Table 3 Upstream and missense candidate causal variants for heat tolerance (slope) traits at genomic sites that are highly conserved (conservation score > 0.9) across 100 vertebrate species*.

SNP	Chr	BP	Annotation	VEP_impact	Gene	HTMYslope	HTFYslope	HTPYslope	Meta-analysis^a	Conditional analysis^b	p value^c
rs209684414	3	34,215,670	Upstream	MODIFIER	KIAA1324				✓		5.98E–07
rs207668220	3	34,273,899	Upstream	MODIFIER	C3H1orf194				✓		6.5E–07
rs210324395	10	46,503,113	Upstream	MODIFIER	USP3				✓		8.66E–09
rs210468775	10	46,505,212	Upstream	MODIFIER	USP3				✓		1.89E–09
rs207681599	14	432,274	Upstream	MODIFIER	LRRC14	✓	✓	✓	✓	✓	1.46E–52\|1.13E–63\|1.13E–28\|8.8E–243\|7.92E–08
rs136474298	14	471,951	Missense	MODERATE	KIFC2	✓	✓	✓	✓	✓	6.11E–53\|4.83E–63\|5.59E–29\|2.5E–242\|7.77E–08
rs207886320	14	479,761	Upstream	MODIFIER	KIFC2	✓	✓	✓	✓	✓	6.18E–52\|4.17E–64\|4.55E–28\|3.9E–242\|7.85E–08
rs137472016	14	494,621	Upstream	MODIFIER	TONSL	✓	✓	✓	✓	✓	6.28E–53\|8.39E–63\|5.94E–29\|9.1E–242\|7.87E–08
rs445616049	14	64,454,721	Missense	MODERATE	VPS13B	✓			✓		4.18E–08\|1.75E–32
rs41946451	20	37,085,370	Missense	MODERATE	CPLANE1					✓	1.14E–07
rs41255693	26	21,272,422	Missense&splice	MODERATE	SCD		✓		✓		4.11E–07\|1.85E–08

*Conservation scores (PhastCon score) of variants at conserved genomic sites were computed by³⁴ based on the LiftOver (https://genome.ucsc.edu/cgi-bin/hgLiftOver) human sites calculated across 100 vertebrate species; single-trait GWAS for heat tolerance milk (HTMYslope), fat (HTFYslope), and protein (HTPYslope) yield slope traits.
^aMeta-analysis combining single-trait GWAS results for slope traits.
^bMeta-analysis combining single-trait conditional GWAS results for slope traits.
^cFor each analysis that identified this variant as significant.

Quick links

Search