Markup | Genome Research

Table 3.

Relative Frequencies of APOE Sequence Variants Within Major Genotype Classes (OLA-Typed Samples)

Position[ii]		Variant type		Population		Relative SNP frequency[iii] by ɛ2/ɛ3/ɛ4 genotype		Prob[iv]
Position[ii]		Variant type		Population		ɛ3/ɛ3	ɛ3/ɛ2	Prob[iv]	ɛ4/ɛ3
73	C/T	J	0.089	0.030	0.036	^***
		N[v]	—	—	—	—
		R[v]	—	—	—	—
308	C/T	J	0.018	0.022	0.011	NS
		N[v]	—	—	—	—
		R[v]	—	—	—	—
471	A/G	J	0.006	0.004	0.185	^***
		N[v]	—	—	—	—
		R[v]	—	—	—	—
545	C/T	J	0.004	—	0.002	NS
		N[v]	—	—	—	—
		R[v]	—	—	—	—
560	A/T	J	0.258	0.193	0.378	^***
		N	0.109	0.333	0.085	^***
		R	0.163	0.312	0.075	^***
624	T/C	J	0.025	0.077	0.019	^***
		N	0.028	0.188	0.013	^***
		R	0.076	0.270	0.058	^***
832	G/T	J	0.175	0.142	0.353	^***
		N	0.337	0.120	0.641	^***
		R	0.483	0.298	0.605	^***
1163	G/C	J	0.180	0.136	0.082	^***
		N	0.333	0.120	0.185	^***
		R	0.455	0.246	0.217	^***
1522	G/A	J[v]	—	—	—	—
		N	0.013	—	0.006	NS
		R[v]	—	—	—	—
1575	C/T	J[v]	—	—	—	—
		N	0.011	—	0.003	NS
		R	0.043	0.016	0.013	^*
1998	G/A	J	—	—	0.068	^***
		N	0.005	—	0.469	^***
		R	0.002	0.004	0.391	^***
2440	G/A	J	0.532	0.225	0.271	^***
		N	0.654	0.375	0.317	^***
		R	0.527	0.256	0.281	^***
2907	T/G	J[v]	—	—	—	—
		N	0.011	—	0.003	NS
		R	0.013	—	0.007	NS
3106	T/C	J	—	—	—	—
		N	—	—	0.016	NS
		R	0.001	—	0.018	^**
3673	C/G	J	0.017	0.022	0.011	NS
		N[v]	—	—	—	—
		R[v]	—	—	—	—
4036	C/T	J	0.039	0.004	0.009	^***
		N[v]	—	—	—	—
		R[v]	—	—	—	—
4951	A/C	J	—	—	0.084	^***
		N	—	—	0.016	^***
		R	—	—	0.102	^***
5361	T/C	J	0.020	0.004	0.015	NS
		N	0.243	0.083	0.137	^***
		R	0.112	0.039	0.035	^***

[i] “—” means site did not vary. SNP = single nucleotide polymorphisms; J = Jackson; N = North Karelia; R = Rochester.

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

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

[iv] Probabilities were assessed by a Fisher exact test for the resulting 2 × 3 table: *P < 0.05; ** = P < 0.01; *** = P < 0.001; NS = nonsignificant.

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