SUPPLEMENTAL TABLE S1. Mouse HDL QTL map.

Chr / Crossa / Peak (Mb)a / 95% CI
(Mb)b / LODc / Sex / High Allele / Ref. d
1 / (NZW X B6).129-Apoe-/- F2 / 79 / 74-105 / 5.1 / M+F / NZW / (1)
1 / (NZB X NZW) F2 / 102 / 80-125 / (3.3) / M+F / NZW / (2)
1 / (NOD X B6).129-Apoe-/- F2 / 148 / 95-174 / 2.8 / M+F / NOD / (1)
1 / (SM X A) F2 / 149 / 127-164 / 2 / M+F / SM / (3)
1 / (B6 X A) F2 / 155 / 90-171 / 6.4 / M+F / A / (4)
1 / (KK X RR) F2 / 158/176 / 149-182 / 7.5, 9.2 / M+F / ? / (5)
1 / (B6 X KK-Ay) F2 / 159/177 / 154-184 / 4.6, 4.7 / M+F / KK / (6)
1 / (B6 X KK) F2 / 164/177 / 154-184 / 3.9, 4.5 / M+F / KK / (6)
1 / (PERA X DBA/2) F2 / 164 / 154-171 / (6.4) / M+F / PERA / (7)
1 / (CAST X 129) F2 / 164 / 115-180 / (5.1) / M+F / 129 / (8)
1 / (NOD X B6) F2 / 170 / 148-176 / 4.1 / M+F / NOD / (1)
1 / (RIII X 129) F2 / 170 / 138-192 / (4.8) / M+F / 129 / (9)
1 / (B6 X FVB).129-Apoe-/- F2 / 170 / 156-184 / 3.6 / M+F / FVB / (10)
1 / (B6 X NZB) F11 / 170 / 166-174 / 37.0 (13.6) / F / NZB / (11)
1 / (B6 X C3H) F2 / 171 / 165-184 / 10.9 (15.2) / F / C3H / (12)
1 / (B6 X 129) F2 / 173 / 170-175 / 68.6 (30) / M+F / 129 / (13)
1 / (B6 X C3H)-Apoe-/- F2 / 173 / 157-192 / (3) / F / C3H / (14)
1 / (NZB X SM) F2 / 173 / 164-176 / 4.9 / F / NZB / (15)
1 / (MRL X SJL) F2 / 175 / 167-180 / 23.3 / F / MRL / (16)
1 / (NZB X SM) F2 / 175 / 173-191 / 11.0 (4.1) / M+F / NZB / (17)
1 / (B6 X C3H) F2 / 176 / 167-192 / (9.1) / F / C3H / (2)
1 / (NZW X B6) F2 / 176 / 170-179 / 16 / M+F / NZW / (1)
1 / (PERA X I) F2 / 176 / 137-197 / (2) / M+F / PERA / (7)
1 / (NZW X B6).129-Apoe-/- F2 / 179 / 173-180 / 17 / M+F / NZW / (1)
1 / (B6 X NZB) F11 / 179 / 176-190 / (11.4) / F / NZB / (11)
1 / (B6 X DBA/2) F2 / 184 / 161-191 / 2.8 / M / DBA/2 / (2)
1 / (NZO X NON) x NON / 189 / 0-189 / 2.4 / M / NON / (2)
1 / (B6 X 129) F2 / 191 / 176-194 / (9.7) / F / 129 / (18)
1 / (B6 X NZB) X B6 / 192 / 182-197 / 5.5 (5.8) / F / NZB / (11)
2 / (DBA/1 X DBA/2) BC / 16/42 / 8-118 / (3.3, 3.6) / M+F / DBA/2 / (19)
2 / (B6 X CAST) F2 / 65 / 31-78 / (5.6) / M+F / B6 / (20)
2 / (DBA/2 X CAST) F2 / 80 / 69-125 / (5.4) / M / D2 / (21)
2 / (B6 X CAST) F2 / 116 / 96-136 / 3.5 (3.4) / M+F / B6 / (20)
2 / (B6 X C3H) F2 / 120 / 74-166 / (2.4) / F / C3H / (2)
2 / (NOD X B6).129-Apoe-/- F2 / 158 / 32-179 / 3.6 / M+F / NOD / (1)
2 / (NZB X NZW) F2 / 161 / 141-163 / (2.8) / M+F / NZB / (2)
2 / (B6 X DBA/2) F2 / 162 / 131-182 / (3.1) / F / D2 / (22)
3 / (DBA/1 X DBA/2) BC / 4 / 0-28 / (4) / M+F / DBA/2 / (19)
3 / (B6 X CSS-3) / 33 / 25-57 / 4.2 / M+F / B6 / (4)
3 / (SM X A) F2 / 39 / 25-64 / 2.5 / M+F / A / (3)
3 / (NZB x NZW) F2 / 49 / 37-73 / (4.5) / M+F / NZB / (2)
3 / (B6 X DBA/2) F2 / 51 / 33-77 / 5.3 / F / B6 / (22)
3 / (B6 X C3H) F2 / 54 / 0-88 / (2.5) / F / C3H / (12)
3 / (MRL X SJL) F2 / 88 / 87-101 / 7 / F / MRL / (16)
3 / (B6 X CAST) F2 / 101 / 83-125 / 3.5 (4.2) / M+F / B6 / (20)
3 / KK/Ta X (BALB X KK/Ta) / 101 / 67-122 / 4 / M / KK / (23)
3 / (KK X RR) F2 / 102 / 73-122 / 3.4 / M+F / ? / (5)
3 / (B6 X KK) F2 / 102 / 87-125 / 3.9 / M+F / ? / (6)
3 / (NZB X SM) F2 / 122 / 72-125 / 4.0 (3.8) / M+F / NZB / (17)
3 / (B6 X 129) F2 / 125 / 117-129 / 5.4 (2.5) / M+F / B6 / (13)
3 / (B6 X C3H)-Apoe-/- F2 / 125 / 101-139 / (2.3) / F / B6 / (14)
3 / (B6 X DBA/2) F2 / 138 / 115-145 / 3 / M / B6 / (2)
4 / (NOD X B6) F2 / 12 / 7-26 / 3.5 / M+F / B6 / (1)
4 / (DBA/1 X DBA/2) BC / 23 / 0-39 / 2.5 / M+F / DBA/2 / (19)
4 / (NZB x NZW) F2 / 47 / 30-63 / (3.5) / M+F / NZW / (2)
4 / (PERA X I) F2 / 47 / 33-85 / (3.2) / M+F / PERA / (7)
4 / (DBA/2 X CAST) F2 / 47 / 35-62 / (5.9) / M / CAST / (21)
4 / (CAST X 129) F2 / 47 / 35-62 / (3.7) / M+F / CAST / (8)
4 / (B6 X C3H) F2 / 53 / 39-64 / (2.8) / F / ? / (12)
4 / (PERA X DBA/2) F2 / 53 / 40-82 / (3.4) / M+F / PERA / (7)
4 / (NOD X B6).129-Apoe-/- F2 / 55 / 43-73 / 2.9 / M+F / NOD / (1)
4 / (B6 X A) F2 / 108 / 64-136 / 4.4 / M+F / B6 / (4)
4 / (DBA/1 X DBA/2) BC / 126 / 104-141 / (2.9) / M / DBA/2 / (19)
4 / (B6 X DBA/2) F2 / 129 / 80-149 / 2.2 / M / DBA/2 / (2)
4 / (B6 X DBA/2) F2 / 144 / 136-155 / (4.1) / F / B6 / (22)
4 / (SM X A) F2 / 150 / 142-155 / 2.1 / M+F / SM / (3)
5 / (PERA X I) F2 / 0 / 0-24 / (5.6) / M+F / PERA / (7)
5 / (B6 X 129) F2 / 23 / 7-33 / 2.1 (3.6) / M+F / 129 / (13)
5 / (NZB X SM) F2 / 32 / 25-38 / 5.2 (7.6) / M+F / NZB / (17)
5 / (NZB x NZW) F2 / 53 / 30-68 / (9) / M+F / NZB / (2)
5 / (B6 X NZB) F11 / 53 / 42-55 / 12.0 (7.8) / F / NZB / (11)
5 / (NZW X B6) F2 / 61 / 43-82 / 2.1 / M+F / NZW / (1)
5 / (B6 X NZB) X B6 / 72 / 66-78 / 4.7 / F / NZB / (11)
5 / (SM X NZB) X NZB / 78 / 54-124 / (3.6) / F / NZB / (24)
5 / (NZO X NON) x NON / 82 / 53-102 / 3.4 / M / het / (2)
5 / (B6 X 129) F2 / 91/114/122 / 79-127 / 3.3 (2.5), 3.3, 3.4 / M+F / 129 / (13)
5 / (B6 X C3H) F2 / 91 / 36-113 / (3.4) / F / C3H / (12)
5 / (MRL X SJL) F2 / 91 / 54-108 / 4.9 / F / MRL / (16)
5 / (NZB X SM) F2 / 98 / 67-109 / 7.6 (10.8) / M+F / NZB / (17)
5 / (B6 X CAST) F2 / 102/130 / 65-144 / (6.0), (3.8) / M+F / CAST / (20)
5 / (NZB x RF) F2 / 105 / 104-121 / 16.7 / F / NZB / (25)
5 / (B6 X NZB) X B6 / 112 / 76-119 / 2.1 / F / NZB / (11)
5 / (B6 X NZB) F11 / 113 / 107-117 / (3.6) / F / NZB / (11)
5 / (NZB X SM) F2 / 113/130 / 67-145 / 6.2 (5.6), 5.3 / M+F / NZB, ? / (15)
5 / (NZB x NZW) F2 / 115 / 104-125 / (12.7) / M+F / NZB / (2)
5 / (SM X NZB) X NZB / 120 / 66-141 / 2.7 / F / NZB / (24)
5 / (NZB X SM) F2 / 120 / 115-150 / 10.1 (12.1) / M+F / nzb / (17)
5 / (B6 X NZB) F11 / 125 / 120-127 / 7.1 (5.8) / F / NZB / (11)
6 / (B6 X SPRET) X B6 / 10 / 0-38 / 5.6 / M+F / B6 / (26)
6 / (B6 X 129) F2 / 16 / 6-26 / (2.9) / M+F / 129 / (13)
6 / (NZB X SM) F2 / 51 / 32-74 / 4.2 / F / NZB / (17)
6 / (NOD X B6) F2 / 52 / 33-107 / 2.5 / M+F / NOD / (1)
6 / (B6 X DBA/2) F2 / 85 / 48-110 / 2.8 / M / DBA/2 / (2)
6 / (PERA X I) F2 / 98 / 74-119 / (3) / M+F / PERA / (7)
6 / (DBA/2 X CAST) F2 / 112 / 97-125 / (4.2) / M / D2 / (21)
6 / (B6 X C3H) F2 / 125 / 97-145 / (2.7) / F / B6 / (2)
6 / (NZB X SM) F2 / 137 / 116-145 / 6.3 / M+F / NZB / (17)
6 / (B6 X DBA/2) F2 / 137 / 114-145 / 7 / F / D2 / (22)
6 / (DBA/2 X CAST) F2 / 142 / 135-150 / (4.9) / M / D2 / (21)
6 / (B6.C-H25c X BALB F2 / 147 / 135-150 / 5 / M+F / B6 / (27)
7 / (MRL-lpr X BALB) F2 / 1 / 0-29 / (2.1) / M+F / ? / (28)
7 / (NZW X B6) F2 / 26 / 23-36 / 2.2 / M+F / B6 / (1)
7 / (MRL X SJL) F2 / 28 / 0-43 / 2.9 / F / ? / (16)
7 / (B6 X C3H) F2 / 40 / 25-72 / 4 / F / ? / (12)
7 / (NOD X B6) F2 / 123 / 108-126 / 3.9 / M+F / B6 / (1)
7 / (B6 X SPRET) X B6 / 131 / 123-145 / 4.3 / M+F / B6 / (26)
7 / (PERA X I) F2 / 144 / 92-145 / (2.7) / M+F / I / (7)
7 / (B6 X DBA/2) F2 / 144 / 126-145 / (3.6) / F / B6 / (22)
8 / (NZB X SM) F2 / 0 / 0-33 / (4.2) / M+F / NZB / (17)
8 / (NZB x NZW) F2 / 32 / 23-68 / (2.9) / M+F / NZB / (2)
8 / (B6 X A) F2 / 52 / 38-90 / 9.4 / M+F / B6 / (4)
8 / (B6 X 129) F2 / 80 / 71-90 / 4.3 / M+F / B6 / (13)
8 / (B6 X 129) F2 / 97 / 83-107 / (2.6) / F / 129 / (18)
8 / (B6 X CSS-8) / 103 / 93-109 / 10.8 / M+F / B6 / (4)
8 / (B6 X 129) F2 / 108 / 94-121 / 3.4 / M+F / B6 / (13)
8 / (B6 X CAST) F2 / 111 / 70-128 / 3.6 / M+F / B6 / (20)
8 / (B6 X DBA/2) F2 / 111 / 89-111 / 4.6 / M / B6 / (2)
8 / (B6 X CASA) F2 / 129 / 117-132 / 4.7 / M+F / B6 / (29)
9 / (DBA/1 X DBA/2) BC / 0 / 0-34 / (4.1) / M+F / DBA/2 / (19)
9 / (RIII X 129) F2 / 32 / 31-43 / (9.4) / M+F / 129 / (9)
9 / (B6 X 129) F2 / 35 / 27-43 / 8.0 (5.4) / M+F / 129 / (13)
9 / (B6 X CAST) F2 / 37 / 26-48 / 4.2 / M+F / CAST / (20)
9 / (B6 X CASA) F2 / 40 / 26-51 / 7.5 / M+F / CASA / (29)
9 / (NOD X B6).129-Apoe-/- F2 / 41 / 20-48 / 2.6 / M+F / NOD / (1)
9 / (B6 X 129) F2 / 42 / 34-60 / (2.9) / F / 129 / (18)
9 / (KK X RR) F2 / 45 / 0-61 / 4.4 / M+F / KK / (5)
9 / (B6 X KK-Ay) F2 / 49 / 0-63 / 3 / M+F / ? / (6)
9 / (B6 X 129) F2 / 91 / 60-95 / 3.5(4.8) / M+F / 129 / (13)
10 / (B6 X FVB).129-Apoe-/- F2 / 10 / 0-21 / 2.6 / M+F / FVB / (10)
10 / (DBA/1 X DBA/2) BC / 71/86 / 53-100 / 2.5 (3.3) / M+F / DBA/2 / (19)
10 / (NZB X SM) F2 / 130 / 109-130 / (4.1) / F / NZB / (17)
11 / (B6 X CSS-11) / 36 / 0-53 / 2.3 / M+F / B6 / (4)
11 / (NZW X B6).129-Apoe-/- F2 / 44 / 44-59 / 3.4 / M+F / B6 / (1)
11 / (PERA X DBA/2) F2 / 54 / 18-77 / (2.8) / M+F / PERA / (7)
11 / (PERA X I) F2 / 54 / 19-90 / (3.5) / M+F / PERA / (7)
11 / (B6 X C3H) F2 / 68/84 / 36-107 / (2.5), (3.4) / F / C3H / (2)
11 / (B6 X 129) F2 / 115 / 110-117 / (2.6) / M+F / 129 / (13)
12 / (NZW X B6).129-Apoe-/- F2 / 5 / 5-81 / 2.3 / M+F / NZW / (1)
12 / (NZB x RF) F2 / 34 / 0-76 / 4.7 / F / NZB / (25)
12 / (B6 X 129) F2 / 44 / 34-55 / (5.9) / F / 129 / (18)
12 / (RIII X 129) F2 / 44 / 0-105 / (5) / M+F / 129 / (9)
12 / (DBA/1 X DBA/2) BC / 75 / 44-87 / 2.5 / M+F / DBA/2 / (19)
12 / (B6 X DBA/2) F2 / 89 / 34-104 / 2.2 / M / B6 / (2)
12 / (NZB x NZW) F2 / 113 / 82-113 / (4.1) / M+F / NZB / (2)
13 / (B6 X 129) F2 / 24 / 4-52 / 3 / M+F / 129 / (13)
13 / (B6.C-H25c X BALB F2 / 75 / 44-99 / 4.8 / M+F / BALB / (27)
14 / (B6 X CAST) F2 / 21 / 0-46 / 3.4 / M+F / B6 / (20)
14 / (DBA/1 X DBA/2) BC / 25 / 0-47 / (2.6) / M+F / DBA/2 / (19)
14 / (SM X A) F2 / 35 / 11-59 / 2.4 / M+F / A / (3)
14 / (MRL X SJL) F2 / 90 / 68-105 / 2.4 / F / ? / (16)
14 / (B6 X 129) F2 / 100 / 94-117 / (3.9) / M+F / 129 / (13)
15 / (B6 X A) F2 / 39 / 2-62 / 2.6 / M+F / B6 / (4)
15 / (B6 X C3H) F2 / 61 / 9-81 / (2.5) / F / B6 / (2)
15 / (MRL-lpr X BALB) F2 / 62 / 39-74 / (2.7) / M+F / MRL / (28)
15 / (NZB X SM) F2 / 81 / 75-102 / 4.2 / F / NZB / (17)
15 / (PERA X I) F2 / 87 / 40-103 / 2.3 / M+F / PERA / (7)
15 / (B6.C-H25c X BALB F2 / 87 / 68-102 / 2.2 / M+F / B6 / (27)
16 / (NZB x NZW) F2 / 3 / 0-25 / (3.2) / M+F / NZW / (2)
16 / (NZW X B6).129-Apoe-/- F2 / 10 / 5-41 / 3.3 / M+F / NZW / (1)
16 / (B6 X CAST) F2 / 30 / 15492 / 4.4 / M+F / B6 / (20)
16 / (NZB X SM) F2 / 35 / 0-91 / 3.7 / M+F / NZB / (17)
16 / (DBA/1 X DBA/2) BC / 80 / 72-92 / 3.9 / M+F / DBA/2 / (19)
17 / (SM X A) F2 / 35 / 16-55 / 2.2 / M+F / A / (3)
17 / (NZB X SM) F2 / 35 / 15-51 / 4.4 / M+F / ? / (15)
17 / (MRL X SJL) F2 / 49 / 29-66 / 2.5 / F / ? / (16)
17 / (B6 X A) F2 / 50 / 23-72 / 3.4 / M+F / B6 / (4)
17 / (B6 X CAST) F2 / 53 / 47-65 / (6.5) / M+F / CAST / (20)
17 / (NZB X SM) F2 / 63 / 52-72 / (4.5) / M / NZB / (17)
17 / (B6 X 129) F2 / 64 / 38-86 / 2.9 (2.7) / M+F / B6 / (13)
17 / (PERA X DBA/2) F2 / 79 / 72-83 / (1.6) / M+F / D2 / (7)
17 / (PERA X I) F2 / 79 / 49-83 / (1.6) / M+F / I / (7)
18 / (B6 X 129) F2 / 23 / 10-36 / 3.8 / M+F / 129 / (13)
18 / (SM X NZB) X NZB / 26 / 5-44 / 3.2 / F / NZB / (24)
18 / (B6 X 129) F2 / 52 / 36-63 / 3.4 / M+F / 129 / (13)
18 / (B6 X A) F2 / 53 / 33-59 / 3 / M+F / B6 / (4)
18 / (NZB x NZW) F2 / 65 / 58-82 / (5.1) / M+F / NZB / (2)
18 / (B6 X C3H) F2 / 67 / 30-76 / 3.5 (3.0) / F / ? / (12)
18 / (B6 X DBA/2) F2 / 73 / 60-86 / 3 / F / D2 / (22)
18 / (B6 X C3H) F2 / 76 / 69-91 / (2.8) / F / C3H / (2)
18 / (B6 X CAST) F2 / 76 / 62-87 / (3.8) / M+F / B6 / (20)
18 / (NZB X SM) F2 / 83 / 69-91 / 4.1 (5.2) / M+F / NZB / (17)
18 / (NOD X B6) F2 / 91 / 76-91 / 3 / M+F / NOD / (1)
19 / (B6 X C3H) F2 / 4 / 0-36 / (2.1) / F / B6 / (2)
19 / (B6 X A) F2 / 8 / 0-21 / 2.1 / M+F / B6 / (4)
19 / (B6.C-H25c X BALB F2 / 13 / 0-23 / 2.2 / M+F / BALB / (27)
19 / (MRL-lpr X BALB) F2 / 39 / 22-41 / (8.4) / M+F / BALB / (28)
19 / (NZB X SM) F2 / 39 / 15-61 / (4) / F / NZB / (17)
19 / (NZB x RF) F2 / 49 / 40-54 / 5.7 / F / NZB / (25)
19 / (SM X A) F2 / 50 / 41-61 / 2.1 / M+F / SM / (3)

Abbreviations: M=Males; F=Females; 129=129S1/SvImJ; A=A/J; B6=C57BL/6J; BALB=BALB/cJ; C3H=C3H/HeJ;
CASA=CASA/RkJ; CAST=CAST/EiJ; CSS=Chromosome Substitution Strains or Consomic; DBA/1=DBA/1J; DBA/2=DBA/2J; FVB=FVB/NJ; I=I/LnJ; KK=KK/HIJ; KK-Ay=KK.Cg-Ay/J; MRL=MRL/MpJ; NOD=NOD/ShiLtJ; NON=NON/ShiLtJ;
NZB=NZB/BINJ; NZO=NZO/HILtJ; NZW=NZW/LacJ; PERA=PERA/EiJ; RF=RF/J; RIII=RIIIS/J; SM=SM/J; SJL=SJL/J; SPRET=SPRET/EiJ.

a Cross as reported in the published manuscript indicated in Supplemental Table S2.

b Peak and 95% CI in Mb of the HDL QTL. The 95% CI is reported as calculated by the authors or by applying 10 cM on each side of the peak or by calculating -1.5 LOD. Large 95% CI are representative of low P-values and LOD scores or the presence of multiple QTL peak within the locus.

c LOD score at the peak of the QTL. Suggestive and significant LOD scores for main effect QTL are indicated as reported by the QTL study. QTL identified in a cross on a high fat diet are reported with the LOD score in parentheses.

d Reference publications that identified the HDL QTL as reported in Supplemental Table S2.


SUPPLEMENTAL TABLE S2. References for the reported HDL QTL.

Ref # / Published references
1. / Chen Y., Wang X, Su Z., Paigen B. Manuscript in preparation.
2. / Su, Z., N. Ishimori, Y. Chen, E. H. Leiter, G. A. Churchill, B. Paigen, and I. M. Stylianou. 2009. Four additional mouse crosses improve the lipid QTL landscape and identify Lipg as a QTL gene. J Lipid Res .
3. / Anunciado, R. V., M. Nishimura, M. Mori, A. Ishikawa, S. Tanaka, F. Horio, T. Ohno, and T. Namikawa. 2003. Quantitative trait locus analysis of serum insulin, triglyceride, total cholesterol and phospholipid levels in the (SM/J x A/J)F2 mice. Exp. Anim. 52: 37-42.
4. / Stylianou, I. M., S. W. Tsaih, K. DiPetrillo, N. Ishimori, R. Li, B. Paigen, and G. Churchill. 2006. Complex genetic architecture revealed by analysis of high-density lipoprotein cholesterol in chromosome substitution strains and F2 crosses. Genetics 174: 999-1007.
5. / Suto, J., K. Sekikawa. 2003. Quantitative trait locus analysis of plasma cholesterol and triglyceride levels in KK x RR F2 mice. Biochem. Genet. 41: 325-341.