Table 3.
Haplotype Analysis to Prioritize Candidate Genes for Atherosclerosis QTLs on Chromosomes 2 and 15
| Gene | Chromosome | Position | Low Allele | High Allele | Consequence | ||
|---|---|---|---|---|---|---|---|
| B6 | AKR/J | C3H/HeJ | DBA/2J | ||||
| Rbm38 | 2 | 172847290 | G | G | c | c | 5′_UTR |
| Rbm38 | 2 | 172847496 | G | G | A | A | 5′_UTR |
| Cdh4 | 2 | 179177190 | C | C | T | T | 5′_UTR |
| Cdh4 | 2 | 179179412 | G | G | A | A | NON_SYNONYMOUS_CODING |
| Ss18l1 | 2 | 179777235 | C | C | G | G | 5′_UTR |
| Hrh3 | 2 | 179835661 | C | C | T | T | NON_SYNONYMOUS_CODING |
| Osbpl2 | 2 | 179854116 | G | G | A | A | 5′_UTR |
| Lama5 | 2 | 179913809 | C | C | A | A | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179915098 | T | T | G | G | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179920402 | C | C | T | T | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179920521 | G | G | T | T | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179921374 | T | T | C | C | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179925043 | C | C | T | T | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179928191 | A | A | G | G | 5′_UTR |
| Lama5 | 2 | 179928517 | G | G | A | A | 5′_UTR |
| Lama5 | 2 | 179929976 | C | C | T | T | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179933048 | G | G | A | A | 5′_UTR |
| Lama5 | 2 | 179933067 | G | G | T | T | NON_SYNONYMOUS_CODING |
| Lama5 | 2 | 179933747 | T | T | A | A | 5′_UTR |
| Lama5 | 2 | 179933873 | G | G | A | A | NON_SYNONYMOUS_CODING |
| Gene | Chromosome | Position | B6 | C3H/HeJ | 129 | Consequence | |
|---|---|---|---|---|---|---|---|
| Rhpn1 | 15 | 75543724 | A | G | G | NON_SYNONYMOUS_CODING | |
| Apol11b | 15 | 77468437 | A | c | C | NON_SYNONYMOUS_CODING | |
| Cacng2 | 15 | 77950358 | G | A | A | 5′_UTR | |
| Ift27 | 15 | 78004380 | C | A | A | 5′_UTR | |
| Ncf4 | 15 | 78075365 | T | C | C | 5′_UTR | |
| Ncf4 | 15 | 78081428 | G | A | A | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78115054 | G | t | t | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78115310 | T | C | c | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78115528 | C | t | t | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78115654 | A | G | G | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78115727 | T | C | C | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78117449 | A | G | G | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78119364 | T | A | A | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78122957 | C | G | g | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78122983 | G | a | A | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78123018 | T | g | G | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78123283 | G | A | A | NON_SYNONYMOUS_CODING | |
| Csf2rb2 | 15 | 78127509 | C | G | G | NON_SYNONYMOUS_CODING | |
| Mpst | 15 | 78240804 | A | G | G | NON_SYNONYMOUS_CODING | |
| Sstr3 | 15 | 78370921 | C | T | T | NON_SYNONYMOUS_CODING | |
| Sstr3 | 15 | 78370941 | G | A | A | NON_SYNONYMOUS_CODING | |
| Sstr3 | 15 | 78371011 | C | G | G | 5′_UTR | |
| Sstr3 | 15 | 78374301 | G | A | A | 5′_UTR | |
| Sstr3 | 15 | 78374693 | A | G | G | 5′_UTR | |
| Sstr3 | 15 | 78374764 | T | C | C | 5′_UTR | |
| Gm6723 | 15 | 78384992 | C | T | T | NON_SYNONYMOUS_CODING | |
| Gm6723 | 15 | 78385151 | G | C | C | NON_SYNONYMOUS_CODING | |
| Mfng | 15 | 78603821 | A | G | G | 5′_UTR | |
| Card10 | 15 | 78633071 | G | A | A | 5′_UTR | |
| Card10 | 15 | 78633319 | T | C | C | 5′_UTR | |
| Cdc42ep1 | 15 | 78677764 | G | A | A | 5′_UTR | |
| Cdc42ep1 | 15 | 78679988 | T | C | C | NON_SYNONYMOUS_CODING | |
| Cdc42ep1 | 15 | 78680104 | G | A | A | NON_SYNONYMOUS_CODING | |
| Cdc42ep1 | 15 | 78680263 | G | A | A | NON_SYNONYMOUS_CODING | |
| Lgals2 | 15 | 78681495 | T | C | C | NON_SYNONYMOUS_CODING | |
| Gcat | 15 | 78873505 | A | G | G | NON_SYNONYMOUS_CODING | |
| Micall1 | 15 | 78957630 | C | T | T | NON_SYNONYMOUS_CODING | |
| Pick1 | 15 | 79060137 | A | G | G | 5′_UTR | |
| Pick1 | 15 | 79079229 | A | G | G | NON_SYNONYMOUS_CODING | |
| Pick1 | 15 | 79086211 | A | C | C | NON_SYNONYMOUS_CODING | |
| Pick1 | 15 | 79086466 | G | T | T | NON_SYNONYMOUS_CODING | |
| Pick1 | 15 | 79086508 | A | g | G | NON_SYNONYMOUS_CODING | |
| Pick1 | 15 | 79086512 | C | g | G | NON_SYNONYMOUS_CODING | |
| Tmem184b | 15 | 79209126 | C | A | A | 5′_UTR | |
| Csnk1e | 15 | 79269395 | A | G | G | 5′_UTR | |
| Csnk1e | 15 | 79271799 | C | T | T | 5′_UTR | |
| Nptxr | 15 | 79624881 | T | G | G | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79722929 | C | A | A | 5′_UTR | |
| Apobec3 | 15 | 79725453 | A | T | T | 5′_UTR | |
| Apobec3 | 15 | 79725492 | T | A | A | 5′_UTR | |
| Apobec3 | 15 | 79725494 | T | G | G | 5′_UTR | |
| Apobec3 | 15 | 79725534 | A | G | G | 5′_UTR | |
| Apobec3 | 15 | 79725547 | G | A | A | 5′_UTR | |
| Apobec3 | 15 | 79725550 | T | A | A | 5′_UTR | |
| Apobec3 | 15 | 79725566 | G | A | A | 5′_UTR | |
| Apobec3 | 15 | 79725868 | G | A | A | 5′_UTR | |
| Apobec3 | 15 | 79725887 | G | C | C | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79725897 | A | T | T | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79725900 | G | A | A | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79728257 | A | G | G | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79728260 | G | C | C | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79728323 | G | A | A | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79728327 | A | G | G | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79728339 | C | A | A | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79728604 | G | A | A | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79729463 | T | C | C | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79729537 | G | C | C | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79735878 | A | G | G | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79735881 | G | C | C | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79735885 | C | T | T | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79735953 | C | G | G | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79736838 | C | T | T | NON_SYNONYMOUS_CODING | |
| Apobec3 | 15 | 79737380 | G | A | A | NON_SYNONYMOUS_CODING | |
| Cbx7 | 15 | 79749323 | C | T | T | NON_SYNONYMOUS_CODING | |
| Cbx7 | 15 | 79749453 | G | C | C | NON_SYNONYMOUS_CODING | |
| Cbx7 | 15 | 79764235 | T | G | G | NON_SYNONYMOUS_CODING | |
| Cbx7 | 15 | 79764259 | A | T | T | STOP_GAINED | |
| Cbx7 | 15 | 79764307 | A | T | T | NON_SYNONYMOUS_CODING | |
| Cbx7 | 15 | 79801396 | G | T | T | 5′_UTR | |
| Cbx7 | 15 | 79801461 | A | C | C | 5′_UTR | |
| Pdgfb | 15 | 79830813 | C | T | T | NON_SYNONYMOUS_CODING | |
| Pdgfb | 15 | 79844499 | T | G | G | 5′_UTR | |
| Pdgfb | 15 | 79844550 | A | C | C | 5′_UTR | |
| Pdgfb | 15 | 79844807 | G | T | T | 5′_UTR | |
| Pdgfb | 15 | 79844895 | G | A | A | 5′_UTR |
Analysis was performed using the Sanger SNP database (http://www.sanger.ac.uk/cgi-bin/modelorgs/mousegenomes/snps.pl). QTL indicates quantitative trait locus.