Table 6 Commonly significantly associated SNPs (MAF ≥ 10%) with individual fatty acid traits.

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

Fatty acid	Marker	Ch	Position	RS# or SS#	Classification	Gene(s)	Minor/Major Allele	P-Value ¹	P-Value ¹ BH FDR	Proportion of Variance Explained	MAF ²
Additive and dominant models
C13:0	S25_23425778	25	23425778	ss1850268922	Intergenic		G/T	0.0001(4.28E-05)	0.03736(0.018)	0.018	0.484
C24:0	S9_1901392	9	1901392	ss1850076897	Intronic	MYT1L	G/T	0.0002(2.74E-05)	0.075(0.040)	0.017	0.294
C16:1	S26_22572364	26	22572364	rs110405215	Intergenic		C/T	1.7E-08(1.23E-09)	0.001(9.4E-05)	0.037	0.225
C22:5n3	S9_106922517	9	106922517	rs466855972	Intergenic		T/G	4.24E-07(2.93E-07)	0.032(0.011)	0.036	0.140
C6:0	S13_54790999	13	54790999	ss1850134585	Intergenic		C/A	1.29E-05(1.12E-05)	0.014(0.022)	0.022	0.130
C8:0	S13_54790999	13	54790999	ss1850134585	Intergenic		C/A	5.85E-06(3.72E-06)	0.013(0.043)	0.024	0.130
C13:0	S2_121572829	2	121572829	rs43327289	Intergenic		A/G	0.0003(0.0003)	0.078(0.053)	0.015	0.110
C13:0	S21_65126271	21	65126271	rs209872748	Intronic	EVL	G/A	5.06E-05(0.0006)	0.024(0.081)	0.019	0.110
C23:0	S2_21504102	2	21504102	ss1849977641	Intergenic		C/A	1.9E-05(2.56E-05)	0.096(0.0723)	0.027	0.106
C4:0	S9_104910843	9	104910843	rs379509819	Intergenic		C/T	3.59E-05(3.8E-06)	0.053(0.017)	0.02	0.104
Additive model
C23:0	S19_60864657	19	60864657	rs136101412	Intergenic		C/G	1.33E-05	0.09199	0.028	0.488
C4:0	S28_39747506	28	39747506	rs210570524	Intergenic		C/G	1.44E-05	0.02929	0.022	0.484
C4:0	S21_19933271	21	19933271	rs42850142	Intronic	LOC512150	T/C	0.000119	0.0999	0.018	0.463
C8:0	S23_15260292	23	15260292	rs453839711	Intergenic		A/C	1.82E-05	0.02778	0.022	0.429
C24:0	S3_125969441	3	125969441	rs439184439	Intergenic		G/A	8.19E-05	0.04775	0.019	0.394
C6:0	S21_65164887	21	65164887	rs432423874	Intronic	EVL	G/A	0.000191	0.09392	0.016	0.365
C20:5n3	S24_40818403	24	40818403	rs109764724	Intergenic		C/T	6.74E-06	0.02144	0.025	0.357
C4:0	S23_44081116	23	44081116	rs42030314	Intergenic		C/A	8.52E-05	0.088	0.018	0.323
C4:0	S15_2204384	15	2204384	rs133014695	Intergenic		A/G	3.68E-05	0.05308	0.02	0.320
C24:0	S8_1667147	8	1667147	rs109630798	Intergenic		G/A	0.000119	0.05878	0.018	0.280
C24:0	S15_84435339	15	84435339	rs110379736	Intergenic		A/G	8.15E-05	0.04775	0.019	0.265
C24:0	S28_44246992	28	44246992	rs42155039	Intronic	MARCH8	T/C	8.18E-05	0.04775	0.019	0.226
C4:0	S18_34969902	18	34969902	rs383910840	Intronic	CDH1	A/G	7.33E-05	0.08446	0.019	0.212
C8:0	S6_84481246	6	84481246	ss1850043060	Intergenic		C/T	7.76E-05	0.07165	0.018	0.212
C11:0	S6_84481246	6	84481246	ss1850043060	Intergenic		C/T	2.33E-06	0.0889	0.026	0.211
C13:0	S11_6782323	11	6782323	rs207538712	Intergenic		C/T	0.000384	0.08464	0.015	0.192
C24:0	S18_26865059	18	26865059	rs209759354	Intergenic		G/A	0.000229	0.08772	0.017	0.191
C24:0	S11_69400708	11	69400708	ss1850107740	Intronic	ANTXR1	C/T	0.000278	0.09614	0.016	0.186
C4:0	S10_104486629	10	104486629	rs109791124	Intergenic		G/A	6.59E-06	0.01937	0.024	0.185
C4:0	S28_24883940	28	24883940	rs208750352	Intronic	HK1	T/C	3.65E-05	0.05308	0.02	0.179
C4:0	S28_24883941	28	24883941	rs210345641	Intronic	HK1	T/C	3.65E-05	0.05308	0.02	0.179
C13:0	S24_60265567	24	60265567	ss1850262310	Intergenic		T/C	0.000396	0.08542	0.015	0.173
C6:0	S18_5423381	18	5423381	rs41856683	Intergenic		A/G	1.03E-05	0.01212	0.023	0.158
C8:0	S18_5423381	18	5423381	rs41856683	Intergenic		A/G	4.24E-06	0.01045	0.025	0.158
C24:0	S6_106786751	6	106786751	rs133693494	Intergenic		C/T	0.000117	0.05846	0.018	0.151
C13:0	S15_64028144	15	64028144	rs41776609	Intronic	CD59	T/C	7.75E-05	0.03149	0.018	0.142
C13:0	S11_94106253	11	94106253	rs135845527	Intergenic		G/C	0.000323	0.07741	0.015	0.133
C24:0	S3_25023007	3	25023007	rs135236823	Intergenic		G/C	0.000132	0.063	0.018	0.132
C6:0	S8_88522633	8	88522633	rs463987848	Intronic	BICD2	C/T	0.000177	0.0907	0.017	0.131
C4:0	S4_119339436	4	119339436	rs378444093	Intergenic		T/C	0.000116	0.09929	0.018	0.130
C4:0	S4_119339451	4	119339451	rs381758710	Intergenic		A/G	0.000116	0.09929	0.018	0.130
C13:0	S13_44358829	13	44358829	ss1850314106	Intergenic		C/G	0.000491	0.09547	0.014	0.128
C4:0	S9_106369166	9	106369166	ss1850086265	Intergenic		A/G	0.000112	0.09853	0.018	0.116
C4:0	S9_106369170	9	106369170	rs470906002	Intergenic		A/G	0.000112	0.09853	0.018	0.116
C13:0	S4_4330240	4	4330240	rs207853593	Intergenic		T/C	0.000215	0.06039	0.016	0.116
C20:5n3	S28_43479268	28	43479268	rs470755489	Coding	ERCC6	G/C	2.49E-05	0.05012	0.022	0.112
C6:0	S21_31073148	21	31073148	rs207776812	Intronic	PSMA4	T/A	0.000205	0.09734	0.016	0.103
C8:0	S21_31073148	21	31073148	rs207776812	Intronic	PSMA4	T/A	7.82E-05	0.07165	0.018	0.103
Dominant model
C13:0	S21_26707088	21	26707088	rs110179128	Intergenic		T/C	0.000395	0.06482	0.015	0.482
C23:0	S8_58122774	8	58122774	rs135761549	Intergenic		C/T	2.7E-05	0.07352	0.026	0.397
C6:0	S13_83809385	13	83809385	rs208127058	Intergenic		G/A	9.73E-05	0.07238	0.018	0.360
SFA	S17_74491357	17	74491357	rs41855732	Intergenic		G/C	1.38E-06	0.05285	0.027	0.328
C18:1n9c	S17_74491357	17	74491357	rs41855732	Intergenic		G/C	3.3E-06	0.08392	0.025	0.328
MUFA	S17_74491357	17	74491357	rs41855732	Intergenic		G/C	2.39E-06	0.05623	0.026	0.328
C23:0	S2_94271418	2	94271418	rs481169913	Intergenic		C/A	5.37E-06	0.03054	0.03	0.324
SFA	S16_48622152	16	48622152	rs465358414	Intergenic		G/C	1.03E-05	0.09875	0.023	0.270
SFA	S14_277266	14	277266	rs135581384	Intronic	TONSL	G/A	3.48E-06	0.07814	0.025	0.260
C18:1n9c	S14_277266	14	277266	rs135581384	Intronic	TONSL	G/A	1.53E-06	0.05824	0.027	0.260
C24:0	S10_20831159	10	20831159	rs211405588	Intergenic		T/C	0.000146	0.09791	0.018	0.243
C4:0	S25_11286202	25	11286202	rs109779107	Intergenic		G/C	2.22E-05	0.0584	0.021	0.226
C13:0	S29_8375318	29	8375318	rs208360098	Intergenic		C/T	0.000692	0.09006	0.014	0.219
C13:0	S29_8375314	29	8375314	rs211269917	Intergenic		T/C	0.000833	0.09972	0.013	0.216
C13:0	S1_130615136	1	130615136	rs208659424	Intronic	CLSTN2	T/C	0.000196	0.04411	0.016	0.209
C13:0	S27_39615226	27	39615226	rs135921072	Intergenic		C/T	0.000202	0.04533	0.016	0.202
C13:0	S8_97716573	8	97716573	rs135846930	Intergenic		T/C	0.000547	0.07852	0.014	0.199
C13:0	S27_39607188	27	39607188	rs207920200	Intergenic		C/T	0.00052	0.07685	0.014	0.191
C23:0	S10_100984214	10	100984214	rs110395591	Intergenic		C/T	2.34E-05	0.07249	0.026	0.174
C20:4n6	S27_16628049	27	16628049	rs42116637	Intergenic		A/C	5.03E-06	0.02745	0.025	0.169
C24:0	S1_4948474	1	4948474	rs137452899	Intergenic		A/G	7.62E-05	0.07742	0.019	0.164
C13:0	S25_38252119	25	38252119	rs108953935	Upstream	PILRA	A/G	0.000776	0.09531	0.013	0.156
C23:0	S10_100494903	10	100494903	rs380814997	Intergenic		T/C	2.43E-05	0.07249	0.026	0.151
C13:0	S1_130624357	1	130624357	rs210558202	Intronic	CLSTN2	T/C	0.000767	0.09461	0.013	0.143
C13:0	S26_48673391	26	48673391	rs133171238	Intergenic		A/G	7.55E-05	0.02452	0.019	0.135
C24:0	S8_14848948	8	14848948	rs110198610	Intergenic		G/C	0.000133	0.09462	0.018	0.133
C24:0	S8_14848943	8	14848943	rs110923026	Intergenic		T/C	9.01E-05	0.07814	0.019	0.132
C13:0	S2_121574985	2	121574985	rs109350928	Intergenic		A/G	0.000322	0.05826	0.015	0.112
C23:0	S17_47372617	17	47372617	ss1850179088	Intergenic		C/T	5E-05	0.09826	0.024	0.11
C13:0	S2_125566351	2	125566351	rs110334370	Intergenic		A/G	0.000317	0.05775	0.015	0.11
C4:0	S9_104908398	9	104908398	rs382936674	Intergenic		G/A	7.4E-06	0.02826	0.024	0.108
C6:0	S12_84413041	12	84413041	rs136905662	Coding	F7	T/G	0.000105	0.07469	0.018	0.104
C4:0	S9_104910742	9	104910742	rs467296387	Intergenic		T/C	1.31E-05	0.03991	0.022	0.101

¹Values in brackets were obtained with the dominant model.
²MAF: Minor allele frequency.

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Table 6 Commonly significantly associated SNPs (MAF ≥ 10%) with individual fatty acid traits.

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