| 2303168 | Bp330 | Blood pressure QTL 330 | 4.25 | .017 | Blood pressure | | 4 | 456799 | 149181446 | Rat | n/a | region | qtl |
| 631261 | Tcas3 | Tongue tumor susceptibility QTL 3 | 6 | | Tongue tumor susceptibility | | 4 | 6179441 | 91330582 | Rat | n/a | region | qtl |
| 2316958 | Gluco58 | Glucose level QTL 58 | 10 | | Glucose level | postprandial | 4 | 6690606 | 185398530 | Rat | n/a | region | qtl |
| 1358352 | Srcrt3 | Stress Responsive Cort QTL 3 | 2.29 | | Hypothalamic-pituitary-adrenal axis | corticosterone post-stress | 4 | 8819982 | 149560340 | Rat | n/a | region | qtl |
| 1300139 | Hrtrt6 | Heart rate QTL 6 | 2.85 | | Heart rate | salt-loaded | 4 | 36611842 | 117887968 | Rat | n/a | region | qtl |
| 1576305 | Emca6 | Estrogen-induced mammary cancer QTL 6 | 5.8 | | Mammary tumor susceptibility | estradiol-induced | 4 | 41729583 | 159115617 | Rat | n/a | region | qtl |
| 1354612 | Foco1 | Food consumption QTL 1 | 8.87 | | Consumption level | food intake | 4 | 41729771 | 151158666 | Rat | n/a | region | qtl |
| 1354660 | Salc1 | Saline consumption QTL 1 | 11.26 | | Consumption level | saline intake | 4 | 41729771 | 151158666 | Rat | n/a | region | qtl |
| 2312567 | Glom19 | Glomerulus QTL 19 | 1.9 | .006 | Renal pathology | | 4 | 43686352 | 149560340 | Rat | n/a | region | qtl |
| 1298082 | Stresp4 | Stress response QTL 4 | | | Hormone level | corticosterone | 4 | 47889730 | 149560340 | Rat | n/a | region | qtl |
| 70200 | Alc18 | Alcohol consumption QTL 18 | 9.2 | | Consumption level | alcohol preference | 4 | 54828166 | 152570244 | Rat | n/a | region | qtl |
| 1641833 | Alc21 | Alcohol consumption QTL 21 | 8.6 | .0001 | Consumption level | alcohol preference | 4 | 54879077 | 127941994 | Rat | n/a | region | qtl |
| 631546 | Bp86 | Blood pressure QTL 86 | 3.2 | | Blood pressure | systolic | 4 | 55369931 | 91330856 | Rat | n/a | region | qtl |
| 1358363 | Sradr3 | Stress Responsive Adrenal Weight QTL 3 | 6.19 | | Hypothalamic-pituitary-adrenal axis | adrenal gland weight | 4 | 56690161 | 101690161 | Rat | n/a | region | qtl |
| 1558651 | Swd3 | Spike wave discharge measurement QTL 3 | 4.62 | .000024 | Spike wave discharge measurement | frequency | 4 | 56704868 | 91916048 | Rat | n/a | region | qtl |
| 738009 | Sach4 | Saccharine consumption QTL 4 | 4.9 | .000016 | Consumption level | saccharin preference | 4 | 58421110 | 158108528 | Rat | n/a | region | qtl |
| 738016 | Alc16 | Alcohol consumption QTL 16 | 3.6 | .00015 | Consumption level | alcohol preference | 4 | 58421110 | 158108528 | Rat | n/a | region | qtl |
| 738031 | Alc14 | Alcohol consumption QTL 14 | 7.6 | .00003 | Consumption level | alcohol preference | 4 | 58421110 | 158108528 | Rat | n/a | region | qtl |
| 634344 | Hcar7 | Hepatocarcinoma resistance QTL 7 | 7.8 | | Liver tumor resistance | 3-methyl-4-dimethylaminoazobenzene induced | 4 | 58550170 | 93498821 | Rat | n/a | region | qtl |
| 2300179 | Bmd50 | Bone mineral density QTL 50 | 5.9 | .0001 | Bone mineral density | | 4 | 60200806 | 105200806 | Rat | n/a | region | qtl |
| 1549843 | Bw53 | Body weight QTL 53 | | .0001 | Body weight | | 4 | 60262965 | 104415981 | Rat | n/a | region | qtl |
| 1549839 | Bw52 | Body weight QTL 52 | | .0001 | Body weight | | 4 | 60262965 | 116780394 | Rat | n/a | region | qtl |
| 61418 | Pia5 | Pristane induced arthritis QTL 5 | 4.5 | | Joint/bone inflammation | inflammation score | 4 | 60974346 | 130228614 | Rat | n/a | region | qtl |
| 1578657 | Bss12 | Bone structure and strength QTL 12 | 8.9 | | Bone structure | femoral neck total area | 4 | 61483655 | 106483655 | Rat | n/a | region | qtl |
| 1578658 | Bss13 | Bone structure and strength QTL 13 | 8 | | Bone structure | femoral neck polar moment of inertia (Ip) | 4 | 61483655 | 106483655 | Rat | n/a | region | qtl |
| 70192 | BpQTLcluster5 | Blood pressure QTL cluster 5 | 2.6 | | Blood pressure | | 4 | 61646915 | 116611046 | Rat | n/a | region | qtl |
| 6478684 | Anxrr30 | Anxiety related response QTL 30 | | .00087 | Anxiety response | | 4 | 62386644 | 107386644 | Rat | n/a | region | qtl |
| 6478743 | Anxrr40 | Anxiety related response QTL 40 | | .83076 | Anxiety response | pen field inner locomotion | 4 | 62386644 | 107386644 | Rat | n/a | region | qtl |
| 6478772 | Anxrr49 | Anxiety related response QTL 49 | | .15488 | Anxiety response | open field inner locomotion | 4 | 62386644 | 107386644 | Rat | n/a | region | qtl |
| 631651 | Bp124 | Blood pressure QTL 124 | 3 | | Blood pressure | systolic | 4 | 62514126 | 107514126 | Rat | n/a | region | qtl |
| 1641919 | Alc22 | Alcohol consumption QTL 22 | | .0005 | Consumption level | alcohol preference | 4 | 62832008 | 127941994 | Rat | n/a | region | qtl |
| 631674 | Iddm14 | Insulin dependent diabetes mellitus QTL 14 | | | Glucose level | | 4 | 63276741 | 160891592 | Rat | n/a | region | qtl |
| 2312569 | Pur19 | Proteinuria QTL 19 | 3.4 | .001 | Renal function | urine protein level | 4 | 63787419 | 96623433 | Rat | n/a | region | qtl |
| 61330 | Eau1 | Experimental allergic uveoretinitis QTL 1 | | .0003 | Uvea inflammation score | | 4 | 69183301 | 134858710 | Rat | n/a | region | qtl |
| 631646 | Stl4 | Serum triglyceride level QTL 4 | 6.5 | .0001 | Lipid level | triglyceride | 4 | 72160227 | 134858710 | Rat | n/a | region | qtl |
| 61476 | Aia3 | Adjuvant induced arthritis QTL 3 | 3.9 | | Joint/bone inflammation | arthritis severity | 4 | 73972453 | 133939659 | Rat | n/a | region | qtl |
| 61406 | Scwia1 | Streptococcal cell wall induced arthritis QTL 1 | 2.3 | | Joint/bone inflammation | streptococcal cell wall induced | 4 | 73972453 | 154937227 | Rat | n/a | region | qtl |
| 724522 | Bp146 | Blood pressure QTL 146 | 2.2 | .0021 | Blood pressure | systolic | 4 | 74123346 | 119123346 | Rat | n/a | region | qtl |
| 2302051 | Pia28 | Pristane induced arthritis QTL 28 | 5.3 | .001 | Joint/bone inflammation | pristane induced | 4 | 74123346 | 119123346 | Rat | n/a | region | qtl |
| 70167 | Bw22 | Body weight QTL 22 | 3.1 | | Body weight | | 4 | 75732943 | 119369308 | Rat | n/a | region | qtl |
| 1357342 | Bw40 | Body weight QTL 40 | | .001 | Body weight | | 4 | 75732943 | 119369308 | Rat | n/a | region | qtl |
| 631662 | Hcar2 | Hepatocarcinoma resistance QTL 2 | 3.1 | .0003 | Liver tumor resistance | nodule volume | 4 | 78035196 | 135074488 | Rat | n/a | region | qtl |
| 631556 | Bp135 | Blood pressure QTL 135 | | .05 | Blood pressure | | 4 | 78038013 | 119369308 | Rat | n/a | region | qtl |
| 2306899 | Bp338 | Blood pressure QTL 338 | | .071 | Blood pressure | salt-loaded systolic | 4 | 80205349 | 121829076 | Rat | n/a | region | qtl |
| 738015 | Pia9 | Pristane induced arthritis QTL 9 | 4.5 | .048 | Joint/bone inflammation | arthritis severity | 4 | 81916057 | 126916057 | Rat | n/a | region | qtl |
| 2306794 | Ean2 | Experimental allergic neuritis QTL 2 | 6.4 | | Peripheral nerve inflammation | demyelination | 4 | 82700691 | 96313512 | Rat | n/a | region | qtl |
| 1576316 | Ept5 | Estrogen-induced pituitary tumorigenesis QTL 5 | 3.8 | | Gland mass | pituitary | 4 | 82700691 | 182307104 | Rat | n/a | region | qtl |
| 70177 | Xhs1 | X-ray hypersensitivity QTL 1 | 25.1 | | X-ray sensitivity | | 4 | 82861630 | 155893772 | Rat | n/a | region | qtl |
| 634334 | Xhs3 | X-ray hypersensitivity QTL 3 | 10 | | X-ray sensitivity | | 4 | 84355208 | 131969855 | Rat | n/a | region | qtl |
| 1582232 | Gluco25 | Glucose level QTL 25 | 3.6 | .0023 | Glucose level | uptake | 4 | 84886545 | 151158853 | Rat | n/a | region | qtl |
| 1358202 | Gluco11 | Glucose level QTL 11 | 2.4 | .02 | Glucose level | uptake | 4 | 85014031 | 171204531 | Rat | n/a | region | qtl |
| 2317587 | Eae26 | Experimental allergic encephalomyelitis QTL 26 | | | Brain/spinal cord inflammation | severity of disease | 4 | 88462327 | 104416171 | Rat | n/a | region | qtl |
| 1578662 | Bss15 | Bone structure and strength QTL 15 | 19.6 | | Bone structure | femoral neck width | 4 | 89539438 | 134539438 | Rat | n/a | region | qtl |
| 1578670 | Bss14 | Bone structure and strength QTL 14 | 16.4 | | Bone structure | femoral neck trabecular area | 4 | 89539438 | 134539438 | Rat | n/a | region | qtl |