. 2021 Mar 6;22(5):2679. doi: 10.3390/ijms22052679

Table 2.

Genomic features and annotation of the TOP-SNPs identified between HF and LF boars using Genomic-Wide Association Studies (GWAS) (the CG seqCpG is marked in red).

Location	Site Summary in the Analyzed Population n = 7						Annotation
Location	Ref	Alt	A1	F_A1 HF	F_A 1 LF	A2	SeqCpG	Annotation	Distance to TSS	ENSEMBL ID	GENE ID	Description
chr1:13745053	G	A	A	0.5	0.25	G	GC	Intron	28,711	ENSSSCG00000004081
chr1:13745059	T	C	C	0.5	0.25	T	TC		28,717
chr1:13745092	C	T	T	0.5	0.25	C	CG		28,750
chr1:54055492	A	G	G	0	0.625	A	AG	Distal Intergenic	33,321	ENSSSCG00000035731	−
chr1:54055493	G	C	C	0	0.625	G	GC		33,320
chr1:54055625	G	C	C	0	0.625	G	GA		33,188
chr1:57269839	T	A	A	0	0.625	T	TG	Intron	−3712	ENSSSCG00000024249	GABRR2	gamma-aminobutyric acid type A receptor subunit rho2 [Source:NCBI gene (formerly Entrezgene);Acc:100522289]
chr1:57269858	T	C	C	0	0.625	T	TC		−3731
chr1:57277143	C	A	A	0	0.625	C	CA		−11,016
chr1:57528770	G	A	A	0	0.625	G	GC	Intron	61,949	ENSSSCG00000050825
chr1:57621352	G	A	A	0	0.625	G	GC	Promoter	2902	ENSSSCG00000004322	ANKRD6	ankyrin repeat domain 6 [Source:NCBI gene (formerly Entrezgene);Acc:102167335]
chr1:57621367	G	A	A	0	0.625	G	GG		2917
chr1:57621370	T	C	C	0	0.625	T	TT		2920
chr1:128707723	C	T	T	0	0.625	C	TG	Promoter	1229	ENSSSCG00000022039
chr1:140846691	A	C	C	0.5	0.25	A	AT	Intron	170,343	ENSSSCG00000038547	GABRB3	gamma-aminobutyric acid type A receptor subunit beta3 [Source:VGNC Symbol;Acc:VGNC:88308]
chr1:167452422	C	G	G	0	0.625	C	GA	Distal Intergenic	63,364	ENSSSCG00000045133
chr1:168947778	T	G	G	0	0.625	T	TG	Intron	−147,253	ENSSSCG00000045715
chr2:10168387	C	T	C	0	0.625	T	TC	Intron	3002	ENSSSCG00000013087	TKFC	triokinase and FMN cyclase [Source:NCBI gene (formerly Entrezgene);Acc:100520121]
chr2:10168389	C	G	G	0	0.625	C	CA	Intron	3000	ENSSSCG00000013087	TKFC
chr2:13387750	G	T	T	0	0.625	G	TG	Promoter	−2942	ENSSSCG00000031163		smoothelin like 1 [Source:NCBI gene (formerly Entrezgene);Acc:110259259]
chr2:13387762	G	A	A	0	0.625	G	AA	Promoter	−2954	ENSSSCG00000031163
chr3:16873170	G	C	C	0.5	0.25	G	GT	Distal Intergenic	−4753	ENSSSCG00000007748	PSPH	phosphoserine phosphatase [Source:VGNC Symbol;Acc:VGNC:91931]
chr6:3925771	C	G	G	0	0.625	C	CA	Intron	18,808	ENSSSCG00000002669	CRISPLD2	cysteine rich secretory protein LCCL domain containing 2 [Source:VGNC Symbol;Acc:VGNC:96958]
chr6:3925776	C	G	G	0	0.625	C	CC		18,803
chr6:3925779	C	T	T	0	0.625	C	CC		18,800
chr6:7702343	G	C	C	0	0.625	G	GG	Intron	−4397	ENSSSCG00000045637
chr6:7702375	G	A	A	0	0.625	G	GG	Intron	−4429	ENSSSCG00000045637
chr6:101129470	A	G	G	0	0.625	A	AT	Distal Intergenic	35,288	ENSSSCG00000049298
chr7:87106399	G	T	T	0.5	0.25	G	GA	Distal Intergenic	−3090	ENSSSCG00000002263	SLCO3A1	solute carrier organic anion transporter family member 3A1 [Source:VGNC Symbol;Acc:VGNC:93197]
chr7:115966284	C	T	T	0	0.625	C	CG	Intron	5808	ENSSSCG00000030371	SERPINA3-2	alpha-1-antichymotrypsin 2 [Source:NCBI gene (formerly Entrezgene);Acc:396686]
chr7:115966307	C	T	T	0	0.625	C	CC		5785
chr7:115982628	C	A	A	0	0.625	C	AA		4776
chr7:115982655	G	T	T	0	0.625	G	TG		4749
chr8:1318578	C	T	T	0.5	0.25	C	CG	Intron	5424	ENSSSCG00000034633	CFAP99	cilia and flagella associated protein 99 [Source:VGNC Symbol;Acc:VGNC:86608]
chr8:1328667	A	G	G	0.5	0.25	A	AG	Intron	15,513	ENSSSCG00000034633	CFAP99
chr9:40003949	A	G	G	0.5	0.25	A	GC	Distal Intergenic	−46,046	ENSSSCG00000050685
chr9:40003978	T	C	C	0.5	0.25	T	TG	Distal Intergenic	−46,017	ENSSSCG00000050685
chr9:45947327	G	T	T	0.5	0.25	G	TT	Intron	15,089	ENSSSCG00000028204	TREH	trehalase [Source:VGNC Symbol;Acc:VGNC:94382]
chr11:7034734	A	T	T	0.5	0.25	A	AA	Intron	50,584	ENSSSCG00000009326	KATNAL1	katanin catalytic subunit A1 like 1 [Source:VGNC Symbol;Acc:VGNC:89310]
chr11:16127229	G	A	A	0.5	0.25	G	GG	Intron	67,905	ENSSSCG00000040538	WDFY2	WD repeat and FYVE domain containing 2 [Source:VGNC Symbol;Acc:VGNC:94902]
chr11:61861680	G	C	C	0	0.625	G	GG	Intron	323,962	ENSSSCG00000048281
chr12:19677123	G	A	A	0	0.625	G	GC	Intron	−4345	ENSSSCG00000040316	U2	U2 spliceosomal RNA [Source:RFAM;Acc:RF00004]
chr12:41648810	G	A	A	0.5	0.25	G	GT	Intron	−78,192	ENSSSCG00000040177	ASIC2	acid sensing ion channel subunit 2 [Source:VGNC Symbol;Acc:VGNC:97893]
chr12:41648838	T	C	C	0.5	0.25	T	TC	Intron	−78,164	ENSSSCG00000040177	ASIC2
chr12:42246850	A	G	G	0	0.625	A	AA	Intron	−61,012	ENSSSCG00000050001
chr14:4991961	T	G	G	1	0.125	T	TT	Distal Intergenic	419,328	ENSSSCG00000018795
chr14:24479770	A	G	G	0	0.625	A	GT	Intron	46,536	ENSSSCG00000009748	RIMBP2	RIMS binding protein 2 [Source:VGNC Symbol;Acc:VGNC:92306]
chr14:56252347	G	C	C	0.5	0.25	G	GG	Promoter	−1423	ENSSSCG00000043646
chr15:63579255	C	T	T	0.5	0.25	C	CC	Distal Intergenic	−13,443	ENSSSCG00000015872	GPD2	glycerol-3-phosphate dehydrogenase 2 [Source:VGNC Symbol;Acc:VGNC:96330]
chr15:63579295	A	G	G	0.5	0.25	A	AA	Distal Intergenic	−13,403	ENSSSCG00000015872	GPD2
chr15:140048049	C	T	T	0.5	0.25	C	CG	Intron	−12,312	ENSSSCG00000016368	FARP2	FERM, ARH/RhoGEF and pleckstrin domain protein 2 [Source:VGNC Symbol;Acc:VGNC:95809]
chr15:140089430	A	T	T	0.5	0.25	A	AA	Intron	14,636	ENSSSCG00000016368	FARP2
chr16:53406651	T	C	C	0	0.625	T	CC	Intron	−81,737	ENSSSCG00000017003	KCNIP1	potassium voltage-gated channel interacting protein 1 [Source:VGNC Symbol;Acc:VGNC:89348]
chrY:5970972	T	A	T	1	0	A	AA	Intron	24,002	ENSSSCG00000039894
chrY:5970979	G	C	G	1	0	C	CG	Intron	24,009	ENSSSCG00000039894