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Table 3 List of genomic regions of extended homozygosity detected in Shanghai Holstein cattle population

From: Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Chr Start (bp) End (bp) Length (bp) SNPs No. of Genes Candidate Genes
13 39,852,457 41,196,648 1,344,191 120 3 KIZ、NKX2-2、XRN2
2 135,983,904 137,968,708 1,984,804 134 17 ALPL、CAMK2N1、CDA、CDC42、CELA3B、DDOST、ECE1、HP1BP3、KIF17、LOC515042、LOC789612、MIR2284U、MUL1、PINK1、RAP1GAP、SH2D5、ZBTB40
12 30,773,910 33,562,640 2,788,730 117 21 ATP8A2、CDX2、FLT1、GPR12、GSX1、GTF3A、LNX2、MIR2285O-2、MIR2300A、MIR2300B、MTIF3、PDX1、POLR1D、POMP、RNF6、RPL21、SHISA2、SLC46A3、URAD、USP12、WASF3
21 31,435,280 33,563,201 2,127,921 81 17 COMMD4、CSPG4、ETFA、HMG20A、IMP3、ISL2、MAN2C1、MIR631、NEIL1、ODF3L1、PSTPIP1、PTPN9、RCN2、SNUPN、SNX33、TMEM266、TSPAN3
10 18,844,833 21,194,474 2,349,641 98 43 ADCY4、ADPGK、ARIH1、BBS4、CBLN3、CELF6、CHMP4A、CIDEB、DCAF11、DHRS1、FITM1、GMPR2、HEXA、INSYN1、IPO4、IRF9、KHNYN、LTB4R、LTB4R2、MDP1、MIR11989、MIR12031、NEDD8、NFATC4、NOP9、NPTN、NR2E3、NYNRIN、PARP6、PKM、PSME1、PSME2、RABGGTA、REC8、RIPK3、RNF31、SDR39U1、TBC1D21、TGM1、THSD4、TINF2、TM9SF1、TSSK4
23 27,948,371 29,204,475 1,256,104 85 4 MIR12033、OR12D2、TRIM27、UBD
3 123,888,189 124,870,683 982,494 92 10 ASB1、ESPNL、HES6、ILKAP、MIR2902、PER2、SCLY、TRAF3IP1、TWIST2、UBE2F
4 98,248,048 100,380,507 2,132,459 95 5 CHCHD3、EXOC4、MIR2423、MIR320B、PLXNA4
25 15,526,462 16,728,810 1,202,348 91 2 ABCC1、ABCC6
6 107,592,661 108,740,633 1,147,972 58 3 EVC、EVC2、MSX1
21 61,326,146 64,094,599 2,768,453 103 6 AK7、ATG2B、BDKRB1、GSKIP、PAPOLA、VRK1
29 30,857,817 31,924,963 1,067,146 105 8 DCPS、FAM118B、FOXRED1、KIRREL3、RPUSD4、SRPRA、ST3GAL4、TIRAP
1 144,773,205 145,465,387 692,182 49 4 C2CD2、RIPK4、TMPRSS2、ZBTB21
9 99,670,895 101,121,625 1,450,730 85 10 ACAT2、AGPAT4、AIRN、IGF2R、MRPL18、PLG、SLC22A1、SOD2、TCP1、WTAP
19 62,790,612 63,501,716 711,104 48 8 ABCA9、AMZ2、ARSG、MGC134105、PRKAR1A、RGS9、SLC16A6、WIPI1
11 25,226,313 25,905,694 679,381 29 2 PKDCC、MIR12030
20 780,499 2,012,217 1,231,718 70 5 FOXI1、KCNMB1、LCP2、SLIT3、SPDL1
2 139,926,793 140,719,836 793,043 69 0 ——