Table 1

Osteosarcoma associated loci identified by independent GWAS in three dog breeds with high rates of the disease
SNP chr Position P Risk allele OR f (A) f (U) Region start-end Size (kb) Genes
Greyhound
BICF2P133066 11 44405676 6.4E-07 A 1.26 0.84 0.65 44392734-44414985 22 None
BICF2P1421479 8 35448126 3.4E-05 C 1.36 0.12 0.03 35433142-35454649 22 OTX2 (50 kb)
BICF2S23118341 13 14588716 1.1E-04 T 1.20 0.34 0.19 14549973-14645634 96 None
BICF2S23325120 25 21912859 1.3E-04 A 1.19 0.56 0.41 21831580-21921256 90 None
BICF2P66597 14 49193217 1.6E-04 G 1.19 0.37 0.23 48831824-49203827 372 BMPER
BICF2P1194727 5 16085937 1.8E-04 G 1.23 0.28 0.14 16071171-16152955 82 GRIK4
BICF2G63051809 19 34134931 2.8E-04 T 1.21 0.80 0.67 33963105-34145310 182 EN1, MARCO
BICF2G630813090 16 43669044 3.0E-04 C 1.16 0.64 0.48 43665149-43737129 72 MTMR7
BICF2G630418573 15 63780452 3.4E-04 A 1.26 0.91 0.81 63767963-63800415 32 None
TIGRP2P215623 16 40896559 3.5E-04 C 1.36 0.97 0.89 40883517-41081510 198 SGCZ
TIGRP2P331221 25 43485109 3.8E-04 G 1.23 0.22 0.11 43476429-43528145 52 CCL20
BICF2S23516022 1 112990983 3.8E-04 C 1.21 0.82 0.69 112977233-113081800 105 CD3EAP, ERCC1, ERCC2, FOSB, PPP1R13L
TIGRP2P45171 3 5564882 4.0E-04 T 1.20 0.79 0.68 5162058-6465753 1,304 FER, MAN2A1, PJA2
BICF2P1090686 7 64672328 4.2E-04 C 1.16 0.57 0.43 64631053-64703475 72 CHST9
Rottweiler
BICF2P1115364 1 116524913 5.0E-07 G 1.32 0.71 0.39 115582915-116790630 1,208 Many (35 genes)
BICF2P411325 2 19515571 5.8E-06 C 1.43 0.91 0.73 19212450-19542015 330 KIAA1462
BICF2P1210630 1 122048812 1.1E-05 C 1.30 0.73 0.46 122033806-122051988 18 C19orf40, CEP89, RHPN2
TIGRP2P407733 35 18338700 1.8E-05 A 1.28 0.51 0.29 18326079-18345318 19 None
BICF2P341331 9 47659782 7.6E-05 A 1.28 0.53 0.28 47647012-47668054 21 BLMH, TMIGD1
BICF2P1129874 38 11714169 9.4E-05 T 1.24 0.49 0.26 11252518-11739329 487 FAM5C
TIGRP2P286750 21 46283811 1.1E-04 C 1.37 0.84 0.70 46231985-46363479 131 NELL1
BICF2S23533459 17 14472761 1.3E-04 C 1.39 0.18 0.01 14465884-14482152 16 None
BICF2G630590368 32 25147661 2.7E-04 A 1.35 0.95 0.81 25136302-25156153 20 EMCN
BICF2P92014 36 29651125 3.0E-04 A 1.22 0.66 0.42 29637804-29663408 26 None
TIGRP2P200071 15 38987072 3.1E-04 T 1.27 0.82 0.59 37986345-39974762 1,988 Many (15 genes)
BICF2P1164085 1 29775073 3.3E-04 G 1.24 0.46 0.23 29405587-29914411 509 EYA4, TCF21
BICF2S23712115 26 32385934 3.7E-04 G 1.35 0.91 0.76 32374093-32428448 54 ARVCF, C22orf25, COMT
BICF2G63095567 25 29671618 3.9E-04 G 1.30 0.23 0.05 29658978-29767164 108 XKR6
BICF2P841536 26 3537143 4.2E-04 A 1.26 0.48 0.30 3529343-3550075 21 FBRSL1
Irish Wolfhound
BICF2S23746532 5 15264066 2.1E-05 A 1.40 0.45 0.16 14720254-15466603 746 BLID
BICF2P1466354 18 4937944 2.7E-05 C 1.36 0.56 0.21 4266743-5854451 1,588 C7orf72, COBL, DDC, FIGNL1, GRB10, IKZF1, VWC2, ZPBP
BICF2P1225386 1 17742179 3.2E-04 C 1.31 0.46 0.19 16768869-18150476 1,382 BCL2, KIAA1468, PHLPP1, PIGN, RNF152, TNFRSF11A, ZCCHC2
BICF2P1125643 9 19623231 4.3E-04 C 1.75 0.14 0.02 18896060-19633155 737 ABCA5, KCNJ16, KCNJ2, MAP2K6

OR is the conditional odds ratio estimated from beta values calculated by EMMAX.

Karlsson et al.

Karlsson et al. Genome Biology 2013 14:R132   doi:10.1186/gb-2013-14-12-r132

Open Data