Table 1.
eQTL Hot Spots Identified in Backcross BMDMs Derived from WKY and LEW
| SNP | Chr. | Position (Mb) | Transcripts Mapping to Each SNP | Five Most Strongly Regulated Genes |
|---|---|---|---|---|
| Rn34_1071564105 | 1 | 71564105 | 7 | RGD1562091 / Zfp61 / Vasp / F1LU75_RAT / Slc26a11 |
| Rn34_1071580649 | 1 | 71580649 | 6 | Gemin7l1 / TMED5_RAT / LOC691921 / Kcnn4 / Trove2 |
| Rn34_1084462932 | 1 | 84462932 | 7 | F1M372_RAT / D3ZBY1_RAT / Flna / Plek / Fn1 |
| Rn34_1253288627 | 1 | 253288627 | 6 | Blnk / LOC689756 / Oasl / Apoc1 / Egr3 |
| Rn34_2146742392 | 2 | 146742392 | 6 | RGD1359508 / Dtwd2 / Hrh1 / RGD1561662 / Lce1l |
| Rn34_2164452465 | 2 | 164452465 | 6 | Sucnr1 / Tuft1 / Mgrn1 / Dlgap4 / Ptch1 |
| Rn34_9003266206 | 9 | 3266206 | 29 | Phlda1 / Pak6 / Xylt1 / Slc30a1 / RGD1565705 |
| Rn34_9003796216 | 9 | 3796216 | 9 | RGD1566226 / D4AE99_RAT / Slc35e4 / RGD1311946 / Hprt1 |
| Rn34_9004824426 | 9 | 4824426 | 15 | Plk3 / Capn5 / Bag3 / F1LTZ3_RAT / Ccl22 |
| Rn34_9005917596 | 9 | 5917596 | 7 | Tgfb2 / Leprot / RGD1310371 / Creb3l2 / RTN1_RAT |
| Rn34_9006863573a | 9 | 6863573 | 40 | Tspan7 / Rdh10 / F1LRS4_RAT / Plcd1 / D3ZC56_RAT |
| Rn34_9007659609a | 9 | 7659609 | 53 | D3ZC56_RAT / D3ZC56_RAT / Ms4a6b / Myo1d / Bend6 |
| Rn34_9008096016a | 9 | 8096016 | 97 | Kcnn4 / Slco4a1 / Flna / Bcat1 / Atp1a3 |
| Rn34_9010210028 | 9 | 10210028 | 6 | D4ACH5_RAT / St6gal1 / Myh9 / Plek / E9PU51_RAT |
n = 200. eQTL hot spots were defined as significant overrepresentation of trans-eQTLs (i.e., any SNP is associated with more than five transcripts; see Experimental Procedures).
a
SNPs delineate a genomic region of 1.2 Mb linked to the expression of 190 transcripts, which were located elsewhere in the genome and regulated in trans (i.e., trans-eQTLs).