| 1586018 | LOC500283 | similar to Proteasome 26S subunit subunit 4 ATPase CG5289-PA | 4 | 144640123 | 144641406 | Rat |
| 2322887 | LOC100360058 | D-tyrosyl-tRNA deacylase 1-like | 4 | 145965076 | 146055581 | Rat |
| 2324315 | LOC100362643 | CDC28 protein kinase regulatory subunit 2 | 4 | 146600529 | 146600768 | Rat |
| 619857 | Grm7 | glutamate receptor, metabotropic 7 | 4 | 146952340 | 147270225 | Rat |
| 1596937 | LOC678747 | hypothetical protein LOC678747 | 4 | 147754404 | 147807555 | Rat |
| 1308963 | Lmcd1 | LIM and cysteine-rich domains 1 | 4 | 148071431 | 148130313 | Rat |
| 1562010 | Ssuh2 | ssu-2 homolog | 4 | 148211602 | 148229983 | Rat |
| 2281 | Cav3 | caveolin 3 | 4 | 148294428 | 148310380 | Rat |
| 3239 | Oxtr | oxytocin receptor | 4 | 148314089 | 148326797 | Rat |
| 1306993 | Rad18 | RAD18 homolog (S. cerevisiae) | 4 | 148452664 | 148543743 | Rat |
| 1563152 | Srgap3 | SLIT-ROBO Rho GTPase activating protein 3 | 4 | 148562981 | 148798613 | Rat |
| 1585950 | LOC679639 | hypothetical protein LOC679639 | 4 | 148867112 | 148870978 | Rat |
| 1560852 | Thumpd3 | THUMP domain containing 3 | 4 | 148918100 | 148941045 | Rat |
| 1310433 | Setd5 | SET domain containing 5 | 4 | 148949819 | 149027459 | Rat |
| 727967 | Lhfpl4 | lipoma HMGIC fusion partner-like 4 | 4 | 149049668 | 149072608 | Rat |
| 1585900 | LOC679689 | hypothetical protein LOC679689 | 4 | 149121732 | 149122055 | Rat |
| 1304842 | Mtmr14 | myotubularin related protein 14 | 4 | 149121980 | 149165007 | Rat |
| 1309212 | Cpne9 | copine family member IX | 4 | 149165857 | 149189090 | Rat |
| 1584828 | Brpf1 | bromodomain and PHD finger containing, 1 | 4 | 149191088 | 149207605 | Rat |
| 621168 | Ogg1 | 8-oxoguanine DNA glycosylase | 4 | 149209745 | 149219081 | Rat |
| 629473 | Camk1 | calcium/calmodulin-dependent protein kinase I | 4 | 149220661 | 149229168 | Rat |
| 2319531 | LOC100361743 | chaperonin containing Tcp1, subunit 3 (gamma) | 4 | 149236389 | 149238604 | Rat |
| 2319475 | LOC100361799 | cDNA sequence BC006662-like | 4 | 149242075 | 149242657 | Rat |
| 1564009 | Tada3 | transcriptional adaptor 3 | 4 | 149247795 | 149259252 | Rat |
| 1310096 | Arpc4 | actin related protein 2/3 complex, subunit 4 | 4 | 149259767 | 149271500 | Rat |
| 1311255 | Ttll3 | tubulin tyrosine ligase-like family, member 3 | 4 | 149280690 | 149282413 | Rat |
| 1307582 | Rpusd3 | RNA pseudouridylate synthase domain containing 3 | 4 | 149297259 | 149301491 | Rat |
| 1562113 | Cidec | cell death-inducing DFFA-like effector c | 4 | 149307986 | 149321303 | Rat |
| 2319333 | LOC100361844 | mCG51413-like | 4 | 149326712 | 149329894 | Rat |
| 735148 | Il17re | interleukin 17 receptor E | 4 | 149348600 | 149361697 | Rat |
| 1306392 | Il17rc | interleukin 17 receptor C | 4 | 149362504 | 149374934 | Rat |
| 1309412 | Creld1 | cysteine-rich with EGF-like domains 1 | 4 | 149375373 | 149384983 | Rat |
| 1562419 | Prrt3 | proline-rich transmembrane protein 3 | 4 | 149387967 | 149393829 | Rat |
| 1311566 | Emc3 | ER membrane protein complex subunit 3 | 4 | 149405742 | 149422064 | Rat |
| 1303172 | Fancd2 | Fanconi anemia, complementation group D2 | 4 | 149424558 | 149500006 | Rat |
| 1565997 | Fancd2os | FANCD2 opposite strand | 4 | 149500797 | 149504275 | Rat |
| 1598136 | Brk1 | BRICK1, SCAR/WAVE actin-nucleating complex subunit | 4 | 149507741 | 149522713 | Rat |
| 3960 | Vhl | von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase | 4 | 149529396 | 149536289 | Rat |
| 1309584 | Irak2 | interleukin-1 receptor-associated kinase 2 | 4 | 149543029 | 149599463 | Rat |
| 1598100 | LOC679970 | hypothetical protein LOC679970 | 4 | 149601735 | 149602210 | Rat |
| 1586017 | Tatdn2 | TatD DNase domain containing 2 | 4 | 149602011 | 149617752 | Rat |
| 632283 | Ghrl | ghrelin/obestatin prepropeptide | 4 | 149622566 | 149628111 | Rat |
| 1359555 | Sec13 | SEC13 homolog (S. cerevisiae) | 4 | 149637058 | 149650449 | Rat |
| 2176 | Atp2b2 | ATPase, Ca++ transporting, plasma membrane 2 | 4 | 149655651 | 149907813 | Rat |
| 2303168 | Bp330 | Blood pressure QTL 330 | 4.25 | .017 | Blood pressure | | 4 | 456799 | 149181446 | Rat |
| 2316958 | Gluco58 | Glucose level QTL 58 | 10 | | Glucose level | postprandial | 4 | 6690606 | 185398530 | Rat |
| 1358352 | Srcrt3 | Stress Responsive Cort QTL 3 | 2.29 | | Hypothalamic-pituitary-adrenal axis | corticosterone post-stress | 4 | 8819982 | 149560340 | Rat |
| 1576305 | Emca6 | Estrogen-induced mammary cancer QTL 6 | 5.8 | | Mammary tumor susceptibility | estradiol-induced | 4 | 41729583 | 159115617 | Rat |
| 1354612 | Foco1 | Food consumption QTL 1 | 8.87 | | Consumption level | food intake | 4 | 41729771 | 151158666 | Rat |
| 1354660 | Salc1 | Saline consumption QTL 1 | 11.26 | | Consumption level | saline intake | 4 | 41729771 | 151158666 | Rat |
| 2312567 | Glom19 | Glomerulus QTL 19 | 1.9 | .006 | Renal pathology | | 4 | 43686352 | 149560340 | Rat |
| 1298082 | Stresp4 | Stress response QTL 4 | | | Hormone level | corticosterone | 4 | 47889730 | 149560340 | Rat |
| 70200 | Alc18 | Alcohol consumption QTL 18 | 9.2 | | Consumption level | alcohol preference | 4 | 54828166 | 152570244 | Rat |
| 738009 | Sach4 | Saccharine consumption QTL 4 | 4.9 | .000016 | Consumption level | saccharin preference | 4 | 58421110 | 158108528 | Rat |
| 738016 | Alc16 | Alcohol consumption QTL 16 | 3.6 | .00015 | Consumption level | alcohol preference | 4 | 58421110 | 158108528 | Rat |
| 738031 | Alc14 | Alcohol consumption QTL 14 | 7.6 | .00003 | Consumption level | alcohol preference | 4 | 58421110 | 158108528 | Rat |
| 631674 | Iddm14 | Insulin dependent diabetes mellitus QTL 14 | | | Glucose level | | 4 | 63276741 | 160891592 | Rat |
| 61406 | Scwia1 | Streptococcal cell wall induced arthritis QTL 1 | 2.3 | | Joint/bone inflammation | streptococcal cell wall induced | 4 | 73972453 | 154937227 | Rat |
| 1576316 | Ept5 | Estrogen-induced pituitary tumorigenesis QTL 5 | 3.8 | | Gland mass | pituitary | 4 | 82700691 | 182307104 | Rat |
| 70177 | Xhs1 | X-ray hypersensitivity QTL 1 | 25.1 | | X-ray sensitivity | | 4 | 82861630 | 155893772 | Rat |
| 1582232 | Gluco25 | Glucose level QTL 25 | 3.6 | .0023 | Glucose level | uptake | 4 | 84886545 | 151158853 | Rat |
| 1358202 | Gluco11 | Glucose level QTL 11 | 2.4 | .02 | Glucose level | uptake | 4 | 85014031 | 171204531 | Rat |
| 634335 | Anxrr16 | Anxiety related response QTL 16 | 7.22 | | Anxiety response | | 4 | 93498821 | 171204377 | Rat |
| 61434 | Cia3 | Collagen induced arthritis QTL 3 | 4.8 | | Joint/bone inflammation | type II collagen induced | 4 | 104415843 | 149415843 | Rat |
| 737821 | Hcar9 | Hepatocarcinoma resistance QTL 9 | 3.7 | | Liver tumor resistance | nodule number | 4 | 106554769 | 171204531 | Rat |
| 6478680 | Anxrr29 | Anxiety related response QTL 29 | | .00092 | Anxiety response | open field inner locomotion | 4 | 106808891 | 151808891 | Rat |
| 6478740 | Anxrr39 | Anxiety related response QTL 39 | | .07528 | Anxiety response | open field inner locomotion | 4 | 106808891 | 151808891 | Rat |
| 2302049 | Pia32 | Pristane induced arthritis QTL 32 | 5.1 | .001 | Joint/bone inflammation | pristane induced | 4 | 107728559 | 152728559 | Rat |
| 731165 | Uae21 | Urinary albumin excretion QTL 21 | 2.4 | .0001 | Renal function | urine albumin level | 4 | 108641841 | 153641841 | Rat |
| 1331759 | Hrtrt13 | Heart rate QTL 13 | 3.54628 | | Heart rate | | 4 | 111754988 | 172369380 | Rat |
| 1549832 | Bss3 | Bone structure and strength QTL 3 | 11 | | Bone structure | Femoral midshaft cortical area | 4 | 112039347 | 157039347 | Rat |
| 7207480 | Bss105 | Bone structure and strength QTL 105 | 8.1 | | Bone structure | Femoral midshaft moment of inertia | 4 | 112039347 | 157039347 | Rat |
| 6478760 | Anxrr45 | Anxiety related response QTL 45 | | .06717 | Anxiety response | response in light-dark box | 4 | 113136999 | 158136999 | Rat |
| 6478763 | Anxrr46 | Anxiety related response QTL 46 | | .07428 | Anxiety response | response in light-dark box | 4 | 113136999 | 158136999 | Rat |
| 1331802 | Srn5 | Serum renin concentration QTL 5 | 3.045 | | Renin concentration | serum | 4 | 115896404 | 160896404 | Rat |
| 1300116 | Hrtrt5 | Heart rate QTL 5 | 3.76 | | Heart rate | salt-loaded | 4 | 117887605 | 154283969 | Rat |
| 724535 | Cm18 | Cardiac mass QTL 18 | 2.6 | | Cardiac mass | | 4 | 121375269 | 166375269 | Rat |
| 2293840 | Kiddil9 | Kidney dilation QTL 9 | 2.9 | | Renal pathology | kidney dilation | 4 | 122550935 | 151158853 | Rat |
| 631683 | Bp116 | Blood pressure QTL 116 | | .0001 | Blood pressure | salt-loaded systolic | 4 | 127060280 | 172060280 | Rat |
| 6478778 | Anxrr51 | Anxiety related response QTL 51 | | .25384 | Anxiety response | open field inner locomotion | 4 | 127547983 | 172547983 | Rat |
| 61451 | Ciaa4 | CIA Autoantibody QTL 4 | 3.1 | | Anti-type II collagen autoantibody titer | | 4 | 128179957 | 171204531 | Rat |
| 1358364 | Sradr4 | Stress Responsive Adrenal Weight QTL 4 | 4.92 | | Hypothalamic-pituitary-adrenal axis | adrenal gland weight | 4 | 132846974 | 177846974 | Rat |
| 631511 | Pia7 | Pristane induced arthritis QTL 7 | 4.3 | | Joint/bone inflammation | arthritis severity | 4 | 133939407 | 171204531 | Rat |
| 737978 | Pia23 | Pristane induced arthritis QTL 23 | 5.3 | | Joint/bone inflammation | arthritis severity | 4 | 133939407 | 171204531 | Rat |
| 61422 | Cia13 | Collagen induced arthritis QTL 13 | 4.5 | | Joint/bone inflammation | arthritis severity | 4 | 134858561 | 171204531 | Rat |
| 1549827 | Scl46 | Serum cholesterol level QTL 46 | 3.5 | | Lipid level | baseline serum cholesterol | 4 | 135601855 | 180601855 | Rat |
| 724558 | Plsm2 | Polydactyly-luxate syndrome (PLS) morphotypes QTL 2 | | .0003 | Limb morphology | hind feet phalanges number | 4 | 135628567 | 180628567 | Rat |
| 61362 | Oia2 | Oil induced arthritis QTL 2 | | .001 | Joint/bone inflammation | arthritis severity | 4 | 136668162 | 181668162 | Rat |
| 1298524 | Oia8 | Oil induced arthritis QTL 8 | | | Joint/bone inflammation | arthritis severity | 4 | 136668162 | 181668162 | Rat |
| 2303623 | Vencon2 | Ventilatory control QTL 2 | 3.8 | | Ventilatory control | re-oxygenation after hypoxia | 4 | 138523557 | 183523557 | Rat |
| 1578674 | Bmd12 | Bone mineral density QTL 12 | 3.8 | | Bone mineral density | femoral neck cortical vBMD | 4 | 140398530 | 185398530 | Rat |
| 2293659 | Bmd35 | Bone mineral density QTL 35 | 4.5 | .0001 | Bone mineral density | | 4 | 140454608 | 186104310 | Rat |
| 70201 | Gcr1 | Gastric cancer resistance QTL 1 | 2.7 | | Gastric tumor resistance | tumor size | 4 | 144600129 | 150048167 | Rat |
| 1581561 | Eae22 | Experimental allergic encephalomyelitis QTL 22 | | | Brain/spinal cord inflammation | | 4 | 145746752 | 187126005 | Rat |
| 6478693 | Anxrr32 | Anxiety related response QTL 32 | | .00092 | Anxiety response | response in light-dark box | 4 | 148704454 | 187126005 | Rat |
| 6478700 | Anxrr33 | Anxiety related response QTL 33 | | .00896 | Anxiety response | response in light-dark box | 4 | 148704454 | 187126005 | Rat |
| 6478718 | Anxrr34 | Anxiety related response QTL 34 | | .00896 | Anxiety response | response in light-dark box | 4 | 148704454 | 187126005 | Rat |
| 6478748 | Anxrr42 | Anxiety related response QTL 42 | | .28008 | Anxiety response | pen field inner locomotion | 4 | 148704454 | 187126005 | Rat |
| 6478754 | Anxrr43 | Anxiety related response QTL 43 | | .14035 | Anxiety response | pen field inner locomotion | 4 | 148704454 | 187126005 | Rat |
| 634342 | Cia24 | Collagen induced arthritis QTL 24 | 4.5 | | Joint/bone inflammation | type II collagen induced | 4 | 149304432 | 179854843 | Rat |