Table 4.

Top Single-Variant Association Signals for the Cigarettes-Per-Day Phenotype Using Multi-Allelic Analysis. Results are shown for variants with p-values less than 5 × 10⁻⁸. We report the p-values and genetic effect estimates for each alternative allele at multi-allelic sites. As a comparison, we also report the p-values and test statistics from single-allelic analysis, as well as the omnibus test that collapses multiple alleles.

Position	Ref Allele	Alt Allele	Alt Allele Freq	p-Value	β	β SD	N	Direction of Effects*	Anno	Stat Single-Allelic Analysis	p-Value Single-Allelic Analysis	p-Value Collapsing Multi-Allelic Sites
15:78915370	CT	C	0.41	1.6 × 10−11	0.078	0.012	17,512	-+++++++	Intergenic	44.67	2.3 × 10−11	1.0 × 10−10
15:78915370	CT	CTTT	0.019	0.61	0.022	0.044	17,512	-++++-+-	Intergenic	0.34	0.55
15:78859605	AAAAAG	A	0.33	2.3 × 10−11	0.079	0.012	17,512	-+++++++	Deletion; CHRNA5	43.74	3.8 × 10−11	5.1 × 10−10
15:78859605	A	G	0.00077	0.38	0.29	0.33	17,512	+++-+-+-	Intron; CHRNA5	0.091	0.76
15:78913353	CGCGGGCGG	C	0.47	2.4 × 10−9	0.072	0.012	17,512	-+++++++	Deletion; CHRNA3	33.31	7.8 × 10−9	2.8 × 10−7
15:78913353	CGCGGGCGG	CGCGGGCGGGCGG	0.033	0.10	−0.057	0.035	17,512	+--+----	Insertion; CHRNA3	0.75	0.38
15:78785944	AT	ATT	0.29	7.7 × 10−9	0.079	0.014	17,512	-+++++++	Insertion; IREB2	31.81	1.7 × 10−8	1.5 × 10−4
15:78785944	AT	A	0.18	0.71	0.0056	0.016	17,512	+------+	Deletion; IREB2	0.00057	0.98
15:78871382	CT	CTT	0.40	1.4 × 10−8	0.080	0.014	13,723	XX++++++	Insertion; CHRNA5	27.81	1.3 × 10−7	6.2 × 10−7
15:78871382	CT	C	0.070	0.37	0.022	0.025	17,512	-+-----+	Deletion; CHRNA5	0.29	0.58
15:78751667	G	GTTTTTTGTTTGTTTGT	0.29	1.6 × 10−8	0.071	0.013	17,512	-+++++++	Insertion; IREB2	22.25	2.4 × 10−6	1.1 × 10−7
15:78751667	G	GTTTTTTTGTTTGTTTG	0.0019	0.97	0.0048	0.14	17,512	++--+---	Insertion; IREB2	0.065	0.80

*: “+” and “-“ denote the direction of relationship between alternative alleles and Cigarettes-Per-Day phenotype.