| 1590913 | LOC298314 | similar to solute carrier family 25, member 5 | 1 | 106616095 | 106617796 | Rat |
| 1583961 | LOC691412 | similar to ADP/ATP translocase 2 | 1 | 106616978 | 106618063 | Rat |
| 1591914 | LOC502339 | hypothetical LOC502339 | 1 | 106619036 | 106634295 | Rat |
| 1583954 | LOC691419 | similar to Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing protein) (Single-strand RNA-binding protein) (hnRNP core protein A1) (HDP) | 1 | 106919624 | 106920720 | Rat |
| 1310401 | Siglech | sialic acid binding Ig-like lectin H | 1 | 107126060 | 107130290 | Rat |
| 1583938 | LOC691435 | hypothetical protein LOC691435 | 1 | 107155725 | 107159218 | Rat |
| 1304689 | Tubgcp5 | tubulin, gamma complex associated protein 5 | 1 | 107171399 | 107206919 | Rat |
| 1583933 | LOC691440 | similar to dynein, cytoplasmic, light peptide | 1 | 107217514 | 107218413 | Rat |
| 1583930 | LOC691443 | hypothetical protein LOC691443 | 1 | 107245652 | 107246498 | Rat |
| 1310332 | Cyfip1 | cytoplasmic FMR1 interacting protein 1 | 1 | 107245993 | 107334337 | Rat |
| 2320162 | LOC100361403 | hypothetical LOC100361403 | 1 | 107310574 | 107311473 | Rat |
| 1306051 | Nipa2 | non imprinted in Prader-Willi/Angelman syndrome 2 | 1 | 107335238 | 107359088 | Rat |
| 1305401 | Nipa1 | non imprinted in Prader-Willi/Angelman syndrome 1 | 1 | 107373113 | 107390777 | Rat |
| 1307989 | Herc2 | HECT and RLD domain containing E3 ubiquitin protein ligase 2 | 1 | 107440126 | 107645117 | Rat |
| 1559691 | LOC308670 | Dnmt3a-ps2 pseudogene | 1 | 107695006 | 107705733 | Rat |
| 2319958 | LOC100361509 | hypothetical LOC100361509 | 1 | 107908499 | 107909105 | Rat |
| 621735 | Gabrg3 | gamma-aminobutyric acid (GABA) A receptor, gamma 3 | 1 | 108189311 | 108821051 | Rat |
| 61859 | Gabra5 | gamma-aminobutyric acid (GABA) A receptor, alpha 5 | 1 | 108843086 | 108955130 | Rat |
| 1583910 | LOC691463 | hypothetical protein LOC691463 | 1 | 108954589 | 108955933 | Rat |
| 1583906 | LOC691467 | hypothetical protein LOC691467 | 1 | 109035998 | 109036619 | Rat |
| 2651 | Gabrb3 | gamma-aminobutyric acid (GABA) A receptor, beta 3 | 1 | 109047399 | 109277756 | Rat |
| 1583789 | LOC365263 | similar to hydroxysteroid dehydrogenase like 1 | 1 | 109360718 | 109362706 | Rat |
| 2319766 | LOC100361605 | hypothetical LOC100361605 | 1 | 109416034 | 109416802 | Rat |
| 1583896 | LOC691477 | similar to 60S ribosomal protein L29 (P23) | 1 | 109451787 | 109452125 | Rat |
| 2319686 | LOC100361687 | SET translocation-like | 1 | 109560501 | 109563090 | Rat |
| 1565871 | RGD1565871 | similar to airway trypsin-like 5 | 1 | 110047484 | 110086137 | Rat |
| 1306150 | Atp10a | ATPase, class V, type 10A | 1 | 110175554 | 110360215 | Rat |
| 1582811 | LOC691503 | similar to Ornithine decarboxylase (ODC) | 1 | 110609794 | 110611252 | Rat |
| 2319143 | LOC100361937 | protein BEX1-like | 1 | 110708014 | 110708403 | Rat |
| 1306361 | Ube3a | ubiquitin protein ligase E3A | 1 | 110729142 | 110816491 | Rat |
| 621306 | Snrpn | small nuclear ribonucleoprotein polypeptide N | 1 | 111570605 | 111592659 | Rat |
| 69269 | Snurf | SNRPN upstream reading frame | 1 | 111576073 | 111592853 | Rat |
| 1596942 | LOC678742 | similar to ras homolog gene family, member G | 1 | 111606068 | 111606715 | Rat |
| 1583788 | LOC365268 | similar to COMM domain containing 9 | 1 | 111898397 | 111900612 | Rat |
| 1561206 | RGD1561206 | similar to solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19 | 1 | 111906267 | 111907208 | Rat |
| 1584837 | LOC679704 | similar to zinc responsive protein ZD7 | 1 | 114279285 | 114280359 | Rat |
| 1560408 | RGD1560408 | similar to Mannoside acetylglucosaminyltransferase 4, isoenzyme A | 1 | 114404654 | 114406486 | Rat |
| 1562541 | RGD1562541 | RGD1562541 | 1 | 114662733 | 114663533 | Rat |
| 2323216 | LOC100363327 | Small nuclear ribonucleoprotein-associated protein B-like | 1 | 116018816 | 116019715 | Rat |
| 1310526 | Ndn | necdin, melanoma antigen (MAGE) family member | 1 | 116594603 | 116596202 | Rat |
| 1583615 | Magel2 | MAGE-like 2 | 1 | 116625779 | 116629840 | Rat |
| 1311197 | Mkrn3 | makorin, ring finger protein, 3 | 1 | 116673748 | 116675369 | Rat |
| 1591913 | LOC502342 | hypothetical LOC502342 | 1 | 116689320 | 116691350 | Rat |
| 1307664 | Peg12 | paternally expressed 12 | 1 | 116710210 | 116711065 | Rat |
| 1598109 | LOC679961 | similar to mortality factor 4 like 1 | 1 | 116721809 | 116722830 | Rat |
| 1598078 | LOC679992 | similar to HBxAg transactivated protein 2 | 1 | 116739429 | 116739875 | Rat |
| 1596884 | LOC680003 | similar to HBxAg transactivated protein 2 | 1 | 116739888 | 116740535 | Rat |
| 1596870 | LOC680017 | similar to Zinc finger CCCH-type domain-containing protein 11A | 1 | 116759829 | 116762608 | Rat |
| 1626035 | Vom2r-ps62 | vomeronasal 2 receptor, pseudogene 62 | 1 | 116879735 | 116897162 | Rat |
| 1596829 | LOC680059 | similar to non-POU domain containing, octamer-binding | 1 | 117009731 | 117011160 | Rat |
| 1596803 | A26c2 | ANKRD26-like family C, member 2 | 1 | 117256549 | 117296873 | Rat |
| 2323907 | LOC100362872 | hypothetical LOC100362872 | 1 | 117278699 | 117280283 | Rat |
| 2348 | Chrna7 | cholinergic receptor, nicotinic, alpha 7 (neuronal) | 1 | 117587580 | 117716267 | Rat |
| 1595473 | LOC680151 | similar to ribosomal protein L36 | 1 | 118006812 | 118007132 | Rat |
| 1595462 | LOC680162 | similar to Nucleosome binding protein 1 (Nucleosome binding protein 45) (NBP-45) (GARP45 protein) | 1 | 118081249 | 118081946 | Rat |
| 1308736 | Hmgn5b | | 1 | 118081347 | 118083725 | Rat |
| 1563721 | Otud7a | OTU domain containing 7A | 1 | 118142100 | 118247638 | Rat |
| 1565099 | Klf13 | Kruppel-like factor 13 | 1 | 118368164 | 118398938 | Rat |
| 1597140 | Trpm1 | transient receptor potential cation channel, subfamily M, member 1 | 1 | 118583516 | 118700653 | Rat |
| 1305958 | Mtmr10 | myotubularin related protein 10 | 1 | 118726116 | 118777543 | Rat |
| 1566323 | Fan1 | FANCD2/FANCI-associated nuclease 1 | 1 | 118784938 | 118811928 | Rat |
| 1307633 | Mphosph10 | M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein) | 1 | 118815636 | 118832462 | Rat |
| 1309966 | Mcee | methylmalonyl CoA epimerase | 1 | 118832889 | 118856087 | Rat |
| 1593008 | LOC680320 | hypothetical protein LOC680320 | 1 | 118943749 | 118950496 | Rat |
| 620845 | Apba2 | amyloid beta (A4) precursor protein-binding, family A, member 2 | 1 | 118970882 | 119156605 | Rat |
| 1592985 | Fam189a1 | family with sequence similarity 189, member A1 | 1 | 119161912 | 119225215 | Rat |
| 1309206 | Ndnl2 | necdin-like 2 | 1 | 119276434 | 119278432 | Rat |
| 2324715 | LOC100363175 | matrin 3-like | 1 | 119538226 | 119541809 | Rat |
| 1306305 | Tjp1 | tight junction protein 1 | 1 | 119684774 | 119750532 | Rat |
| 1590653 | LOC680507 | hypothetical protein LOC680507 | 1 | 119931478 | 119932335 | Rat |
| 2324277 | LOC100362681 | rCG24613-like | 1 | 120037501 | 120042976 | Rat |
| 1311308 | Tarsl2 | threonyl-tRNA synthetase-like 2 | 1 | 120050878 | 120087520 | Rat |
| 1564929 | Tm2d3 | TM2 domain containing 3 | 1 | 120102507 | 120117091 | Rat |
| 1590620 | LOC680540 | similar to RIKEN cDNA 0610040D20 | 1 | 120179468 | 120180146 | Rat |
| 3246 | Pcsk6 | proprotein convertase subtilisin/kexin type 6 | 1 | 120324843 | 120476913 | Rat |
| 2320494 | Snrpa1 | small nuclear ribonucleoprotein polypeptide A' | 1 | 120490921 | 120503974 | Rat |
| 628897 | Vimp | VCP-interacting membrane protein | 1 | 120509100 | 120518867 | Rat |
| 1311904 | Chsy1 | chondroitin sulfate synthase 1 | 1 | 120539002 | 120600102 | Rat |
| 1308000 | Lrrk1 | leucine-rich repeat kinase 1 | 1 | 120695657 | 120836324 | Rat |
| 628662 | Aldh1a3 | aldehyde dehydrogenase 1 family, member A3 | 1 | 120847746 | 120881883 | Rat |
| 1305154 | Asb7 | ankyrin repeat and SOCS box-containing 7 | 1 | 121091586 | 121142773 | Rat |
| 1308792 | Lins | lines homolog (Drosophila) | 1 | 121162852 | 121169099 | Rat |
| 1564356 | Cers3 | ceramide synthase 3 | 1 | 121213298 | 121298770 | Rat |
| 1595478 | LOC680146 | similar to Heat shock protein cognate 1 CG8937-PA, isoform A | 1 | 121283910 | 121285894 | Rat |
| 1308783 | Adamts17 | ADAM metallopeptidase with thrombospondin type 1 motif, 17 | 1 | 121324404 | 121491594 | Rat |
| 1590894 | LOC308706 | similar to glyceraldehyde-3-phosphate dehydrogenase | 1 | 122130238 | 122131489 | Rat |
| 1307209 | Lrrc28 | leucine rich repeat containing 28 | 1 | 122267092 | 122385096 | Rat |
| 1310409 | Ttc23 | tetratricopeptide repeat domain 23 | 1 | 122395433 | 122469865 | Rat |
| 727872 | Synm | synemin, intermediate filament protein | 1 | 122474205 | 122504176 | Rat |
| 2323523 | LOC100359717 | ribosomal protein L15-like | 1 | 122538751 | 122546084 | Rat |
| 1587035 | LOC680848 | similar to 60S ribosomal protein L29 (P23) | 1 | 122633537 | 122634664 | Rat |
| 2320273 | LOC100361392 | thymosin, beta 10-like | 1 | 122640219 | 122640353 | Rat |
| 2869 | Igf1r | insulin-like growth factor 1 receptor | 1 | 122704976 | 122990007 | Rat |
| 631688 | Hcas2 | Hepatocarcinoma susceptibility QTL 2 | 3 | .0001 | Liver tumor susceptibility | nodule number | 1 | 6253946 | 116153262 | Rat |
| 1358359 | Sradr1 | Stress Responsive Adrenal Weight QTL 1 | 4.74 | | Hypothalamic-pituitary-adrenal axis | adrenal gland weight | 1 | 28716493 | 124749065 | Rat |
| 2313051 | Bss57 | Bone structure and strength QTL 57 | 3.7 | .0001 | Bone strength | | 1 | 37646940 | 119780561 | Rat |
| 2313059 | Bss55 | Bone structure and strength QTL 55 | 3.2 | .0001 | Bone structure | | 1 | 37646940 | 119780561 | Rat |
| 2313072 | Bss53 | Bone structure and strength QTL 53 | 4.3 | .0001 | Bone structure | | 1 | 37646940 | 119780561 | Rat |
| 2313078 | Bss54 | Bone structure and strength QTL 54 | 3.5 | .0001 | Bone structure | | 1 | 37646940 | 119780561 | Rat |
| 2313094 | Bss58 | Bone structure and strength QTL 58 | 3.7 | .0001 | Bone strength | | 1 | 37646940 | 119780561 | Rat |
| 2313098 | Bmd70 | Bone mineral density QTL 70 | 3.6 | .0001 | Bone mineral density | | 1 | 37646940 | 119780561 | Rat |
| 2313099 | Bss56 | Bone structure and strength QTL 56 | 2.4 | .0001 | Bone structure | | 1 | 37646940 | 119780561 | Rat |
| 2313402 | Anxrr24 | Anxiety related response QTL 24 | | | Anxiety response | domestication | 1 | 43426139 | 146971983 | Rat |
| 1578654 | Bss10 | Bone structure and strength QTL 10 | 4 | | Bone structure | femoral neck cortical area | 1 | 43872710 | 162735928 | Rat |
| 634314 | Niddm44 | Non-insulin dependent diabetes mellitus QTL 44 | | | Glucose level | | 1 | 43872827 | 204280278 | Rat |
| 2298545 | Neuinf8 | Neuroinflammation QTL 8 | 2.9 | | Neuroinflammation | | 1 | 55083934 | 154002647 | Rat |
| 1300121 | Hrtrt1 | Heart rate QTL 1 | 3.7 | | Heart rate | salt-loaded | 1 | 64744882 | 116153262 | Rat |
| 1549903 | Bp267 | Blood pressure QTL 267 | | | Blood pressure | systolic, nighttime | 1 | 77541583 | 106445306 | Rat |
| 1582234 | Gluco18 | Glucose level QTL 18 | 3.4 | .0003 | Glucose level | uptake | 1 | 79749065 | 124749065 | Rat |
| 4889494 | Scort2 | Serum corticosterone level QTL 2 | 4.2 | | Hormone level | corticosterone | 1 | 80851478 | 125851478 | Rat |
| 1578780 | Cm52 | Cardiac mass QTL 52 | 3.3 | .0001 | Cardiac mass | | 1 | 81342810 | 225814178 | Rat |
| 2313083 | Bmd74 | Bone mineral density QTL 74 | 4 | .0001 | Bone mineral density | | 1 | 81947770 | 119780561 | Rat |
| 631519 | Pia11 | Pristane induced arthritis QTL 11 | 5.3 | | Joint/bone inflammation | arthritis severity | 1 | 83489176 | 186472032 | Rat |
| 738022 | Anxrr13 | Anxiety related response QTL 13 | 4.6 | .00039 | Anxiety response | open field inner locomotion | 1 | 83945235 | 128945235 | Rat |
| 724529 | Cm16 | Cardiac mass QTL 16 | 2.7 | | Cardiac mass | | 1 | 87465281 | 153578547 | Rat |
| 1358902 | Bw47 | Body weight QTL 47 | 1.67 | | Body weight | | 1 | 90282040 | 184857893 | Rat |
| 724521 | Uae1 | Urinary albumin excretion QTL 1 | 3.8 | .0001 | Renal function | urine albumin level | 1 | 90282040 | 185923619 | Rat |
| 1302788 | Scl19 | Serum cholesterol QTL 19 | 4.6 | .001 | Lipid level | cholesterol level | 1 | 90306033 | 124749065 | Rat |
| 1300153 | Bp171 | Blood pressure QTL 171 | 3.37 | | Blood pressure | salt-loaded diastolic | 1 | 90448902 | 145865373 | Rat |
| 724567 | Tcas6 | Tongue tumor susceptibility QTL 6 | 6.85 | | Tongue tumor susceptibility | | 1 | 92101613 | 146971983 | Rat |
| 2293142 | Bp314 | Blood pressure QTL 314 | | | Blood pressure | systolic | 1 | 94471673 | 139471673 | Rat |
| 1331800 | Scl25 | Serum cholesterol level QTL 25 | 3.013 | | Lipid level | cholesterol | 1 | 94473940 | 134980682 | Rat |
| 1331793 | Bp200 | Blood pressure QTL 200 | 3.71601 | | Blood pressure | systolic | 1 | 94473940 | 176855135 | Rat |
| 1331751 | Bp199 | Blood pressure QTL 199 | 3.60022 | | Blood pressure | diastolic | 1 | 94473940 | 186472032 | Rat |
| 1331749 | Hrtrt11 | Heart rate QTL 11 | 2.973 | | Heart rate | | 1 | 94473940 | 203303100 | Rat |
| 70209 | Niddm23 | Non-insulin dependent diabetes mellitus QTL 23 | 2.82 | | Glucose level | fasting | 1 | 94473940 | 203416143 | Rat |
| 731168 | Bp154 | Blood pressure QTL 154 | 3.4 | | Blood pressure | systolic | 1 | 94624828 | 220639653 | Rat |
| 61399 | Tcat1 | Tongue tumor resistance QTL 1 | 3.3 | | Tongue tumor resistance | | 1 | 101971983 | 146971983 | Rat |
| 1641897 | Alcrsp1 | Alcohol response QTL 1 | | | Alcohol response | loss of righting reflex | 1 | 102248992 | 147248992 | Rat |
| 2317833 | Alcrsp19 | Alcohol response QTL 19 | 12.4 | .001 | Alcohol response | loss of righting reflex | 1 | 102248992 | 147248992 | Rat |
| 61370 | Mcs3 | Mammary carcinoma susceptibility QTL 3 | 2.15 | | Mammary tumor susceptibility | | 1 | 102532145 | 134980682 | Rat |
| 1354623 | Rf46 | Renal function QTL 46 | 3.8 | | Creatinine level | serum | 1 | 103149923 | 154075310 | Rat |
| 1354591 | Cm36 | Cardiac mass QTL 36 | 4.1 | | Cardiac mass | left ventricle adjusted for tibia length | 1 | 103149923 | 206567907 | Rat |
| 1354615 | Cm32 | Cardiac mass QTL 32 | 5.2 | | Cardiac mass | left ventricle | 1 | 103149923 | 206567907 | Rat |
| 1354606 | Bp246 | Blood pressure QTL 246 | 3.6 | | Blood pressure | pulse pressure | 1 | 103149923 | 224426393 | Rat |
| 2303591 | Gluco41 | Glucose level QTL 41 | 2 | | Glucose level | fasting | 1 | 103483490 | 148483490 | Rat |
| 631569 | Bp93 | Blood pressure QTL 93 | | .0001 | Blood pressure | systolic | 1 | 106445165 | 122992360 | Rat |
| 631496 | Bp97 | Blood pressure QTL 97 | 3.08 | | Blood pressure | systolic | 1 | 106445165 | 163516043 | Rat |
| 1600363 | Hc6 | Hypercalciuria QTL 6 | 2.7 | | Renal function | calcium excretion | 1 | 112148733 | 250430505 | Rat |
| 631684 | Bp117 | Blood pressure QTL 117 | 8.3 | | Blood pressure | systolic | 1 | 112480604 | 157480604 | Rat |
| 1300158 | Bp173 | Blood pressure QTL 173 | 3.48 | | Blood pressure | salt-loaded time series calculation | 1 | 115946374 | 189900838 | Rat |
| 2313060 | Bss71 | Bone structure and strength QTL 71 | 2.6 | .0001 | Bone structure | | 1 | 119780411 | 186391852 | Rat |
| 631205 | Bp196 | Blood pressure QTL 196 | 4 | .0001 | Blood pressure | mean arterial | 1 | 119780561 | 204280278 | Rat |
| 2293140 | Bp313 | Blood pressure QTL 313 | | | Blood pressure | systolic | 1 | 122991895 | 167991895 | Rat |