Table 3

Significant SNPs for T-cell subpopulations
Trait No. SNPs SNP Name SSC. Position Significance levelb Nearest gene Distance (bp)
(bp)a
CD4-CD8- T% 3 ALGA0006170 SSC1 147676962 A SELS 101263
ALGA0027442 SSC4 106255554 A LOC100515138 15207
MARC0035862 SSC17 26683704 A FLRT3 999166
CD4+CD8+ T% 15 ASGA0000475 SSC1 5393161 A QKI 197563
MARC0090836 SSC5 18263549 A LOC100523435 8399
H3GA0016197 SSC5 30846602 A LOC100514286 within
DRGA0005876 SSC5 52631994 A LOC100153016 7905
ASGA0093882 SSC8 27821389 A LOC100515221 68339
MARC0103793 SSC9 117134341 A NCF2 within
ALGA0061180 SSC11 18408471 A LOC100518860 within
ALGA0062506 SSC11 55628913 A RNF219 152990
DRGA0012994 SSC13 116721928 A LOC100518275 Within
ASGA0059251 SSC13 116794774 A LOC100518275 within
H3GA0037561 SSC13 117065279 A LOC100518275 within
MARC0024545 SSC13 117511306 A LOC100739759 within
H3GA0037568 SSC13 117963270 A CLDN11 within
ALGA0072642 SSC13 118134975 A SLC7A14 22223
ASGA0077977 SSC17 59215829 A CBLN4 within
CD4+CD8- T% 31 SIRI0000967 SSC1 65386385 A MAP3K7 93369
ALGA0109882 SSC1 65402776 A MAP3K7 76978
ALGA0003935 SSC1 67256904 A LOC100152346 within
MARC0008049 SSC6 74003688 A LOC100738715 within
ALGA0105115 SSC9 127202082 A CD46 12474
MARC0076632 SSC9 127394064 B LOC100514786 within
ASGA0046812 SSC10 16205420 A LOC100513811 within
ALGA0057450 SSC10 16220722 A LOC100513811 within
ALGA0061535 SSC11 23576083 A TRNAE-UUC 42913
M1GA0015162 SSC11 61231196 A LOC100154696 within
ASGA0051093 SSC11 61450492 A LOC100154696 112456
ALGA0108362 SSC12 6596691 A LOC100518214 225784
MARC0009109 SSC12 6637944 A SOX9 229926
ALGA0106073 SSC12 6663787 A SOX9 204083
ASGA0052986 SSC12 6791202 A SOX9 76668
ASGA0052974 SSC12 6826155 A SOX9 41715
ALGA0064738 SSC12 6891741 A SOX9 20500
H3GA0033370 SSC12 6976387 B LOC100518393 21514
ASGA0053002 SSC12 7105246 A LOC100519105 55408
ASGA0104370 SSC12 7185885 A LOC100519105 136047
ALGA0064767 SSC12 7400177 A LOC100519105 350339
ALGA0078815 SSC14 76804400 A LOC100521406 85124
H3GA0041012 SSC14 77946383 A PSAP within
ASGA0065687 SSC14 107127514 A HTR7 260753
ALGA0087956 SSC15 123078022 A LOC100516232 22744
INRA0055474 SSC18 21991584 A LOC100622672 28674
ALGA0097499 SSC18 22003396 A LOC100513190 3075
ASGA0079256 SSC18 22055859 A LOC100525548 1899
ALGA0098112 SSC18 38463920 A BMPER 113622
MARC0089391 SSC18 38488630 A BMPER 88912
MARC0024065 SSC18 50965324 A LOC100622432 within
CD4-CD8+ T% 3 ASGA0022812 SSC4 126976845 A LOC100737939 107579
H3GA0041012 SSC14 77946383 A PSAP within
ALGA0103427 SSC15 127742340 A IKZF2 within
CD4+ T% 6 ASGA0023262 SSC4 130826499 A LOC100151966 174827
ALGA0030335 SSC5 7606208 A LOC100512654 6682
ALGA0122248 SSC16 73417692 A LOC100518939 70693
INRA0055474 SSC18 21991584 A LOC100513190 within
ASGA0079256 SSC18 22055859 A LOC100525548 1899
ASGA0080319 SSC18 49513089 A LOC100516656 43287
CD8+ T% 1 ALGA0006170 SSC1 147676962 B SELS 101263
CD4+:CD8+ 5 H3GA0041012 SSC14 77946383 A PSAP within
ALGA0117513 SSC15 123215784 A LOC100518938 11678
ALGA0122248 SSC16 73417692 A LOC100738933 403285
ALGA0098112 SSC18 38463920 A BMPER 113622
MARC0089391 SSC18 38488630 A BMPER 88912

a: Derived from the recent porcine genome sequence assembly (Sscrofa9.2) ( http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9823&build=previous webcite).

b: A means chromosome-wise significance level, B means genome-wise significance level.

Lu et al.

Lu et al. BMC Genomics 2012 13:488   doi:10.1186/1471-2164-13-488

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