Table 2 List of candidate genes and corresponding significant identified SNPs within or very close (±100 kb) to the SNPs for subclinical ketosis in second and later lactations (SCK2)
SNP_name | rs_snp_name | chromosome | position | Ensembl_gene _id | Entrez_gene_id |
|---|---|---|---|---|---|
BovineHD0300010696; BovineHD0300010697 | rs109078663; rs110789481 | 3 | 34314659; 34316156 | ENSBTAG00000001136 | KIAA1324 |
BovineHD0300010081 | rs42784745 | 3 | 32149527 | ENSBTAG00000023535 | NA |
BovineHD0300010059 | rs43333803 | 3 | 32082026 | ENSBTAG00000034841 | NA |
Hapmap60224-rs29001782 | rs29001782 | 6 | 85178107 | ENSBTAG00000000438 | GNRHR |
BovineHD0600024201; BovineHD0600024204; Hapmap54015-rs29022799; | rs109901151; rs110246305; rs29022799; rs43473311 | 6 | 88494442; 88498400; 88421804; 88212890 | ENSBTAG00000002348 | SLC4A4 |
Hapmap50857-BTA-107920 | rs41610991 | 6 | 86819633 | ENSBTAG00000004040 | UGT2A1 |
BovineHD0600025086 | rs42606224 | 6 | 91447170 | ENSBTAG00000004237 | BTC |
BovineHD0600025613; BovineHD0600025593 | rs109510145; rs137505966 | 6 | 92951049; 92919992 | ENSBTAG00000004921 | FAM47E |
BovineHD0600025431; BovineHD0600025432; BovineHD0600025421 | rs133065719; rs134889097; rs43476314 | 6 | 92584159; 92585321; 92567521 | ENSBTAG00000007639 | SDAD1 |
BovineHD4100005289; BovineHD4100005290 | rs110786992; rs110899052 | 6 | 87136725; 87145250 | ENSBTAG00000007695 | CSN1S1 |
BovineHD0600024406 | rs137844449 | 6 | 89050323 | ENSBTAG00000009070 | NPFFR2 |
BovineHD0600022837; BovineHD0600022838; BovineHD0600022835; BovineHD0600022833; BovineHD0600022839; BovineHD0600022830; BovineHD0600022831; BovineHD0600022834 | rs132864694; rs134101925; rs134383135; rs135577932; rs135693518; rs136048407; rs136499310; rs136560941 | 6 | 82920849; 82925435; 82912559; 82905087; 82929947; 82896236; 82898792; 82907694 | ENSBTAG00000009438 | EPHA5 |
BovineHD0600024752 | rs110185652 | 6 | 90382995 | ENSBTAG00000011935 | RASSF6 |
BovineHD0600023861 | rs135052123 | 6 | 87039570 | ENSBTAG00000011952 | SULT1E1 |
ARS-BFGL-NGS-112872 | rs110707460 | 6 | 88069548 | ENSBTAG00000012397 | DCK |
BovineHD0600024291; BovineHD0600024289; BovineHD0600024288; BovineHD0600024294; BovineHD0600021907; Hapmap52479-rs29018853 | rs109547247; rs110310151; rs133300430; rs137023501; rs132666893; rs29018853 | 6 | 88732184 88728581; 88724389; 88735599; 79273130; 79203343 | ENSBTAG00000013718 | GC |
BovineHD0600023797 | rs135797682 | 6 | 86686282 | ENSBTAG00000015047 | LOC781988 |
BovineHD0600023599; BovineHD0600023609 | rs135335675; rs136617775 | 6 | 85838311; 85861013 | ENSBTAG00000015572 | YTHDC1 |
BovineHD0600024791 | rs109793149 | 6 | 90557327 | ENSBTAG00000019716 | CXCL8 |
Hapmap43767-BTA-113302 | rs41618641 | 6 | 85646902 | ENSBTAG00000038520 | NA |
Hapmap60224-rs29001782 | rs29001782 | 6 | 85178107 | ENSBTAG00000038648 | LOC100140490 |
BovineHD0600023676 | rs136388495 | 6 | 86188921 | ENSBTAG00000039991 | UGT2B10 |
BovineHD0600023659 | rs136518898 | 6 | 86122072 | ENSBTAG00000040337 | NA |
BovineHD0600024923; BovineHD0600024884 | rs133534783; rs133586557 | 6 | 90977968; 90863255 | ENSBTAG00000043960 | MTHFD2L |
BovineHD0600024601 | rs135618950 | 6 | 89677070 | ENSBTAG00000047335 | NA |
BovineHD0600023628 | rs110240917 | 6 | 85933714 | ENSBTAG00000048013 | LOC100138004 |
BovineHD1100004827; BovineHD1100004831 | rs110571223; rs43672311 | 11 | 15050414; 15081731 | ENSBTAG00000027932 | BIRC6 |
BovineHD1100004868; BovineHD1100004913 | rs110243275; rs42050566 | 11 | 15212371; 15369971 | ENSBTAG00000033010 | TTC27 |
BovineHD1400000443; BovineHD1400000446 | rs133518905; rs136122630 | 14 | 2758369; 2763621 | ENSBTAG00000000158 | LY6K |
BovineHD1400000275 | rs133271979 | 14 | 2019390 | ENSBTAG00000000312 | GRINA |
Hapmap52798-ss46526455 | rs41256919 | 14 | 1923292 | ENSBTAG00000000658 | WDR97 |
Hapmap30383-BTC-005848 | rs109752439 | 14 | 1489496 | ENSBTAG00000000879 | C14H8orf33 |
Hapmap30374-BTC-002159 | rs109529219 | 14 | 2468020 | ENSBTAG00000002104 | RHPN1 |
Hapmap30086-BTC-002066; BovineHD1400000389 | rs110199901; rs110382236 | 14 | 2524432; 2518104 | ENSBTAG00000003606 | NA |
BovineHD1400018136; BovineHD1400018139 | rs135447252; rs41632852 | 14 | 64993498; 64996863 | ENSBTAG00000004518 | GRHL2 |
ARS-BFGL-NGS-3122 | rs109476905 | 14 | 2721633 | ENSBTAG00000004595 | GML |
BovineHD1400000434 | rs110295964 | 14 | 2707911 | ENSBTAG00000004596 | LOC787628 |
ARS-BFGL-NGS-57820 | rs109146371 | 14 | 1651311 | ENSBTAG00000004761 | FOXH1 |
BovineHD1400000187; | rs136580003 | 14 | 1585385 | ENSBTAG00000007186 | ARHGAP39 |
ARS-BFGL-NGS-94706 | rs17870736 | 14 | 1696470 | ENSBTAG00000007749 | TONSL |
BovineHD1400000305 | rs137757978 | 14 | 2164419 | ENSBTAG00000008079 | NRBP2 |
BovineHD4100010523; BovineHD4100010524; UA-IFASA-8997 | rs110288957; rs110502044; rs41602530 | 14 | 2198215; 2201929; 2194228 | ENSBTAG00000008421 | SCRIB |
ARS-BFGL-NGS-107379; BovineHD1400000288 | rs109350371; rs135270011 | 14 | 2054457; 2084067 | ENSBTAG00000011922 | LOC786966 |
BovineHD1400000400; BovineHD4100010548 | rs109221516; rs110651119 | 14 | 2568452; 2566015 | ENSBTAG00000011939 | LY6H |
Hapmap52798-ss46526455 | rs41256919 | 14 | 1923292 | ENSBTAG00000012235 | SHARPIN |
Hapmap52798-ss46526455 | rs41256919 | 14 | 1923292 | ENSBTAG00000012242 | MAF1 |
Hapmap30383-BTC-005848 | rs109752439 | 14 | 1489496 | ENSBTAG00000012353 | ZNF34 |
BovineHD1400000239; BovineHD1400000246 | rs133299034; rs137787931 | 14 | 1855090; 1880378 | ENSBTAG00000014458 | MROH1 |
BovineHD1400000262 | rs135549651 | 14 | 1967325 | ENSBTAG00000015040 | SMPD5 |
BovineHD1400000457 | rs135781491 | 14 | 2833552 | ENSBTAG00000016209 | SLURP1 |
BovineHD1400000457 | rs135781491 | 14 | 2833552 | ENSBTAG00000016210 | LYPD2 |
BovineHD1400000262 | rs135549651 | 14 | 1967325 | ENSBTAG00000017281 | OPLAH |
BovineHD1400018541 | rs136940827 | 14 | 66276813 | ENSBTAG00000017833 | RNF19A |
BTA-34956-no-rs | rs41630614 | 14 | 1514056 | ENSBTAG00000018456 | ZNF7 |
BovineHD1400018582 | rs134747221 | 14 | 66468090 | ENSBTAG00000019793 | RGS22 |
ARS-BFGL-NGS-4939 | rs109421300 | 14 | 1801116 | ENSBTAG00000020751 | HSF1 |
BovineHD4100010534 | rs110706284 | 14 | 2398876 | ENSBTAG00000021472 | ZC3H3 |
ARS-BFGL-NGS-94706 | rs17870736 | 14 | 1696470 | ENSBTAG00000026320 | NA |
BovineHD1400000474; BovineHD1400000480; BovineHD1400000473; BovineHD1400000482 | rs108968192; rs136634846; rs137202573; rs137438227 | 14 | 2916658; 2936478; 2915391; 2940147 | ENSBTAG00000026340 | NA |
BovineHD1400000262; BovineHD1400000271; UA-IFASA-6878 | rs135549651; rs136792973; rs41629750 | 14 | 1967325; 2002126; 2002873 | ENSBTAG00000026350 | NA |
ARS-BFGL-NGS-4939 | rs109421300 | 14 | 1801116 | ENSBTAG00000026356 | DGAT1 |
ARS-BFGL-NGS-34135 | rs109968515 | 14 | 1675278 | ENSBTAG00000035254 | CYHR1 |
BovineHD1400000305 | rs137757978 | 14 | 2164419 | ENSBTAG00000037493 | PUF60 |
BovineHD1400000324 | rs137181538 | 14 | 2257386 | ENSBTAG00000040360 | CCDC166 |
BovineHD1400000246 | rs137787931 | 14 | 1880378 | ENSBTAG00000044406 | MIR1839 |
BovineHD1400000300; BovineHD4100010521 | rs109342545; rs110053839 | 14 | 2147133; 2135276 | ENSBTAG00000045727 | NA |
BovineHD1400000706 | rs135132676 | 14 | 3583221 | ENSBTAG00000046467 | PTP4A3 |
BTA-35941-no-rs | rs41627764 | 14 | 2276443 | ENSBTAG00000046866 | NA |
BovineHD1400024339 | rs136939758 | 14 | 1308359 | ENSBTAG00000046932 | NA |
BovineHD1400000462 | rs132789965 | 14 | 2857000 | ENSBTAG00000047022 | PSCA |
BovineHD1700015848 | rs137100268 | 17 | 55864167 | ENSBTAG00000004457 | ORAI1 |
BovineHD2000016332 | rs109823133 | 20 | 58638275 | ENSBTAG00000000672 | OTULINL |
ARS-BFGL-NGS-84494 | rs109643490 | 20 | 57301571 | ENSBTAG00000003219 | FBXL7 |
BovineHD2000016490; BovineHD2000016482; BovineHD2000016480; BovineHD2000016463; ARS-BFGL-NGS-71622; BovineHD2000016473; BovineHD2000016468; BovineHD2000016401; BovineHD2000016466; BovineHD2000016477; BovineHD2000016465; BovineHD2000016474; BovineHD2000016471; BovineHD2000016486; BovineHD2000016464; BovineHD2000016485; BovineHD2000016476; BovineHD2000016470; BovineHD2000016479; BovineHD2000016445; BovineHD2000016487; BovineHD2000016478; BovineHD2000016491; BovineHD2000016475; BovineHD2000016469; BovineHD2000016481; BovineHD2000016467; BovineHD2000016394; BovineHD2000016484; BovineHD2000016392; BovineHD2000016472; BovineHD2000016364; | rs108957596; rs108964368; rs109059391; rs109148196; rs109243453; rs109671324; rs109939825; rs110078451; rs110093810; rs110410028; rs110554011; rs110608216; rs110681006; rs110881846; rs132765887; rs133138163; rs133624494; rs133732006; rs133761028; rs134168996; rs135516192; rs135821345; rs135888983; rs136263201; rs136340192; rs136561486; rs136576574; rs136944246; rs137465525; rs137486152; rs137528125; rs41950612 | 20 | 58947745; 58932752; 58929832; 58904206; 58928800; 58922307; 58915583; 58796750; 58911097; 58925687; 58908876; 58923230; 58919595; 58936512; 58906478; 58935497; 58925004; 58917974; 58927712; 58878031; 58938683; 58926579; 58948689; 58924069; 58916701; 58931087; 58914355; 58771588; 58934789; 58762885; 58920803; 58709513 | ENSBTAG00000005514 | TRIO |
BovineHD2000016248; ARS-BFGL-NGS-111931; BovineHD2000016258; BovineHD2000016246; BovineHD2000016226; BovineHD2000016190; BovineHD2000016253; BovineHD2000016252; BovineHD2000016203; BovineHD2000016239; BovineHD2000016237; BovineHD2000016240; BovineHD2000016232; BovineHD2000016238; BovineHD2000016241; BovineHD2000016236; BovineHD4100014800; BovineHD2000016206; BovineHD2000016208; BovineHD2000016210; BovineHD2000016227; BovineHD2000016216; BovineHD2000016217; BovineHD2000016218 | rs108968188; rs109102596; rs109167035; rs109439555; rs110470671; rs110589026; rs110630125; rs110862310; rs110983331; rs133021030; rs133648068; rs134090885; rs134817611; rs135781363; rs135920407; rs137840204; rs41642545; rs41951107; rs41951130; rs41951335; rs42640155; rs42640157; rs42640164; rs42640170 | 20 | 58493410; 58405641; 58522200; 58491204; 58445208; 58374946; 58501904; 58500982; 58417934; 58465508; 58462053; 58468597; 58455297; 58463540; 58470255; 58459086; 58392839; 58421319; 58425019; 58426752; 58445701; 58433919; 58435724; 58436944 | ENSBTAG00000013391 | ANKH |
BovineHD2000015474; BovineHD2000015529 | rs137602919; rs42809077 | 20 | 56327023; 56449013 | ENSBTAG00000020126 | MYO10 |
BovineHD2000016591; BovineHD2000016689; UA-IFASA-2314; BovineHD2000016639 | rs110554444; rs134140692; rs29012816; rs41953112 | 20 | 59283222; 59484278; 59514189; 59416887 | ENSBTAG00000021972 | DNAH5 |
BovineHD2000016248; BovineHD2000016246 | rs108968188; rs109439555 | 20 | 58493410; 58491204 | ENSBTAG00000045869 | NA |
BovineHD2500007120 | rs42062457 | 25 | 25174707 | ENSBTAG00000001602 | IL4R |
BovineHD2500007345 | rs135129780 | 25 | 25895888 | ENSBTAG00000010309 | XPO6 |
BovineHD2500007818 | rs109700166 | 25 | 27974664 | ENSBTAG00000013081 | PSPH |
BovineHD2500007447 | rs135166725 | 25 | 26358012 | ENSBTAG00000016883 | NA |
BovineHD2500007435; BovineHD2500007432 | rs42071217; rs42072596 | 25 | 26317395; 25 | ENSBTAG00000018000 | CLN3 |
BovineHD2500007435 | rs42071217 | 25 | 26317395 | ENSBTAG00000018011 | APOBR |
BovineHD2500007435 | rs42071217 | 25 | 26317395 | ENSBTAG00000018015 | IL27 |