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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)

From: Genome-wide association analysis for β-hydroxybutyrate concentration in Milk in Holstein dairy cattle

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