. 2019 Apr 29;15(4):e1008081. doi: 10.1371/journal.pgen.1008081

Table 2. Genome-wide significant sliding windows identified by various tests in the UK10K TWINSUK cohort and replication in the ALSPAC cohort of UK10K.

Significant p-values are in boldface; only significant p-values in the ALSPAC cohort were reported (TWINSUK p-value/ALSPAC p-value shaded when both are significant). cMAF: cumulative minor allele frequency. Base pair (bp) position based on reference genome hg19.

Trait	Chr	Start position- Stop position (bp)	Gene(s)	cMAF	# SNVs	p-Values
						Globally weighted		Not globally weighted		aSPU _minP	aSPUw _minP	aSPU	FST (combined)	SKAT	T5
						wtFun-SPU	wtFun -SPUw	Fun-SPU	Fun-SPUw	aSPU _minP	aSPUw _minP	aSPU	FST (combined)	SKAT	T5
HDL	1	39,070,016–39,080,016	Intergenic	0.14/0.33	39/38	4.3e-2	2.3e-3	3.3e-2	<1e-8	2.0e-2	3.2e-6	3.6e-2	1.2e-3	5.2e-2	2.0e-4
HDL	2	173,903,159–173,913,159	RAPGEF4	0.084/0.21	33/31	<1e-8	<1e-8	2.4e-6	<1e-8	4.9e-6	8.9e-6	2.4e-5	2.5e-6	1.1e-6	1.2e-4
HDL	3	63,804,000–63,814,000	C3orf49	0.02/0.17	37/36	2.9e-3	<1e-8	4.0e-2	1.8e-5	3.1e-2	4.5e-5	0.12	3.2e-3	1.6e-2	5.2e-2
HDL	5	6,548,648–6,558,648	Intergenic	0.001/0.32	59/59	0.13	<1e-8	0.18	<1e-8	6.2e-2/ <1e-4	$< 1 e ‐ 8 / < 1 e ‐ 4$	0.15	2.0e-5	2.1e-3	0.19
HDL	5	6,557,398–6,567,398	Intergenic	0.34/0.26	48/43	4.3e-2	1.5e-2	0.13	<1e-8	9.5e-3	<1e-8/	0.24	1.2e-8	1.8e-2	0.81
LDL	3	102,287,400–102,297,400	Intergenic	0.25/0.19	56/39	4.4e-5	9.9e-3	<1e-8	3.6e-2	9.0e-6	1.3e-2	8.1e-6	1.3e-4	2.5e-5	4.5e-3
LDL	3	102,427,400–102,437,400	Intergenic	0.16/0.27	32/40	<1e-8	5e-8	<1e-8	1.3e-3	1.2e-6/ <1e-4	5.1e-5	2.5e-4	3.3e-7	1.3e-4	0.68
LDL	5	43,259,958–43,269,958	NIM1K	0.43/0.29	41/46	9e-8	<1e-8	6.5e-7	3.0e-7	1.7e-5/ <1e-4	8.2e-6	2.5e-5	1.5e-5	2.4e-3	4.4e-6
LDL	12	13,771,517–13,781,517	GRIN2B	0.18/0.23	43/48	3.5e-3	5.8e-4	0.80	3.5e-5	5.9e-6	1.7e-6	0.60	2.4e-11	0.23	0.96
LDL	12	13,780,267–13,790,267	GRIN2B	0.26/0.27	45/43	6.0e-2	8.0e-4	0.47	1.3e-4	1.0e-6	1.7e-6	0.33	2.0e-11	4.9e-2	0.53
LDL	19	45,387,096–45,397,096	PVRL2/ TOMM40	0.21/ 0.22	33/ 37	5.4e-2/ 1.8e-3	0.10	3.5e-7/ <1e-4	5.0e-3/ 1.6e-3	2.1e-7/ <1e-4	4.5e-3	$5.0 e ‐ 8 / < 1 e ‐ 4$	2.4e-4	2.4e-4/ 7.9e-6	0.25
LDL	19	45,395,846–45,405,846	TOMM40	0.42/0.59	65/62	8.6e-3/ <1e-4	8.6e-2	$3.0 e ‐ 8 / < 1 e ‐ 4$	1.4e-4/ 1.9e-3	$< 1 e ‐ 8 / < 1 e ‐ 4$	5.8e-5/ <1e-4	5.0e-7	1.2e-4/ 1.0e-10	4.7e-4/ 1.1e-6	0.28
LDL	19	45,439,596–45,449,596	APOC4-APOC2	0.37/0.18	25/25	$< 1 e ‐ 8 / < 1 e ‐ 4$	1.1e-4	1.2e-6/ <1e-4	6.9e-4	2.1e-5/ <1e-4	1.4e-4	2.3e-4	4.7e-5/ 2.4e-7	1.1e-3/ 9.0e-4	0.15
BMI	3	35,619,294–35,629,294	Intergenic	0.24/0.24	39/40	<1e-8	4.2e-5	5.0e-5	1.1e-4	3.9e-5	3.6e-5	8.0e-5	2.9e-6	4.4e-5	1.5e-5
BMI	4	22,825,237–22,835,237	Intergenic	0.18/0.24	47/48	1.3e-3	5.2e-5	1.8e-3	6.0e-5	1.6e-4	3.4e-4/ <1e-4	2.8e-3	2.6e-8	1.4e-6	3.0e-5
BMI	10	13,937,041–13,947,041	FRMD4A	0.28/0.30	49/53	8.5e-2	2.4e-3	0.16	1.4e-4	5.9e-4	2.4e-4	0.18	1.9e-8	0.12	7.2e-2
BMI	12	26,179,017–26,189,017	RASSF8	0.38/0.40	37/37	7.5e-2	1.2e-4	0.12	4.4e-4	2.1e-4	3.5e-4/ <1e-4	0.12	7.5e-8	6.6e-2	2.1e-4
BMI	15	42,935,528–42,945,528	STARD9	0.28/0.23	43/56	<1e-8	2.7e-6	<1e-8	1.2e-5	2.1e-6	4.5e-5	1.2e-6	4.8e-7	8.4e-8	1.1e-7
BMI	16	60,159,304–60,169,304	Intergenic	0.27/0.12	29/28	4.3e-4	<1e-8	2.5e-2	2.1e-4	6.1e-4/ <1e-4	6.4e-6/ <1e-4	5.1e-3	1.4e-5	0.15	3.0e-4
BMI	21	40,851,354–40,861,354	SH3BGR	0.26/0.17	32/26	4.4e-4	<1e-8	2.5e-3	1.1e-4	1.3e-3	6.7e-5 /2.6e-3	1.2e-3	3.9e-4	1.5e-2	3.4e-4
SBP	4	118,855,917–118,865,917	Intergenic	0.36/0.16	32/27	5.5e-2	<1e-8	0.68	8.1e-5	5.2e-2	4.2e-5/ <1e-4	0.75	2.5e-2	0.39	0.34
SBP	6	42,558,580–42,568,580	UBR2	0.96/0.095	28/22	<1e-8	1.3e-4	3.4e-4	5.6e-4	1.1e-6	1.6e-4	3.9e-4	1.7e-6	2.7e-3	7.8e-5
SBP	6	121,241,282–121,251,282	Intergenic	0.50/0.23	53/46	<1e-8	1.8e-4	1.2e-4	1.4e-3	1.6e-4	2.1e-3/ <1e-4	5.5e-4	3.0e-4	1.1e-4	7.0e-4
SBP	11	38,236,659–38,246,659	Intergenic	0.60/0.48	61/61	<1e-8	1.4e-4	8.6e-5	6.4e-6	2.1e-5	1.9e-4	3.8e-3	4.4e-6	8.5e-3	0.36

Significance threshold: p<1.56×10⁻⁷ for TWINSUK and p<2×10⁻³ for ALSPAC