Markup | Genome Research

Table 1.

Relative Frequencies of APOE Sequence Variants in the Core and Large OLA-Typed Samples

Position[i]		Variant type		Relative frequency[ii]
				Jackson		North Karelia		Rochester		Total		F_ST
				core (2n =48)	OLA-typed (2n =1686[iii])	core (2n =48)	OLA-typed (2n =904[iii])	core (2n =48)	OLA-typed (2n =1768[iii])	core (2n =144)	OLA-typed (2n =4358[iii])	core	OLAtyped
73	C/T	0.042	0.055	0.000	0.000[vii]	0.000	0.000[vii]	0.014	0.021	0.028	0.037
308	C/T	0.021	0.014	0.000	0.000[vii]	0.000	0.000[vii]	0.007	0.006	0.014	0.009
471	A/G	0.042	0.088	0.000	0.000[vii]	0.000	0.000[vii]	0.014	0.034	0.028	0.060
545	C/T	0.021	0.003	0.000	0.000[vii]	0.000	0.000[vii]	0.007	0.001	0.014	0.002
560[iv]	A/T	0.292	0.305[viii]	0.125	0.113[viii]	0.271	0.169	0.229	0.210[viii]	0.031	0.041
624[iv]	T/C	0.000	0.033[viii]	0.021	0.037[viii]	0.250	0.107	0.090	0.064[viii]	0.156	0.021
832[iv]	G/T	0.229	0.244	0.542	0.460[viii]	0.438	0.485	0.403	0.386[viii]	0.070	0.049
1163[iv]	G/C	0.208	0.123[viii]	0.333	0.246[viii]	0.354	0.351	0.299	0.242[viii]	0.020	0.048
1522	G/A	0.000	0.000[vii]	0.042	0.009	0.000	0.000[vii]	0.014	0.002	0.028	0.006
1575	C/T	0.000	0.000[vii]	0.000	0.007[viii]	0.042	0.031	0.014	0.014	0.028	0.014
1998	G/A	0.000	0.030[viii]	0.229	0.210[ix]	0.083	0.109	0.105	0.098[viii]	0.096	0.053
2440	G/A	0.521	0.354[ix]	0.396	0.475[x]	0.333	0.407	0.417	0.400[viii]	0.025	0.010
2907	T/G	0.000	0.000[vii]	0.021	0.007[viii]	0.000	0.009	0.005	0.005	0.014	0.003
3106[v]	T/C	0.000	0.000[vii]	0.000	0.007[viii]	0.021	0.005	0.007	0.003	0.014	0.002
3673	C/G	0.021	0.014[viii]	0.000	0.000[vii]	0.000	0.000[vii]	0.007	0.005	0.014	0.009
3937[v]	T/C	0.104	0.222[viii]	0.229	0.226	0.125	0.138	0.153	0.189[viii]	0.023	0.010
4036[v]	C/T	0.042	0.020[viii]	0.000	0.000[vii]	0.000	0.000[vii]	0.014	0.008	0.028	0.013
4075[v]	C/T	0.042	0.103[viii]	0.042	0.040[viii]	0.187	0.093	0.090	0.086[viii]	0.057	0.011
4951	A/C	0.000	0.038[viii]	0.042	0.009	0.042	0.029	0.028	0.028[viii]	0.014	0.006
5229A	delG	0.042	k	0.250	k	0.125	k	0.139	k	0.030	k
	G[vi]	0.542	k	0.417	k	0.333	k	0.431	k
	insG	0.312	k	0.333	k	0.542	k	0.396	k
	insGG	0.104	k	0.000	k	0.000	k	0.035	k
5229B	G/T	0.958	k	0.958	k	0.813	k	0.910	k	0.057	k
5361	T/C	0.021	0.014[viii]	0.167	0.180[ix]	0.042	0.079	0.076	0.074[viii]	0.059	0.056

[i] Position of the variant position in the reference sequence, GenBank AF261279.

[ii] Frequency of the least common allele (nucleotide listed second under Variant Type).

[iii] Total number of chromosomes surveyed; actual nvaries, as frequencies were calculated relative to nonmissing data only.

[iv] Previously identified noncoding sites: 560 = −491, 624 = −427, 832 = −219 or Th/1/E47cs, 1163 = 1E1.

[v] Coding-region variant.

[vi] Allele identified in the baseline sequence for this mononucleotide track.

[vii] These sites were typed in approximately 188 individuals from the population sample without detecting the alternative allele.

[viii] Proportion of sites not scored = 1%–5%.

[ix] Proportion of sites not scored = 5.1%–10%.

[x] Proportion of sites not scored = 10.1%–15%.

[xi] Site not typed.