Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

Cagliani, Rachele; Riva, Stefania; Pozzoli, Uberto; Fumagalli, Matteo; Comi, Giacomo P; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

doi:10.1186/1471-2148-11-171

Table 2 Nucleotide diversity and neutrality tests for the analysed gene regions

From: Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

Gene	L^a	P^b	S^c	θ_W^d		π^e		Tajima's D			Fu & Li's D*			Fu & Li's F*
				value	rank^f	value	rank^f	value	rank^f	p ^g	value	rank^f	p ^g	value	rank^f	p ^g
ZSCAN23	3.3	CEU	7	4.96	0.44	6.52	0.66	0.87	0.78	0.20	0.51	0.72	0.34	0.73	0.74	0.25
VARS2	3.2	CEU	10	7.30	0.69	10.78	0.86	1.43	0.89	0.09	0.24	0.65	0.40	0.73	0.74	0.25
HLA-DMB	3.1	CEU	14	10.60	0.91	12.12	0.89	0.45	0.66	0.30	-0.28	0.47	0.60	-0.050	0.54	0.51
PTPN22	3.5	CEU	7	4.70	0.44	4.57	0.41	-0.077	0.51	0.49	-0.98	0.23	0.80	-0.81	0.31	0.75
BAT3	2.0	CEU	3	3.47	0.21	3.14	0.27	-0.20	0.47	0.57	-0.35	0.46	0.64	-0.36	0.44	0.62
C6orf47	2.0	CEU	3	3.59	0.21	5.21	0.48	0.98	0.81	0.18	0.92	0.85	0.19	1.09	0.84	0.13
IL10	2.3	CEU	3	2.97	0.15	5.95	0.55	2.12	0.97	0.01	0.90	0.84	0.16	1.47	0.94	0.04
CDSN/	4.5	CEU	59	30.80	>0.99	49.42	>0.99	2.17	0.97	0.01	1.40	0.95	0.03	1.98	0.97	0.01
PSORSC1
		YRI	63	32.88	>0.99	46.20	>0.99	1.46	0.99	0.01	1.44	>0.99	<0.01	1.72	>0.99	<0.01
		EAS	64	33.41	>0.99	47.50	>0.99	1.52	0.91	0.08	1.45	0.98	001	1.75	0.98	0.02
TRIM40/	9.1	CEU	68	17.51	0.98	26.13	0.99	1.78	0.96	0.03	1.61	0.98	<0.01	1.98	0.97	<0.01
TRIM10
		YRI	64	16.48	0.96	15.74	0.94	-0.16	0.64	0.22	1.07	0.97	<0.01	0.76	0.93	0.02
		EAS	79	20.34	0.99	19.33	0.98	-0.18	0.46	0.31	-0.20	0.46	0.68	-0.23	0.45	0.71
BTNL2	3.8	CEU	53	33.04	>0.99	39.75	0.99	-0.33	0.42	0.36	1.32	0.93	0.03	0.88	0.78	0.15
		YRI	63	39.28	>0.99	30.01	>0.99	0.043	0.71	0.18	0.67	0.89	0.06	0.53	0.86	0.07
		EAS	94	58.60	>0.99	47.38	>0.99	-0.70	0.31	0.21	0.95	0.88	0.13	0.43	0.69	0.35
TAP2	4.4	CEU	33	17.56	0.98	29.07	0.99	2.27	0.98	0.01	1.59	0.98	0.01	2.16	0.98	<0.01
		YRI	54	28.73	>0.99	34.55	>0.99	0.73	0.94	0.05	1.63	>0.99	<0.01	1.56	0.99	<0.01
		EAS	41	21.81	0.99	32.88	>0.99	1.79	0.97	0.04	1.30	0.96	0.04	1.74	0.98	0.02
TAP2-ctr	2.6	CEU	12	10.71	0.91	12.18	0.89	0.42	0.65	0.32	0.46	0.70	0.29	0.52	0.69	0.18
BTNL2-ctr	2.0	CEU	15	17.47	0.98	16.73	0.96	-0.14	0.50	0.54	1.56	0.97	0.01	1.18	0.90	0.09

^a length of analyzed sequenced region (kb);
^b sampled population (for each population 40 chromosomes were resequenced);
^c number of segregating sites;
^d Watterson's theta estimation per site (×10^-4);
^e nucleotide diversity per site (×10^-4);
^f percentile rank relative to a distribution of 238 5kb segments from NIEHS genes;
^g p value applying demographic coalescent simulations.

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