Table 5 Chromosomal regions (0 to 3 Mbp) harboring four or more significantly associated SNPs with the same or different fatty acid traits and termed association hot spots in this study.

From: High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits

Chromosomal location (size in Mbp)	Marker	Position	RS# or SS#	Minor/Major Allele	Classification	Gene(s)	P-Value	P-Value BH FDR	Proportion Variance Explained	MAF	Fatty acid
Chr 10 81299090 to 83656836 (2.36 Mbp)	S10_81299090	81299090	rs469048969	C/G	UTR3	TMEM229B	0.000679	0.08942	0.014	0.021	C13:0
	S10_81311811	81311811	rs211170312	A/G	Intronic	TMEM229B	3.65E-06	0.005572	0.025	0.037	C6:0
	S10_81311811	81311811	rs211170312	A/G	Intronic	TMEM229B	6E-05	0.064553	0.019	0.037	C8:0
	S10_81524148	81524148	rs379783190	A/C	Intergenic	—	4.91E-05	0.035386	0.019	0.017	C6:0
	S10_82071253	82071253	rs381605268	A/G	Intronic	RAD51B	2.99E-07	0.003042	0.031	0.017	C20:4n6
	S10_83656836	83656836	ss1850096308	G/T	Intronic	SMOC1	0.00013	0.094105	0.018	0.017	C24:0
Chr 11 102189029 to 103096195 (0.91 Mbp)	S11_102189029	102189029	rs472815046	G/T	Intergenic	—	2.78E-06	0.005448	0.027	0.017	C24:0
	S11_102513057	102513057	ss1850113339	G/T	Splicing	ODF2	7.29E-05	0.045339	0.019	0.040	C24:0
	S11_102912346	102912346	ss1850113453	C/A	Intronic	LRRC8A	4.84E-05	0.022963	0.019	0.032	C13:0
	S11_103096195	103096195	ss1850113566	C/A	Intronic	PPP2R4	2.14E-05	0.040245	0.021	0.018	C4:0
	S11_103096195	103096195	ss1850113566	C/A	Intronic	PPP2R4	1.96E-06	0.003555	0.027	0.018	C6:0
	S11_103096195	103096195	ss1850113566	C/A	Intronic	PPP2R4	0.000102	0.083004	0.019	0.018	C8:0
Chr 17 75239193 to 75857466 (0.618 Mbp)	S17_75239193	75239193	rs440208182	G/T	Downstream	MIR130B, MIR301B	3.72E-05	0.019058	0.020	0.016	C13:0
	S17_75451270	75451270	rs468894370	G/T	Intronic	AIFM3	0.000142	0.066741	0.018	0.023	C24:0
	S17_75458648	75458648	rs381895058	G/A	Intronic	LZTR1	0.000384	0.064358	0.015	0.019	C13:0
	S17_75636645	75636645	ss1850185522	G/A	Intronic	KLHL22	0.000432	0.089446	0.015	0.060	C13:0
	S17_75825603	75825603	rs207929394	T/C	Intergenic	—	1.59E-05	0.011326	0.023	0.047	C13:0
	S17_75857466	75857466	ss1850185673	G/T	Intronic	CDC45	2.83E-05	0.0159	0.021	0.039	C13:0
Chr 22 51831131 to 53880151 (2.05 Mbp)	S22_51831131	51831131	rs473131453	G/T	Intronic	SLC25A20	2.27E-06	0.003938	0.026	0.018	C6:0
	S22_51831131	51831131	rs473131453	G/T	Intronic	SLC25A20	1.82E-05	0.02778	0.022	0.018	C8:0
	S22_51965717	51965717	ss1850241844	C/A	UTR3	NCKIPSD	6.41E-06	0.00924	0.025	0.018	C24:0
	S22_52346974	52346974	rs110791336	T/G	Intergenic	—	0.000161	0.050409	0.017	0.066	C13:0
	S22_52379056	52379056	ss1850241914	G/T	Coding	CCDC51	0.000691	0.090064	0.014	0.037	C13:0
	S22_52380263	52380263	ss1850241922	C/T	Coding	CCDC51	0.000451	0.090988	0.015	0.022	C13:0
	S22_53719765	53719765	ss1850242135	G/T	Intronic	MYL3	1.48E-05	0.066302	0.027	0.015	C23:0
	S22_53880151	53880151	rs477695948	C/A	Coding	ALS2CL	0.000107	0.054515	0.019	0.025	C24:0
Chr 22 55449849 to 56791780 (1.35 Mbp)	S22_55449849	55449849	rs110927574	G/A	Intronic	GHRL	1.77E-07	0.000615	0.031996	0.0184	C6:0A
	S22_55449849	55449849	rs110927574	G/A	Intronic	GHRL	2.88E-07	0.001481	0.030908	0.0184	C8:0A
	S22_55451203	55451203	rs109410906	A/G	Intronic	GHRL	0.000111	0.075601	0.017662	0.0314	C6:0D
	S22_55494482	55494482	rs42013770	G/A	Intronic	SEC13	1.44E-06	0.002899	0.027315	0.0329	C6:0A
	S22_55494482	55494482	rs42013770	G/A	Intronic	SEC13	1.05E-05	0.020434	0.022899	0.0329	C8:0A
	S22_55554117	55554117	rs469316661	C/A	Intronic	ATP2B2	1.37E-06	0.005244	0.027425	0.0185	C4:0A
	S22_56478689	56478689	ss1850242913	G/T	Intronic	ATG7	6.25E-05	0.05658	0.018929	0.019	C6:0D
	S22_56478689	56478689	ss1850242913	G/T	Intronic	ATG7	2.83E-05	0.035383	0.02069	0.019	C8:0A
	S22_56791780	56791780	ss1850243003	A/T	Intronic	ATG7	0.000172	0.074627	0.017434	0.0694	C24:0A
Chr 28 41433808 to 43479268 (2.04 Mbp)	S28_41433808	41433808	rs475314514	T/C	Intronic	GLUD1	5.56E-07	0.002831	0.029443	0.0302	C4:0A
	S28_41433849	41433849	rs466502048	C/T	Intronic	GLUD1	0.000165	0.051037	0.016783	0.0155	C13:0A
	S28_41435026	41435026	ss1850132183	A/G	Intronic	GLUD1	2.95E-05	0.064795	0.020599	0.0173	C4:0D
	S28_41634323	41634323	ss1850295121	G/T	Intergenic	—	4.17E-05	0.03122	0.020707	0.0261	C24:0A
	S28_41748027	41748027	ss1850295146	C/A	Intergenic	—	5.7E-07	0.001675	0.030684	0.0165	C24:0A
	S28_41994199	41994199	rs42148747	T/C	Intergenic	—	0.000191	0.054817	0.016462	0.0533	C13:0A
	S28_42004219	42004219	rs42148747	C/A	Coding	RBP3	3.65E-05	0.01884	0.020122	0.0222	C13:0A
	S28_42639526	42639526	ss1850295342	C/A	Intergenic	—	7.74E-05	0.084457	0.018456	0.0168	C4:0A
	S28_43479268	43479268	rs470755489	G/C	Coding	ERCC6	2.49E-05	0.050122	0.022174	0.1121	C20:5n3A
Chr 29 42815829 to 45731092 (2.9 Mbp)	S29_42815829	42815829	rs447920602	G/T	Intronic	SLC22A8	0.000104	0.074691	0.017793	0.0155	C6:0D
	S29_43911453	43911453	rs132922154	C/A	Intronic	MACROD1	0.000459	0.091729	0.014533	0.0167	C13:0A
	S29_43949399	43949399	ss1850302054	A/G	Intronic	MACROD1	2.83E-05	0.024879	0.020684	0.0233	C6:0A
	S29_43949399	43949399	ss1850302054	A/G	Intronic	MACROD1	9.68E-05	0.082102	0.017963	0.0233	C8:0A
	S29_43950350	43950350	rs451632156	T/C	Intronic	MACROD1	4.4E-08	0.000258	0.035107	0.0161	C6:0A
	S29_43950350	43950350	rs451632156	T/C	Intronic	MACROD1	1.86E-07	0.00129	0.031889	0.0161	C8:0A
	S29_44467997	44467997	ss1850302313	C/A	Intronic	NRXN2	0.00018	0.052768	0.016598	0.0161	C13:0A
	S29_44684726	44684726	rs435582482	G/T	Intronic	EHD1	0.00073	0.092593	0.013517	0.0235	C13:0D
	S29_45566049	45566049	ss1850302687	C/G	Coding	DKFZP761E198	2.35E-06	0.002742	0.026226	0.0179	C13:0A
	S29_45731092	45731092	rs436614558	T/G	Coding	C29H11orf68	2.38E-05	0.014305	0.021074	0.0172	C13:0A

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Table 5 Chromosomal regions (0 to 3 Mbp) harboring four or more significantly associated SNPs with the same or different fatty acid traits and termed association hot spots in this study.

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