Common polymorphisms of protein tyrosine phosphate non-receptor type 2 gene are not associated with risk of Crohn’s disease in Indian

Table 1 Baseline characteristics of patients with Crohn’s disease

Characteristic	Frequency (n = 108)
Age (yr)	37.5 + 12.7
Sex (females)	46 (42.6%)
Age at diagnosis
< 17 yr	7 (6.5%)
17-40 yr	75 (69.4%)
> 40 yr	26 (24.1%)
Disease behaviour
Inflammatory	43 (39.8%)
Stricturing	48 (44.4%)
Penetrating	13 (12.1%)
Stricturing and penetrating	4 (3.7%)
Disease location
Ileal	49 (45.4%)
Colonic	16 (14.8%)
Ileo-colonic	42 (38.9%)
Upper gastrointestinal	1 (0.9%)
Perianal disease (Yes)	15 (13.9%)
Surgery for Crohn’s disease (Yes)	37 (34.3%)
Extra-intestinal manifestations (Yes)	19 (17.6%)
Smoking (Yes)	12 (11.1%)

Table 2 Frequency of the single nucleotide polymorphisms in protein tyrosine phosphate non-receptor type 2 gene in cases and controls

	PTPN2 SNP rs7234029
	Homozygote (GG)	Heterozygote (AG)	Wild type (AA)
Cases (n = 108)	8 (7.4%)	30 (27.8%)	70 (64.8%)
Controls (n = 98)	5 (5.1%)	44 (44.9%)	49 (50%)
P value1	0.05
	PTPN2 SNP rs2542151
	Homozygote (GG)	Heterozygote (GT)	Wild type (TT)
Cases (n = 101)	4 (4%)	40 (39.6%)	57 (56.4%)
Controls (n = 100)	4 (4%)	43 (43%)	53 (53%)
P value1	0.73

¹Wild vs variant (homozygote or heterozygote). SNP: Single nucleotide polymorphism; PTPN2: Protein tyrosine phosphate non-receptor type 2.

Table 3 Minor allele frequency of the single nucleotide polymorphisms in protein tyrosine phosphate non-receptor type 2 gene in cases and controls

	Minor allele	Cases	Controls	P value
rs7234029	G	20.9%	27.6%	0.17
rs2542151	G	23.8%	25.5%	0.77

SNP: Single nucleotide polymorphism; PTPN2: Protein tyrosine phosphate non-receptor type 2.

Table 4 Association of the single nucleotide polymorphisms in protein tyrosine phosphate non-receptor type 2 gene with patient and disease characteristics

Characteristic		rs7234029			rs2542151
		Variant (n=38, GG or GA)	Wild type (n=70, AA)	P value	Variant (n=44, GG or GT)	Wild type (n=57, TT)	P value
Sex	Female	37%	63%	0.74	38.1%	61.9%	0.46
	Male	33.9%	66.1%		47.5%	52.5%
Age at onset of illness (yr)	Up to 40 yr	39%	61%	0.21	43.4%	56.6%	0.96
	> 40	23.1%	76.9%		44%	56%
Disease behaviour	NSNP	29.6%	70.4%	0.42	45%	55%	0.98
	SP	39.1%	60.9%		42.6%	57.4%
Disease location	Ileal	34.7%	65.3%	0.98	42.9%	57.1%	0.28
	Colonic	35.3%	64.7%		23.5%	76.5%
	Ileocolonic	36.6%	63.4%		43.9%	56.1%
Perianal disease	Present	46.7%	53.3%	0.32	46.7%	53.3%	0.79
	Absent	33.3%	66.7%		43%	57%
Surgery for Crohn’s disease	Yes	32.4%	67.6%	0.67	29.4%	70.6%	0.07
	No	36.6%	63.4%		50.1%	49.9%
Smoking	Yes	25%	75%	0.43	41.7%	58.3%	0.89
	No	36.5%	63.5%		43.8%	56.2%
EIM	Yes	40%	60%	0.62	29.4%	70.6%	0.31
	No	34.1%	65.9%		46.4%	53.6%

SNP: Single nucleotide polymorphism; PTPN2: Protein tyrosine phosphate non-receptor type 2; NSNP: Non-stricturing and non-penetrating; SP: Stricturing and/or penetrating; EIM: Extraintestinal manifestations.