Table 5. Genome sequence context for ARRDC3 and NFIA SNPs associated with BCHF.

Genome position				SNP identifier					Flanking features in 19 beef breeds d
Chr a	UMD3.1 (bp)	ARS-UCD1.2 (bp)	Gene	Bead Array	rs number	Alias	A 1/A 2 b	200 bp flanking genome sequence c	Type	ARS-UCD1.2 (bp)	Diff. (bp)	MAF
7	93229001	90830012	ARRDC3	BovineHD0700027233	rs110586518	BCHF60	A /G	5′-TACTCCAGAGTATCAGGGACCCATGAGGAATGATCAAGAAATGAAAATGGGGGAAAATGGGATTTTAAAATGGGTGGAAAGAAGTAAG MATTGGGTGAGA [ A/G] GATGAAAACCTAGACGAGGAGGGTAGCAACGGGAGTGGAAGAACAGGGACAGGGACCCTGGAGATCTTACGAGAAGACCGAGGAAACTTCATACCTTACT-3′	SNP SNP	90830000 90830012	-12 0	0.281 0.281
7	93231670	90832681	ARRDC3	BovineHD0700027234	rs135607340	BCHF61	A /G	5′-CTTAGAGAACGAAACGAGTTAATAGATTTTCCTCAAATTGGAGCAATTTTCTTCTTCTTTATTGAATCAGGAAAGCTAACT RTCAAAGAGGCATAGAGTG [ A/G] CGTAGATAATGCCCTAAGGTAACAAAACTCTATTATGTTGTGTTACATTAGCACCGAGCGAAGGGTATTTTA RAAGGAAATTTCACTGTGTAATAAGGGG-3′	SNP SNP SNP	90832662 90832681 90832754	-19 0 +73	0.083 0.281 0.083
7	93243245	90844254	ARRDC3	BovineHD0700027237	rs109439459	BCHF33	A /G	5′-TAAGAGACCAGTCCAATGCTGGGTCAGACTTTGTATTAAGTATTGACAATCTAACTTTTAATCTGTTGTTCAAAATTATTTATTTCTCTCTTACCATGAT [ A/G] ATCAAAACCTAACTGTATTTTCAGAAACTCTGCAATATTGCTTAGTAAGAGTCAGCCCATTTTGTACTTGAGGGTGTGATGCTTACCTCTGAATAAAGGG-3′	SNP	90844254	0	0.281
7	93243714	90844723	ARRDC3	BovineHD0700027238	rs136675904	BCHF34	C /T	5′-GGAAATATACATTTTAAATCTAACATTAGGGGCACACCCCATTCTTCAATACAGACAAATTTTATCTAATCATAAAATATCAGAAGCAAAATTATTTTCT [ C/T] GCAAATACCAGATTAAGCTTAGATACGCATTATCAAATTATTACCTTCAGGTCTTTCAGGTAGGGATAAACCAAGCCAGTTCATGTTCATGCTACACTGA-3′	SNP	90844723	0	0.281
7	93244933	90845941	ARRDC3	BovineHD0700027239 e	rs109901274	BCHF5	T /C	5′-TCAGTCTTGGTGGGAGTCCACCTCATACGTACCTGGCGTATAGCCCTTCCTTTCGATCTTGGCACTTAAGGATATGGGGCCTGAGGTACAGAACCAGCAA [ T/C] AGAGAGTCTTTTCTTTTGTGCCTGCTTGGGGTGACTGTAAGATATAAATTTAGAG RAAAAAATCAAGGTATGAATTGAGACAGGAATAAAATTTTTAAAA-3′	SNP SNP	90845941 90845997	0 +56	0.224 0.177
7	93247780	90848788	ARRDC3	BovineHD0700027240	rs135153741	BCHF35	G /T	5′-ATGACAGACTTGATATGTTCTCTTTTTTCAGCTAATGCTGATGGTGAACTATTAAGTGCTTACTATTTGACTAGCACCTTCCAATTCATTCACTTTAAAT [ G/T] AAATACTTTTAAACACCATACAAATCCTGGGACGGAATATTGAGGTTTGCTTTCTATAATTTTGCCACTCCAGATTAAAAAATAGCTT YTTTTTTTTTAG-3′	SNP SNP	90848788 90848877	0 +89	0.412 0.068
7	93251138	90851664	ARRDC3	BovineHD0700027241	rs110066813	BCHF36	T /C	5′-GTTTGTCCCCGTAAGTCGTATTATTATTCTACTTTTACCCCACTGCACACCACAACTCCTTAAAAACCTGTTTCTTCTAACCCATCTTAAAAAAAGCTAC [ T/C] AGTCAAGGAAGGATCAAATACAAACTCCTGGGCGTCCTGTTCAGCCAATACCAGGACTGTCATTAGGCAGTTCCATTTCTTATGACTGTCAGTGCTTGGA-3′	SNP	90851664	0	0.260
7	93263102	90863630	ARRDC3	BovineHD0700027244	rs109860522	BCHF62	C /T	5′-CAGTGTTTAATCTGTCAGTGTAGGACTCATTAATTGTTGTTGTTGAATTATTCTTTTTTATTTCAGTAGGGCTTCCTTTCCCAAAATAATGTTTAGTTAT [ C/T] AATAAACAACTCTTTACGTGATTGAAGACATTGTTTTCCACAAATTTATACATTTTGCCCCCAGATATGTTTAAAGTATATATATGCAC YATATTTGCTA-3′	SNP SNP	90863630 90863720	0 +90	0.260 0.021
7	93281534	90882079	ARRDC3	BovineHD0700027248	rs110253449	BCHF63	T /C	5′-TTCTTTTTGCCTGG KGCTGCACAGATCTTGAAGTCACTGCCAAACTAACTCTGCAGTGGCAACTTCAGAACACAAAATAAGCACTAGACCTAGAAATGCT [ T/C] GACACCCAAACTTAACGTATAGTCAAATAAATGGTTTAGTCTAGCACCTACCAGCCTTTAAGAAGAGCTTGTCAGTATACTCTTTCCTGTTGAAAGGAAA-3′	SNP SNP	90881993 90882079	-86 0	0.026 0.276
3	85123495	84578325	NFIA	BovineHD0300024307	rs136210820	BCHF31	G /A	5′-TTTTCCCTGGA WGAAATGAACTGCTGACATTCCGTGAACTCTATCTTTGCCTCACTTCTCACCCTGACCGTCAAACAAAGAAATCTGTCTTGAGTTCCAC [ G/A] ATGTACCCCATGTCACTATGACTAATCCAAAGCATTTTTATTTACAGTGTTCAGAAT RAATTTCTATGACAATCTCATGCCATTCTCACGTGCCTTTTGA-3′	SNP SNP SNP	84578236 84578325 84578383	-89 0 +58	0.042 0.448 0.052
3	85125825	84580655	NFIA	BovineHD0300024308	rs133192205	BCHF32	T /C	5′-TTACTAACCATGGACCAAGGACACATTTCTCAGCCTCTTTGTTTCTCAGCAGCATTAAGGCAATTATAAAAGCTCCCCTATCTAAAAGGTAAGATTTACA [ T/C] GAAGAACTAATAAAATAATGTATAAGAACCAACTTAAATATCATAGAAATGAACAACACTAGTCTAGCAGATCTGGCTTTCATCCTGGCTCTGCCACTTA-3′	SNP	84580655	0	0.422
3	85254825	84707876	NFIA	BovineHD0300024366 f	rs42583839	BCHF2	T /C	5′- tatctgcatgcaatgcaggagacctgggttcaatccctgggtcaggaagatcccctggaggagggcatggcaa TACTTCTGCTCTTGCTTAGAATAAAAT [ T/C] CAGTTCCCATGACAACCTGGTGGCCCTGAGGAG MCCGAAC RACTCCTGCTGCAGGGACCTGACCCTGTTCCGCTGCCTCCCTGTACATTCTGATCTGCGG-3′	SNP SNP SNP	84707876 84707910 84707917	0 +34 +41	0.464 0.021 0.073

^a Chromosome.

^b A1 was defined as the most frequent allele in the group of 204 BCHF cases and controls and the orientation is consistent with the ARS-UCD1.2 top strand (antisense strand in ARRDC3 and NFIA genes). The bolded red allele is associated with risk.

^c Sequence orientiation is consistent with the ARS-UCD1.2 top strand. Each sequence aligned uniquely to the reference genome except BovineHD0300024366 (rs42583839) which contained 75 bp of repetative sequence denoted in lowercase (blue).

^d Derived from WGS data with USMARC beef cattle diversity panel version 2.9 (MBCDPV2.9, Heaton et al., 2016), and PLINK software (v1.9, Chang et al., 2015) with filters for MAF greater than or equal to 0.015, and missing genotypes less than or equal to 0.05.

^e SNP BovineHD0700027239 corresponds to ARRDC3 C182Y (codon tRt) in exon 4 where tGt encodes C182 and tAt encodes Y182.

^f SNP BovineHD0300024366 was included for comparison, since it was used in early analyses for obtaining frequency data of U.S. cattle breeds in Table 4.