533	61	49	251	95	0.0284
Triglycerides	0.417955674	52	37	202	78	0.0695
Aneurysm	0.436847165	25	17	103	35	0.0896
Macular degen	0.423410192	45	25	80	45	0.0909
Kawasaki disease	0.449048952	18	11	66	18	0.112
LDL cholesterol	0.401895683	78	47	218	99	0.1148
Cholesterol total	0.388545716	78	55	279	116	0.1798
B function glucose	0.390955994	48	33	150	61	0.2263
Celiac disease	0.374576605	56	30	172	54	0.3688
Breast cancer	0.368659838	131	81	373	141	0.3806
Parkinson disease	0.368841594	67	42	294	81	0.4017
Migraine	0.361138473	133	86	357	165	0.4966
Systemic lupus erythematosus	0.335187216	72	49	260	92	0.7776

*GWAS catalog genes were supplemented with additional CAD genes identified from CARDIoGRAM+C4D, which are not currently included in the GWAS catalog. Traits with bold text are those significant at P<0.05 in both the GWAS gene enrichment analysis shown in Table 4 and the current analysis.