Nucleotide sequence analyses of the MRP 1 gene in four populations suggest negative selection on its coding region

Wang, Zihua; Sew, Pui-Hoon; Ambrose, Helen; Ryan, Stephen; Chong, Samuel S; Lee, Edmund JD; Lee, Caroline GL

doi:10.1186/1471-2164-7-111

Table 5 Comparisons of polymorphisms identified in this study with those reported in HapMap/Perlegen

From: Nucleotide sequence analyses of the MRP 1 gene in four populations suggest negative selection on its coding region

A
			HAPMAP				Perlegen
			CHB		CEPH		CHB		EA
	# common polymorphisms		19		19		14		14
This Study	# non-common polymorphisms	polymorphisms found in HapMap/Perlegen but not in this study	25 (22)		23 (22)		1 (0)		1 (0)
		polymorphisms found in this study but not in HapMap/Perlegen	41 (26)		41 (26)		46 (28)		46 (26)
	() refers to number of monomorphic SNPs in that category in that population
B
SNP ID	dbSNP ID	Popu	N	Our data		N	HapMap		n	Perlegen
I2/26 G>A	rs8187843			A	G		A	G
		CH	36	0.00	100.00	45	0.00	100.00
		CAU	35	7.14	92.86	60	5.83	94.17
I7/31 G>T	rs8187850			G	T		G	T
		CH	35	100.00	0.00	45	100.00	0.00
		CAU	36	98.61	1.39	60	100.00	0.00
I7/54 C>A	rs903880			A	C		A	C
		CH	34	1.47	98.53	45	4.44	95.56
		CAU	36	13.89	86.11	60	25.00	75.00
I7/64 C>G	rs246232			C	G		C	G		C	G
		CH	34	61.76	38.24	44	55.68	44.32	21	50.00	50.00
		CAU	35	80.00	20.00	60	66.67	33.33	24	52.08	47.92
E8/825 T>C	rs246221			C	T		C	T		C	T
		CH	36	36.11	63.89	45	46.67	53.33	24	56.25	43.75
		CAU	36	13.89	86.11	60	28.33	71.67	22	45.45	54.55
E9/1062 T>C	rs35587			C	T		C	T		C	T
		CH	36	38.89	61.11	45	46.67	53.33	24	58.33	41.67
		CAU	36	31.94	68.06	60	28.33	71.67	24	45.83	54.17
I11/-78 G>A	rs35595			A	G		A	G
		CH	36	20.83	79.17	45	31.11	68.89
		CAU	36	13.89	86.11	60	13.33	86.67
I11/-48 C>T	rs3765129			C	T		C	T		C	T
		CH	36	88.89	11.11	45	88.89	11.11	24	93.75	6.25
		CAU	36	90.28	9.72	58	85.34	14.66	24	85.42	14.58
I12/56 C>T	rs17265551			C	T		C	T		C	T
		CH	35	98.57	1.43	45	95.56	4.44	24	97.92	2.08
		CAU	36	97.22	2.78	60	90.83	9.17	24	89.58	10.42
I12/-85 G>A	rs4148348			A	G		A	G
		CH	36	8.33	91.67	45	4.44	95.56
		CAU	36	8.33	91.67	60	7.50	92.50
I12/-37 A>G	rs35604			A	G		A	G		A	G
		CH	36	83.33	16.67	45	72.22	27.78	24	81.25	18.75
		CAU	36	79.17	20.83	60	82.50	17.50	24	91.67	8.33
E13/1684 C>T	rs35605			C	T		C	T		C	T
		CH	36	83.33	16.67	45	72.22	27.78	24	81.25	18.75
		CAU	36	80.56	19.44	60	82.50	17.50	24	91.67	8.33
E13/1704 C>T	rs8187858			C	T		C	T		C	T
		CH	36	100.00	0.00	45	100.00	0.00	24	100.00	0.00
		CAU	36	98.61	1.39	60	90.83	9.17	24	95.83	4.17
E16/2001 C>T	rs8187863			C		T		T		C	T
		CH	36	100.00	0.00	45	100.00	0.00	24	100.00	0.00
		CAU	36	98.61	1.39	60	98.33	1.67	24	95.83	4.17
E16/2007 C>T	rs2301666			C	T		C	T		C	T
		CH	36	98.61	1.39	45	97.78	2.22	24	97.92	2.08
		CAU	36	100.00	0.00	60	100.00	0.00	24	100.00	0.00
I18/-30 G>C	rs2074087			C	G					C	G
		CH	36	15.28	84.72				24	14.58	85.42
		CAU	36	18.06	81.94				24	4.17	95.83
I21/26 T>C	rs11075296			C	T		C	T		C	T
		CH	36	0.00	100.00	45	0.00	100.00	24	0.00	100.00
		CAU	36	0.00	100.00	60	0.00	100.00	24	0.00	100.00
I22/62 T>C	rs3887893			G	A		G	A
		CH	36	58.33	41.67	45	50.00	50.00
		CAU	36	43.06	56.94	59	37.29	62.71
E28/4002 G>A	rs2239330			A	G		A	G		A	G
		CH	36	8.33	91.67	45	11.11	88.89	24	16.67	83.33
		CAU	36	37.50	62.50	60	29.17	70.83	24	31.25	68.75
I28/-45 G>A	rs212087			A	G		A	G		A	G
		CH	36	18.06	81.94	45	20.00	80.00	24	18.75	81.25
		CAU	36	58.33	41.67	60	39.17	60.83	24	43.75	56.25
C
P-value	Our data			HapMap			Perlegen
	CH	EA	Both	CH	EA	Both	CH	EA	Both
Average difference between datasets
Our data	-	-	-	0.77	0.24	0.26	0.28	0.83	0.71
HapMap	0.42	2.11	1.27	-	-	-	0.03	0.16	0.02
Perlegen	2.54	0.83	0.85	3.48	3.57	3.67	-	-	-

Note: Cells in the top right triangular section indicate p values of paired-samples t test, whereas those in the lower triangular section contain the average differences in allele frequencies between comparable SNPs between the respective data sets.

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