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Table 2 Identification of protein-coding genes based on the additive genetic variance (Var) explained by 1 Mb windows of adjacent SNPs

From: A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive

Chr Region (bp) Genes Var
SSC2a 4,239,252-5,222,613 KDM2A, RHOD, C2H11orf86, SYT12, PC, RCE1, C2H11orf80, CCDC87, CCS, CTSF, ACTN3, ZDHHC24, BBS1, DPP3, PELI3, MRPL11, NPAS4, SLC29A2, B4GAT1, BRMS1, RIN1, CD248, TMEM151A, YIF1A, CNIH2, RAB1B, KLC2, PACS1, SF3B2 1.57
SSC2 145,012,848-146,011,865 SPOCK1, KLHL3, HNRNPA0, LOC100517462, MYOT, PKD2L2, LOC100520183, FAM13B, WNT8A, NME5, BRD8, KIF20A, CDC23, GFRA3, CDC25C, SLBP2 1.01
SSC3a 3,981,003-4,980,011 SDK1, FOXK1, AP5Z1, RADIL, PAPOLB, MMD2, WIPI2, SLC29A4, TNRC18, FBXL18, ACTB, FSCN1, RNF216 1.16
SSC4 20,774,634-21,762,434 COLEC10, TNFRSF11B, SAMD12, EXT1 1.07
SSC4 104,642,633-105,640,667 SLC39A1, CRTC2, DENND4B, GATAD2B, SLC27A3, INTS3, NPR1, ILF2, SNAPIN, CHTOP, S100A5, S100A4, S100A3, S100A2, S100A16, S100A14, S100A13, PPGRP-S, S100A9, S100A12, S100A8, LOC102161828, S100A7, PGLYRP3, LOR, PRR9, LELP1, SPRR2E, LOC100737840, SPRR1A, SPRP, IVL, SMCP, KPRP 1.13
SSC11 25,254,733-26,232,874 TNFSF11, AKAP11, DGKH, VWA8, RGCC, NAA16 1.18
SSC12 54,066,400-55,065,792 GP1BA, MINK1, PLD2, ZMYND15, CXCL16, MED11, ARRB2, PSMB6, GLTPD2, VMO1, TM4SF5, PELP1, ALOX15, SLC16A11, SLC16A13, BCL6B, C12H17orf49, RNASEK, ALOX12, CLEC10A, ASGR2, SLC2A4, CLDN7, ELP5, GABARAP, PHF23, DVL2, DLG4, YBX2, NEURL4, ACAP1, KCTD11, TMEM95, TNK1, PLSCR3, POLR2A, SLC35G6, ZBTB4, CHRNB1, FGF11, TMEM102, SPEM2, DNAH2 1.10
SSC12a 56,619,955-57,608,007 CCDC42, MFSD6L, PIK3R6, PIK3R5, NTN1, STX8, CFAP52, USP43, DHRS7C, GSG1L2, GLP2R, RCVRN, GAS7 1.30
SSC13 3,171,064-4,162,557 BTD, ANKRD28, GALNT15, DPH3, OXNAD1, RFTN1, DAZL 1.35
SSC13 10,788,202-11,761,268 UBE2E2 2.27
SSC14 13,059,455-14,032,461 SCARA5, NUGGC, ELP3, PNOC, ZNF395, FBXO16, FZD3, EXTL3, INTS9, HMBOX1, KIF13B 2.14
SSC15 55,188,321-56,161,595 FGFR1, LETM2, NSD3, PLPP5, DDHD2, BAG4, ADRB3, STAR, ASH2L, EIF4EBP1, LSM1, BRF2, ADGRA2, PLPBP, ERLIN2, ZNF703, KCNU1 1.28
SSC15 57,551,770-58,532,159 1.29
SSC15 131,996,123-132,969,736 TNS1, RUFY4, CXCR2, CXCR1 1.09
SSC16 77,028,962-78,013,471 GLRA1, G3BP1, ATOX1, LOC100514500, SPARC, FAT2, SLC36A1, SLC36A2, SLC36A3, GM2A, CCDC69, ANXA6 2.55
SSC17a 17,325,007-18,300,615 BMP2 1.04
  1. aregion also identified in a CNVR