Analysis of common PTPN1gene variants in type 2 diabetes, obesity and associated phenotypes in the French population

Table 3 Type 2 Diabetes association analysis for the seven common haplotypes

Haplotypes	Frequencies				Frequencies				Frequencies
	D1	C1	Individual p-values	Overall p-value	D2	C2	Individual p-values	Overall p-value	D1 + D2 cases	C1 + C2 controls	Individual p-values	Overall p-value
GGCC	37.8	34.3	0.13		31.9	31.5	0.59		33.5	32.3	0.23
CACC	18.3	19.9	0.42		24.0	21.8	0.40		22.4	21.1	0.67
GGCG	13.8	12.2	0.61		13.8	13.3	0.97		13.7	13.0	0.88
GACC	11.8	11.7	0.93	0.44	10.7	11.0	0.97	0.42	11.0	11.3	0.95	0.20
CACG	7.1	9.1	0.17		6.1	8.5	0.07		6.4	8.7	0.02
GACG	5.1	5.4	0.78		6.6	6.5	0.85		6.2	6.1	0.87
CATC	3.9	3.4	0.96		4.2	5.0	0.45		4.2	4.6	0.48

The 7 haplotypes defined by the four most informative SNPs (-7077 G/C, rs941798, rs2282146 and rs914458) were tested for association with T2D in both the individual case-control samples and in the pooled sample. Frequencies were estimated from case and control groups separately using the HTR software. Individual and overall p-values were indicated. We estimated the empirical p-value of the CACG haplotype in the combined sample through 1000 permutations of the dataset using the Cocaphase software (p = 0.20).

ISSN: 1471-2350