Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for Pharmacogenomics

Li, Jing; Lao, Xingzhen; Zhang, Chao; Tian, Lei; Lu, Dongsheng; Xu, Shuhua

doi:10.1186/1471-2156-15-52

Table 1 Summary information of highly differential functional SNPs at ADME core genes

From: Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for Pharmacogenomics

rsID	Gene	allele	f_ASW	f_CEU	f_YRI	He _ASW	He _CEU	He _YRI	Type	Dataset	Related
rs2032582	ABCB1	C/A	0.082	0.453	0.000	0.151	0.496	0.000	NON_SYNONYMOUS	GKB	amitriptyline, atorvastatin, etc.
rs2231164	ABCG2	C/T	0.287	0.912	0.188	0.409	0.161	0.305	INTRONIC	GKB	antineoplastic agents
rs2622628	ABCG2	C/A	0.443	0.012	0.494	0.493	0.023	0.500	INTRONIC	GKB	antiepileptics
rs2606345	CYP1A1	C/A	0.197	0.682	0.006	0.316	0.433	0.011	UPSTREAM	GKB	carbamazepine, phenobarbital, etc.
rs2472304	CYP1A2	C/T	0.131	0.659	0.000	0.228	0.450	0.000	SYNONYMOUS	GKB	caffeine, paroxetine
rs2470890	CYP1A2	G/A	0.139	0.659	0.011	0.240	0.450	0.023	INTRONIC	GKB	caffeine, paroxetine
rs2070673	CYP2E1	A/T	0.369	0.777	0.205	0.466	0.347	0.325	INTRONIC	GKB	cytarabine, ethambutol, etc.
rs12333983	CYP3A4	A/T	0.361	0.924	0.205	0.461	0.141	0.325	DOWNSTREAM	GKB	tacrolimus
rs3735451	CYP3A4	A/G	0.279	0.982	0.199	0.402	0.035	0.319	UPSTREAM	GKB	methadone
rs2242480	CYP3A4	T/C	0.303	0.947	0.142	0.423	0.100	0.244	INTRONIC	GKB	clopidogrel, warfarin, etc.
rs4646437	CYP3A4	C/A	0.353	0.982	0.256	0.456	0.035	0.381	INTRONIC	GKB	methadone, tacrolimus
rs2687116	CYP3A4	C/T	0.344	0.982	0.233	0.452	0.035	0.357	UPSTREAM	GKB	tacrolimus
rs2740574	CYP3A4	C/T	0.344	0.924	0.171	0.452	0.141	0.283	INTRONIC	GKB	carbamazepine, cyclophosphamide, etc.
rs1851426	CYP3A4	A/G	0.303	0.929	0.171	0.423	0.131	0.283	INTRONIC	GKB	tacrolimus
rs4646458	CYP3A5	G/A	0.418	0.947	0.278	0.487	0.100	0.402	3PRIME_UTR	GKB	tacrolimus
rs4646457	CYP3A5	C/A	0.328	0.947	0.159	0.441	0.100	0.268	DOWNSTREAM	GKB	tacrolimus
rs15524	CYP3A5	G/T	0.648	0.988	0.483	0.456	0.023	0.499	DOWNSTREAM	GKB	tacrolimus
rs7780328	CYP3A5	T/C	0.336	0.953	0.159	0.446	0.090	0.268	ESSENTIAL_SPLICE_SITE	GKB	alfentanil, alprazolam, etc.
rs776746	CYP3A5	G/A	0.426	0.959	0.301	0.489	0.079	0.421	INTRONIC	RegulomeDB	-
rs11101985	GSTM1	G/C	0.098	0.418	0.011	0.177	0.486	0.023	INTRONIC	RegulomeDB	-
rs4630	GSTT1	G/A	0.279	0.877	0.091	0.402	0.216	0.165	3PRIME_UTR	GKB	dexamethasone, paclitaxel, etc.
rs145334570	SLCO1B3	G/T	0.516	0.112	0.631	0.499	0.199	0.466	NON_SYNONYMOUS	-	-
rs4762683	SLCO1B3	T/C	0.516	0.112	0.631	0.499	0.199	0.466	SPLICE_SITE	-	-
rs3764009	SLCO1B3	C/T	0.484	0.888	0.369	0.499	0.199	0.466	SPLICE_SITE	-	-
rs7311358	SLCO1B3	G/A	0.484	0.888	0.369	0.499	0.199	0.466	NON_SYNONYMOUS	GKB	docetaxel, mycophenolate mofetil
rs7435827	UGT2B17	A/G	0.098	0.665	0.046	0.177	0.446	0.087	INTRONIC	RegulomeDB	-
rs7434408	UGT2B17	A/G	0.172	0.706	0.068	0.285	0.415	0.127	INTRONIC	RegulomeDB	-
rs74764812	UGT2B17	T/C	0.172	0.665	0.057	0.285	0.446	0.107	INTRONIC	RegulomeDB	-

It is noted that in the column “allele”, the first allele is ancestral state, while the second one highlighted in bold is derived state.

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