Table 1. Genomic loci nominally associated with IgA levels.
| SNP | Chr | Postion | pa | Alleles | Risk allele | Region start-end | Size (kb) | Genes in region | Closest gene to SNP |
|---|---|---|---|---|---|---|---|---|---|
| German shepherd | |||||||||
| BICF2P417629 | 5 | 7,009,995 | 3.0E-05 | G/A | A | 6,498,684–8,172,621 | 1,674 | KIRREL3, ST3GAL4, DCP | KIRREL3 (upstream of) |
| BICF2P853011 | 5 | 29,238,199 | 4.6E-04 | T/C | C | 29,188,112–29,288,253 | 100 | TMEM123, MMP7 | TMEM123 (intron) |
| TIGRP2P118956 | 8 | 63,777,575 | 8.9E-05 | A/G | G | 63,211,755–63,827,575 | 616 | PP4R4, RETNLB, GSC, SERPINA1,2,3–6,9–13 | GSC (upstream of) |
| BICF2S23435776 | 10 | 69,122,184 | 3.9E-04 | A/C | C | 69,072,184–69,174,348 | 102 | ADD2, CLEC4F, FIGLA | ADD2 (upstream of) |
| BICF2G630530840 | 14 | 42,224,407 | 3.8E-04 | A/C | A | 42,174,407–42,291,282 | 117 | CHN2 | CHN2 (intronic) |
| BICF2P168717 | 16 | 46,117,662 | 3.0E-04 | A/C | A | 45,960,356–46,377,153 | 417 | IRF2, ENPP6 | IRF2 (intronic) |
| BICF2G630365408 | 23 | 48,489,474 | 4.1E-05 | C/A | C | 48,439,474–48,539,474 | 100 | DHX36, GPR149 | GPR149 (intronic) |
| BICF2P247941 | 27 | 37,404,652 | 4.6E-04 | T/C | T | 37,248,047–37,454,652 | 207 | SLC2A4,14, NANOG, FOXJ2, C3AR1 | FOXJ2 (upstream of) |
| Golden retriever | |||||||||
| BICF2P856602 | 6 | 18,062,312 | 1.6E-04 | C/T | T | 18,011,946–18,112,312 | 100 | Many! | PPP2CB (intronic) |
| BICF2P442233 | 21 | 45,973,013 | 4.4E-04 | T/C | T | 45,923,013–46,023,013 | 100 | LUZP2 | LUZP2 (intronic) |
| BICF2P261279 | 26 | 7,164,610 | 3.9E-05 | G/A | A | 7,114,611–7,846,707 | 732 | Many! | Lrrc43 (intronic) |
| BICF2G630261705 | 28 | 37,236,337 | 2.5E-04 | T/C | T | 37,228,122–37,362,478 | 134 | none | MKI67 (upstream of) |
| BICF2S232271 | 29 | 11,752,985 | 3.2E-04 | A/G | G | 10,808,328–11,803,162 | 995 | LINC01301, CLVS1, YWHAZ, RAB2A, CHD6, CHD7, CLVS1 | CLVS1 (intronic) |
| BICF2P877790 | 34 | 10,311,397 | 4.4E-04 | C/T | T | 10,261,397–10,685,205 | 424 | IRX2, C5orf38 | IRX2 (downstream of) |
| BICF2P963046 | 34 | 21,820,555 | 4.7E-05 | G/T | G | 21,406,221–22,589,723 | 1183 | TPRG1, TP63, LEPREL1, CLDN1, THEM207, IL1RAD, CLDN16 | TP63 (upstream of) |
| BICF2P1301719 | 34 | 41,393,801 | 4.4E-04 | C/T | C | 41,343,801–41,751,420 | 408 | LRMP | LRMP (upstream of) |
| Labrador retriever | |||||||||
| BICF2G630378390 | 23 | 24,721,148 | 3.8E-04 | G/A | G | 24,665,511–24,771,148 | 106 | SATB1, LOC339862 | SATB1 (downstream of) |
| TIGRP2P306755 | 23 | 42,076,158 | 3.3E-04 | C/T | C | 42,026,107–42,142,835 | 117 | None | PLSCR5 (upstream) |
| BICF2P227171 | 30 | 17,867,239 | 4.9E-04 | T/C | T | 17,817,239–17,917,239 | 100 | GNB5, MYO5C | GNB5 (intronic) |
| Shar-Pei | |||||||||
| BICF2S23136666 | 4 | 31,168,913 | 3.2E-04 | C/A | A | 31,118,913–31,218,913 | 100 | NRG3 | NRG3 (intronic) |
| BICF2G630552985 | 7 | 15,555,664 | 4.1E-04 | G/A | A | 15505664–15,605,664 | 100 | None | ZNF648 (upstream of) |
| BICF2S23410286 | 7 | 16,196,250 | 2.4E-04 | C/T | T | 16,146,250–16,246,197 | 100 | NPL, DHX9 | NPL (intronic) |
| BICF2P1401994 | 7 | 17,786,665 | 1.3E-04 | C/T | T | 17,736,665–17,836,665 | 100 | C1orf21 | C1orf21 (intronic) |
| BICF2S23136652 | 7 | 19,673,829 | 7.1E-05 | T/C | C | 19,623,829–19,723,829 | 100 | MTFR1, PTGS2 | PTGS2 (intronic) |
| BICF2P1436700 | 7 | 22,764,328 | 4.4E-04 | A/G | G | 22,714,328–22,814,328 | 100 | ASTN1, PAPPA2 | ASTN1 & PAPPA2 (downstream of) |
| BICF2P215640 | 8 | 16,058,011 | 2.0E-04 | A/G | G | 16,008,011–16,108,075 | 100 | MIPOL1, FOXA1 | MIPOL1 & FOXA1 (downstream of) |
| BICF2S2361733 | 22 | 20,899,197 | 4.1E-04 | T/G | G | 20,848,859–20,949,206 | 100 | none | none, closest gene is PCDH9 |
| TIGRP2P320304 | 24 | 41,301,998 | 3.3E-04 | T/C | C | 41,251,998–41,351,998 | 100 | CBLN4 | downstream of CBLN4 |
| BICF2S23711428 | 28 | 5,983,856 | 1.2E-04 | G/T | T | 5,933,856–6,033,856 | 100 | HECTD2 | HECTD2 (upstream of) |
| BICF2G630276743 | 28 | 7,733,212 | 2.4E-04 | T/C | T | 7,683,212–7,803,352 | 120 | MYOF, CEP55, FFAR4 | MYOF (intronic) |
| BICF2G630276012 | 28 | 9,909,408 | 1.2E-04 | A/G | G | 9,859,408–9,994,305 | 135 | TLL2, TM9SF3, PIK3AP1 | TM9SF3 (intronic) |
| BICF2G630275788 | 28 | 10,515,232 | 2.7E-05 | G/A | G | 10,446,800–13,077,479 | 2,631 | Many! | SLIT1 (intronic) |
| BICF2P677609 | 28 | 18,823,291 | 2.2E-04 | A/G | G | 18,773,291–18,873,291 | 100 | SORCS1 | SORCS1 (intronic) |
| TIGRP2P404896 | 35 | 1,981,709 | 2.9E-04 | C/T | T | 1,931,709–2,031,709 | 100 | FOXC1 | FOXC1 (intronic) |
| BICF2G630772654 | 35 | 8,300,115 | 2.7E-04 | G/A | A | 8,250,009–8,350,115 | 100 | SLC35B3 | SLC35B3 (downstream of) |
A total of 35 IgA associated regions were defined across four dog breeds based on SNPs in strong linkage disequilibrium (LD, r2 >0.8) and within 1 Mb of the top SNP (plus the flanking 50 kb). All regions except four, contained one or more protein-coding genes. Displayed in the table are the genomic positions (Canfam 3.1) of the associated regions, information about the SNPs including p values (a P1df) and gene content.