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 2 Frequencies of single nucleotide polymorphisms (SNPs) identified at MRP 1

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

No.*	SNP ID**	Region	Protein residue	dbSNP (rs)	Population***	n	Allele frequency (%)		No.	SNP ID	Region	Protein residue	dbSNP (rs)	Population	n	Allele frequency (%)
							C	T								C	T
SNPu1	5'UTR/-51 C>T	5'UTR	-	-	CH	36	100.00	0.00	SNPe4	E8/825 T>C	Exon 8	Val>Val	rs246221	CH	36	36.11	63.89
					ML	35	98.57	1.43						ML	35	24.29	75.71
					IN	35	100.00	0.00						IN	35	11.43	88.57
					CAU	36	100.00	0.00						CAU	36	13.89	86.11
							C	T								C	T
SNPu2	5'UTR/-46 C>T	5'UTR	-	-	CH	36	100.00	0.00	SNPe5	E9/1062 T>C	Exon 9	Asn>Asn	rs35587	CH	36	38.89	61.11
					ML	35	98.57	1.43						ML	35	40.00	60.00
					IN	35	100.00	0.00						IN	35	20.00	80.00
					CAU	36	100.00	0.00						CAU	36	31.94	68.06
							C	T								A	G
SNPe1	E2/218 C>T	Exon 2	Thr>Ile	-	CH	36	98.61	1.39	SNPi11	I9/8 A>G	Intron 9	-	rs35588	CH	36	61.11	38.89
					ML	35	97.14	2.86						ML	35	60.00	40.00
					IN	35	100.00	0.00						IN	35	80.00	20.00
					CAU	36	100.00	0.00						CAU	36	68.06	31.94
							A	G								A	G
SNPi1	I2/26 G>A	Intron 2	-	rs8187843	CH	36	0.00	100.00	SNPi12	I9/79 G>A	Intron 9	-	-	CH	36	0.00	100.00
					ML	35	0.00	100.00						ML	35	0.00	100.00
					IN	35	1.43	98.57						IN	35	1.43	98.57
					CAU	35	7.14	92.86						CAU	36	0.00	100.00
							A	T								G	T
SNPi2	I2/-151 A>T	Intron 2	-	-	CH	36	98.61	1.39	SNPe6	E10/1299 G>T	Exon 10	Arg>Ser	-	CH	36	100.00	0.00
					ML	35	100.00	0.00						ML	35	100.00	0.00
					IN	35	100.00	0.00						IN	35	100.00	0.00
					CAU	36	100.00	0.00						CAU	36	98.61	1.39
							G	T								C	T
SNPi3	I2/-93 G>T	Intron 2	-	-	CH	36	100.00	0.00	SNPi13	I10/64 C>T	Intron 10	-	rs28363993	CH	36	100.00	0.00
					ML	35	100.00	0.00						ML	35	100.00	0.00
					IN	35	98.57	1.43						IN	35	97.14	2.86
					CAU	36	100.00	0.00						CAU	36	100.00	0.00
							C	G								A	C
SNPi4	I2/-33 C>G	Intron 2	-	-	CH	36	100.00	0.00	SNPi14	I10/91 C>A	Intron 10	-	-	CH	36	0.00	100.00
					ML	35	98.57	1.43						ML	35	1.43	98.57
					IN	35	100.00	0.00						IN	35	4.29	95.71
					CAU	36	100.00	0.00						CAU	36	0.00	100.00
							G	T								C	T
SNPi5	I3/-288 T>G	Intron 3	-	rs4148335	CH	36	2.78	97.22	SNPi15	I11/-95 T>C	Intron 11	-	-	CH	36	1.39	98.61
					ML	34	1.47	98.53						ML	35	0.00	100.00
					IN	35	15.71	84.29						IN	35	0.00	100.00
					CAU	34	14.71	85.29						CAU	36	0.00	100.00
							A	C								A	G
SNPi6	I3/-196 A>C	Intron 3	-	rs4148336	CH	36	97.22	2.78	SNPi16	I11/-78 G>A	Intron 11	-	rs35595	CH	36	20.83	79.17
					ML	35	98.57	1.43						ML	35	27.14	72.86
					IN	35	84.29	15.71						IN	35	11.43	88.57
					CAU	36	84.72	15.28						CAU	36	13.89	86.11
							C	T								C	T
SNPi7	I3/-66 T>C	Intron 3	-	rs4148337	CH	36	40.28	59.72	SNPi17	I11/-48 C>T	Intron 11	-	rs3765129	CH	36	88.89	11.11
					ML	35	44.29	55.71						ML	35	91.43	8.57
					IN	35	48.57	51.43						IN	35	97.14	2.86
					CAU	35	74.29	25.71						CAU	36	90.28	9.72
							A	G								C	T
SNPe2	E6/651 G>A	Exon 6	Ser>Ser	-	CH	36	0.00	100.00	SNPi18	I12/56 C>T	Intron 12	-	rs17265551	CH	35	98.57	1.43
					ML	35	0.00	100.00						ML	35	98.57	1.43
					IN	35	2.86	97.14						IN	35	94.29	5.71
					CAU	36	0.00	100.00						CAU	36	97.22	2.78
							G	T								C	T
SNPi8	I7/31 G>T	Intron 7	-	rs8187850	CH	35	100.00	0.00	SNPi19	I12/-143 C>T	Intron 12	-	-	CH	31	100.00	0.00
					ML	34	100.00	0.00						ML	35	100.00	0.00
					IN	35	98.57	1.43						IN	35	98.57	1.43
					CAU	36	98.61	1.39						CAU	36	98.61	1.39
							A	C								A	G
SNPi9	I7/54 C>A	Intron 7	-	rs903880	CH	34	1.47	98.53	SNPi20	I12/-85 G>A	Intron 12	-	rs4148348	CH	36	8.33	91.67
					ML	34	2.94	97.06						ML	35	4.29	95.71
					IN	35	20.00	80.00						IN	35	5.71	94.29
					CAU	36	13.89	86.11						CAU	36	8.33	91.67
							C	G								A	G
SNPi10	I7/64 C>G	Intron 7	-	rs246232	CH	34	61.76	38.24	SNPi21	I12/-37 A>G	Intron 12	-	rs35604	CH	36	83.33	16.67
					ML	34	72.06	27.94						ML	35	85.71	14.29
					IN	35	65.71	34.29						IN	35	57.14	42.86
					CAU	35	80.00	20.00						CAU	36	79.17	20.83
							A	G								C	T
SNPe3	E8/816 G>A	Exon 8	Pro>Pro	rs2230669	CH	36	2.78	97.22	SNPe7	E13/1684 C>T	Exon 13	Leu>Leu	rs35605	CH	36	83.33	16.67
					ML	35	0.00	100.00						ML	35	85.71	14.29
					IN	35	0.00	100.00						IN	35	57.14	42.86
					CAU	36	0.00	100.00						CAU	36	80.56	19.44
							C	T								C	T
No.	SNP ID	Region	Protein residue	dbSNP (rs)	Population	n	Allele frequency (%)		No.	SNP ID	Region	Protein residue	dbSNP (rs)	Population	n	Allele frequency (%)
SNPe8	E13/1704 C>T	Exon 13	Tyr>Tyr	rs8187858	CH	36	100.00	0.00	SNPi28	I20/-31 C>T	Intron 20	-	-	CH	36	100.00	0.00
					ML	35	100.00	0.00						ML	35	100.00	0.00
					IN	35	95.71	4.29						IN	35	100.00	0.00
					CAU	36	98.61	1.39						CAU	36	98.61	1.39
							C	G								C	T
SNPi22	I13/33 I13/33	Intron 13	-	-	CH	36	0.00	100.00	SNPe17	E21/2793 C>T	Exon 21	Thr>Thr	-	CH	36	100.00	0.00
					ML	35	0.00	100.00						ML	35	100.00	0.00
					IN	35	1.43	98.57						IN	35	98.57	1.43
					CAU	36	0.00	100.00						CAU	36	100.00	0.00
							A	G								C	T
SNPe9	E14/1898 G>A	Exon 14	Arg>Gln		CH	36	0.00	100.00	SNPi29	I21/26 T>C	Intron 21	-	rs11075296	CH	36	0.00	100.00
					ML	35	0.00	100.00						ML	35	0.00	100.00
					IN	35	0.00	100.00						IN	35	1.43	98.57
					CAU	36	1.39	98.61						CAU	36	0.00	100.00
							C	T								C	T
SNPe10	E16/2001 C>T	Exon 16	Ser>Ser	rs8187863	CH	36	100.00	0.00	SNPi30	I22/62 T>C	Intron 22	-	rs3887893	CH	36	58.33	41.67
					ML	35	100.00	0.00						ML	35	52.86	47.14
					IN	35	100.00	0.00						IN	35	47.14	52.86
					CAU	36	98.61	1.39						CAU	36	43.06	56.94
							C	T								C	T
SNPe11	E16/2007 C>T	Exon 16	Pro>Pro	rs2301666	CH	36	98.61	1.39	SNPi31	I22/-43 C>T	Intron 22	-	-	CH	35	91.43	8.57
					ML	35	100.00	0.00						ML	35	81.43	18.57
					IN	35	100.00	0.00						IN	35	100.00	0.00
					CAU	36	100.00	0.00						CAU	36	100.00	0.00
							G	T								A	G
SNPe12	E16/2012 G>T	Exon 16	Gly>Val	-	CH	36	100.00	0.00	SNPi32	I24/211 G>A	Intron 24	-	-	CH	36	6.94	93.06
					ML	35	100.00	0.00						ML	35	4.29	95.71
					IN	35	98.57	1.43						IN	35	1.43	98.57
					CAU	36	97.22	2.78						CAU	36	0.00	100.00
							A	G								C	T
SNPe13	E17/2168 G>A	Exon 17	Arg>Gln	rs4148356	CH	36	0.00	100.00	SNPi33	I25/103 C>T	Intron 25	-	-	CH	36	100.00	0.00
					ML	35	2.86	97.14						ML	35	100.00	0.00
					IN	35	0.00	100.00						IN	35	98.57	1.43
					CAU	36	0.00	100.00						CAU	34	100.00	0.00
							C	T								C	T
SNPe14	E17/2217 C>T	Exon 17	Ser>Ser	-	CH	36	100.00	0.00	SNPi34	I25/114 C>T	Intron 25	-	-	CH	36	98.61	1.39
					ML	35	100.00	0.00						ML	35	100.00	0.00
					IN	35	98.57	1.43						IN	35	100.00	0.00
					CAU	36	100.00	0.00						CAU	34	100.00	0.00
							A	G								A	G
SNPe15	E17/2268 G>A	Exon 17	Gly>Gly	-	CH	36	1.39	98.61	SNPi35	I25/146 G>A	Intron 25	-	-	CH	36	0.00	100.00
					ML	35	0.00	100.00						ML	35	1.43	98.57
					IN	35	0.00	100.00						IN	35	0.00	100.00
					CAU	36	0.00	100.00						CAU	34	0.00	100.00
							A	G								C	G
SNPi23	I17/-168 A>G	Intron 17	-	-	CH	31	100.00	0.00	SNPi36	I26/-108 G>C	Intron 26	-	-	CH	36	0.00	100.00
					ML	35	97.14	2.86						ML	35	0.00	100.00
					IN	29	100.00	0.00						IN	35	2.86	97.14
					CAU	32	98.44	1.56						CAU	35	2.86	97.14
							C	G								C	T
SNPi24	I18/-30 G>C	Intron 18	-	rs2074087	CH	36	15.28	84.72	SNPi37	I26/-9 C>T	Intron 26	-	-	CH	36	98.61	1.39
					ML	35	12.86	87.14						ML	35	100.00	0.00
					IN	35	37.14	62.86						IN	35	100.00	0.00
					CAU	36	18.06	81.94						CAU	35	100.00	0.00
							A	G								A	G
SNPi25	I18/-27 G>A	Intron 18	-	rs28363997	CH	36	0.00	100.00	SNPe18	E28/4002 G>A	Exon 28	Ser>Ser	rs2239330	CH	36	8.33	91.67
					ML	35	0.00	100.00						ML	35	7.14	92.86
					IN	35	1.43	98.57						IN	35	20.00	80.00
					CAU	36	2.78	97.22						CAU	36	37.50	62.50
							C	T								A	G
SNPi26	I19/-175 C>T	Intron 19	-	rs4148369	CH	36	91.67	8.33	SNPi38	I28/-45 G>A	Intron 28	-	rs212087	CH	36	18.06	81.94
					ML	35	91.43	8.57						ML	35	27.14	72.86
					IN	35	81.43	18.57						IN	35	38.57	61.43
					CAU	36	91.67	8.33						CAU	36	58.33	41.67
							C	T								C	T
SNPe16	E20/2651 C>T	Exon 20	Thr>Met	-	CH	36	100.00	0.00	SNPi39	I29/-83 C>T	Intron 29	-	-	CH	36	100.00	0.00
					ML	35	98.57	1.43						ML	35	100.00	0.00
					IN	35	100.00	0.00						IN	35	97.14	2.86
					CAU	36	100.00	0.00						CAU	36	98.61	1.39
							C	T								C	G
SNPi27	I20/-59 C>T	Intron 20	-	-	CH	36	100.00	0.00	SNPi40	I30/-51 G>C	Intron 30	-	-	CH	36	0.00	100.00
					ML	35	97.14	2.86						ML	35	0.00	100.00
					IN	35	100.00	0.00						IN	35	2.86	97.14
					CAU	36	100.00	0.00						CAU	35	0.00	100.00

* The numbers of SNPs are defined as SNP(SNP locates the region)(In the certain region, the consequent number of the SNP). For example, SNPu1 means the SNP is located in the untranslated region (UTR) and the first SNP in the UTR.
** SNP ID for these SNPs are defined as (Region)/(position number)(major allele)(minor allele). Region shows whether SNP is in an exon (E) or intron (I). Position number of exonic SNP is the mRNA nucleotide position using the translation start site as position 1. For intronic SNP, the position in the genomic sequence is either upstream (-) of using the 5' boundary of the immediate downstream exon as position -1, or downstream (+) using 3' boundary of the immediate upstream exon as position 1. The same principle is employed to the indel and STR. The position is specific to the first nucleotide in the genomic sequence. (reference mRNA ID:NM_004996.2).
*** CH, ML, IN and CAU represent Chinese, Malay, Indian and Caucasian, respectively.

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