Table 4.

Genes in the Chr 4 QTL interval after narrowing the region by haplotype comparison

GeneStart (bp)Chr 4 LOD Scorecis-QTLHigh AlleleP
M0: ACRM0:ACR|GEXN0:GEXN0:GEX|ACR
Tlr4664886185.65.411.231.26NSM0.632
Ptprd755871435.65.281.711.52NMRL0.478
Mpdz809244095.65.463.613.87YMRL0.059
Nfib819360775.64.681.080.71NMRL0.389
Zdhhc21824446425.65.1816.6916.75YSM4.59 × 10−05
Cer1825276555.65.311.701.58NHet0.609
Frem1825438315.66.602.563.49NSM0.002
Cachd11004492805.65.370.910.82NMRL0.675
Sgip11024139025.65.402.132.42NMRL0.020
Wdr78102690477
Insl51027106705.65.350.500.51NMRL0.839
Mier11027869955.64.721.791.42NMRL0.010
Slc35d11028432545.64.197.095.73YSM2.06 × 10−05
Dab11032919645.65.322.922.65NHet0.567
Gm10271063530225.62.406.964.62YSM0.000
Tmem591068510045.65.421.761.74NSM0.789
Zyg11a1078545395.65.511.822.21NHet0.314
Zcchc111081320315.64.593.041.93NMRL0.002
Hyi1180325955.63.6516.7417.03YSM7.24 × 10−11
Szt21180353485.65.271.601.59NHet0.573
Med81180819425.65.322.082.04NMRL0.207
Elovl11181006985.65.032.021.91NSM0.103
Tmem1251182135465.65.370.540.55NSM0.268
Ppt11225134855.64.347.907.23YSM0.000
Cap11225362905.65.270.900.93NSM0.546
Mfsd2a1226240935.64.645.534.77YSM6.56 × 10−06
Mycl11226728955.65.370.680.65NHet0.998
Oxct2b1227935075.65.310.710.70NMRL0.477
Ppie1228043585.65.091.531.23NMRL0.156
Akirin11234118025.65.371.952.06NSM0.933
Rhbdl21234651175.64.0214.2712.47YMRL4.74 × 10−10
Psmb21263548745.65.361.611.62NMRL0.374
Tcfap2e1263932505.65.381.020.89NHet0.936
Zmym41265391835.64.443.062.88NMRL0.003
Zmym11267243385.65.231.331.36NMRL0.279
Zmym61267546275.65.951.421.49NMRL0.233
Csmd21276651015.65.371.140.91NHet0.789
Hmgb41279374565.65.281.020.80NMRL0.512
Zscan201282607835.65.421.842.01NMRL0.012
Tlr121282926905.61.3340.1838.86YMRL1.88 × 10−27
Phc21283319825.65.291.661.59NHet0.127
A3galt21284326085.65.511.551.65NHet0.675
  • The Chr 4 LOD scores for the ACR model (M0: ACR = Q + ε) and conditional on the gene expression trait (M1: ACR = Q + GEX + ε), likewise, the GEX model (N0: GEX = Q + ε) and the conditional model (N1: GEX = ACR + Q + ε). Transcripts that are cis-QTL at the suggestive level (P < 0.05) are indicated, along with the high allele and the P value for the ANOVA contrast MRL versus SM. Trl12 is the only candidate that upon conditioning reduces the ACR LOD peak below the suggestive level (P < 0.63). Conditioning Trl12 on ACR has little effect on the LOD score. Taken together, this suggests that Trl12 is the most likely upstream candidate gene.