Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

Table 4 Comparison of SNP allele frequencies of the studied Caucasian sample with the data on Africans/African- Americans from databases and literature

Gene	SNP	Reference population	Database or references	Data from a database or reference		Caucasians^a		P
				Frequency^b	n	Frequency	n
APOE	2	African-Americans	dbSNP	0.48	24	0.399	1,839	0.52
	3	African-Americans	dbSNP	0.10	24	0.149	1,858	0.56
	4	African-Americans	dbSNP	0.04	24	0.087	1,783	0.25
ER-α	11	SANGER 12 DNAs of African-American origin	dbSNP	0.08	12	0.257	1,857	0.32
	12	African/African-Americans	dbSNP	0.27	24	0.218	1,859	0.61
	13	TSC panel of African-Americans	dbSNP	0.16	40	0.098	1,863	0.27
	15	African/African-Americans	dbSNP	0.28	23	0.203	1,863	0.42
IL-6	16	African/African-Americans	dbSNP	0.96	24	0.434	1,860	<0.01
LEPR	20	TSC panel of African-Americans	dbSNP	0.45	42	0.353	1,860	0.25
TGF-ß1	26	TSC panel of African-Americans	TSC	0.27	42	0.311	1,840	0.61
		African/African-Americans	dbSNP	0.15	24	0.311	1,840	0.07
UCP3	32	African-American females	[70]	0.15	57	0.265	1,767	0.07
	33	African-Americans	[73]	0.08	18	0.000	295	0.06
	34	African-American females	[70]	0.45	63	0.258	1,862	<0.01
	35	African-American females	[70]	0.247	73	0.447	1,863	<0.01
		African/African-Americans	[74]	0.20	276	0.447	1,863	<0.01
	36	African-Americans	[70]	0.00	18	0.000	295	10.00
VDR	38	African-American males	[77]	0.244	37	0.373	1,861	0.15
	40	African-American males	[77]	0.312	32	0.419	1,860	0.30
		Nigerians	[82]	0.37	93	0.419	1,860	0.41
	41	African/African-Americans	dbSNP	0.35	24	0.408	1,859	0.71
		African-American males	[77]	0.244	39	0.408	1,859	0.06

For gene abbreviations and SNP designations see Table 1. ^a Present study. ^b Frequency of the allele corresponding to a minor allele in the present study.

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