A common regulatory haplotype doubles lactoferrin concentration in milk

Table 2 The top five most significant ChIP-seq and ATAC-seq peaks identified within 1 Mb of the LTF gene

Peak Name	Location (BTA22)	Score	Signal Value	Q-value	TSS
Ac-244	52541892–52549649	7113	64.64	711.34	CCDC12
Ac-592	53325802–53327345	3079	34.48	307.94	FYCO1\(^{\text {U}}\)
Ac-418	52935669–52936535	2764	31.86	276.42	LTF\(^{\text {U}}\)
Ac-630	53398218–53403461	2517	29.77	251.72	FYCO1\(^{*}\)
Ac-64	52136724–52138123	2170	26.77	217.07	ELP6\(^{*}\)
Me1-283	53332642–53338482	323	8.94	32.37	FYCO1
Me1-133	52560161–52586174	268	8.13	26.88	CCDC12\(^{*}\)
Me1-129	52541850–52549226	265	8.02	26.55	CCDC12
Me1-367	53749632–53751815	239	7.66	23.90	LARS2\(^{*}\)
Me1-194	52944846–52949322	239	7.72	23.90	LTF\(^{\text {U}}\)
Me3-482	53325803–53327366	29773	178.25	2977.31	FYCO1\(^{\text {U}}\)
Me3-106	52283328–52285089	29451	176.68	2945.13	PTPN23
Me3-567	53470756–53472052	26738	163.37	2673.81	LZTFL1
Me3-140	52360766–52363004	24267	151.06	2426.73	KLHL18,KIF9
Me3-164	52425038–52427859	22979	144.57	2297.99	–
ATAC-158	53625481–53627252	28987	13.14	2898.77	SACM1L
ATAC-49	52555035–52556223	22154	14.51	2215.48	CCDC12\(^{*}\)
ATAC-145	53470617–53471757	18874	17.63	1887.42	LZTFL1
ATAC-128	53333362–53335224	17271	10.28	1727.13	FYCO1\(^{U}\)
ATAC-54	52578451–52579389	16778	11.02	1677.87	CCDC12\(^{*}\)

Results are shown for each of the three histone modifications, and ATAC-seq peaks within the same window. Peak names are allocated by the peak caller sequentially for each dataset. Peaks are ranked by Q-value (\(-\log _{10}\)-scale). Score, signal value, and q-value are as reported in the narrowPeak or broadPeak files created by the peak caller. The transcription start site (TSS) column lists the genes for which the TSS overlapped with the peak, or, for those marked with an asterisk, the gene within which the peak is located. A superscript U indicates that the peak maps within 20 kb upstream of the indicated gene

ISSN: 1297-9686