PMID: 23555291

Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained.

PLoS genetics
Y Wu, LL Waite, AU Jackson, WH Sheu, S Buyske, D Absher, DK Arnett, E Boerwinkle, LL Bonnycastle, CL Carty, I Cheng, B Cochran, DC Croteau-Chonka, L Dumitrescu, CB Eaton, N Franceschini, X Guo, BE Henderson, LA Hindorff, E Kim, L Kinnunen, P Komulainen, WJ Lee, L Le Marchand, Y Lin, J Lindström, O Lingaas-Holmen, SL Mitchell, N Narisu, JG Robinson, F Schumacher, A Stančáková, J Sundvall, YJ Sung, AJ Swift, WC Wang, L Wilkens, T Wilsgaard, AM Young, LS Adair, CM Ballantyne, P Bůžková, A Chakravarti, FS Collins, D Duggan, AB Feranil, LT Ho, YJ Hung, SC Hunt, K Hveem, JM Juang, AY Kesäniemi, J Kuusisto, M Laakso, TA Lakka, IT Lee, MF Leppert, TC Matise, L Moilanen, I Njølstad, U Peters, T Quertermous, R Rauramaa, JI Rotter, J Saramies, J Tuomilehto, M Uusitupa, TD Wang, M Boehnke, CA Haiman, YD Chen, C Kooperberg, TL Assimes, DC Crawford, CA Hsiung, KE North, KL Mohlke
2013-03

168 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
7-72115190-C-T TYW1B c.1507-21208G>A - intron_variant - 12/14
2-44099433-C-T ABCG8 c.1199C>T p.Thr400Met Missense 8/13 -
9-15293427-G-A TTC39B c.240+13655C>T - IntronicSNV - 1/19
8-19824492-T-C LPL c.*1671T>C - 3-UTRSNV 10/10 -
18-47088655-T-G LIPG c.1-24T>G - 5-UTRSNV 1/10 -
8-18257795-C-T NAT2 c.282C>T p.Tyr94Tyr Synonymous 2/2 -
16-68153062-G-A NFATC3 c.104-2828G>A - IntronicSNV - 1/10
11-47292237-A-T MADD c.-89+440A>T - intron_variant - 1/32
8-19824492-T-A LPL c.*1671T>A - 3-UTRSNV 10/10 -
12-125265689-C-T SCARB1 c.*1540G>A - IntronicSNV 13/13 -
2-165554309-C-A COBLL1 c.1672+1606G>T - IntronicSNV - 11/13
5-74928883-G-T ANKDD1B c.601-1840G>T - IntronicSNV - 5/13
5-156381533-G-A TIMD4 c.293C>T p.Thr98Ile Missense 2/9 -
12-57722187-T-C R3HDM2 c.1-17976A>G - IntergenicSNV - 2/23
9-136145425-C-A ABO c.28+5153G>T - IntronicSNV - 1/7
12-109997164-C-T MMAB c.585-204G>A - IntronicSNV - 7/8
1-230235609-C-T GALNT2 c.126+32456C>T - IntronicSNV - 1/15
9-136145425-C-T ABO c.28+5153G>A - IntronicSNV - 1/7
5-156353296-T-C TIMD4 c.872A>G p.Asn291Ser Missense 6/9 -
2-21260934-G-A APOB c.433C>T p.Pro145Ser Missense 5/29 -
1-25730713-G-A RHCE c.336-1476C>T - IntronicSNV - 2/9
11-116631786-A-T BUD13 c.1037-118T>A - IntronicSNV - 4/9
15-63551941-G-T RAB8B c.480+50G>T - IntronicSNV - 6/7
5-74717767-G-A COL4A3BP c.596-2518C>T - IntronicSNV - 5/17
9-136127601-G-A ABO c.*3452C>T - 3_prime_UTR_variant 8/8 -
15-58730498-C-G LIPC c.88+6179C>G - IntronicSNV - 1/8
15-58730498-C-T LIPC c.88+6179C>T - IntronicSNV - 1/8
9-15305378-G-C TTC39B c.240+1704C>G - IntronicSNV - 1/19
2-165552709-G-A COBLL1 c.1673-366C>T - IntronicSNV - 11/13
20-39889730-G-A ZHX3 c.-151+7900C>T - intron_variant - 2/3
20-43041591-C-T HNF4A c.386-743C>T - IntronicSNV - 3/9
11-47258979-A-C DDB2 c.1024-409A>C - IntronicSNV - 7/9
11-116661392-C-A APOA5 c.553G>T p.Gly185Cys Missense 4/4 -
11-116657561-C-T ZPR1 c.424+124G>A - IntronicSNV - 3/13
12-125265201-G-A SCARB1 c.*2028C>T - IntronicSNV - 12/12
11-46743247-T-C F2 c.316+857T>C - IntronicSNV - 4/13
6-160507298-A-G IGF2R c.6205+1135A>G - IntronicSNV - 41/47
9-107665739-G-A ABCA1 c.66+156C>T - IntronicSNV - 2/49
15-42683787-G-A CAPN3 c.946-1050G>A - IntronicSNV - 6/23
16-67928042-G-A PSKH1 c.-71+768G>A - intron_variant - 1/2
18-47109955-A-C LIPG c.1187A>C p.Asn396Thr Missense 8/10 -
18-47109955-A-G LIPG c.1187A>G p.Asn396Ser Missense 8/10 -
4-88030261-G-T AFF1 c.1512+794G>T - IntronicSNV - 10/19
11-61624414-T-C FADS2 c.745-69T>C - IntronicSNV - 5/11
19-45405062-A-T TOMM40 c.946+495A>T - IntronicSNV - 9/9
8-19824667-C-T LPL c.*1846C>T - 3-UTRSNV 10/10 -
11-126237666-T-G ST3GAL4 c.-61+11469T>G - intron_variant - 1/10
2-21225281-C-T APOB c.13013G>A p.Ser4338Asn Missense 29/29 -
16-57000885-G-A CETP c.234-2413G>A - IntronicSNV - 2/15
11-116653296-C-T ZPR1 c.1093-336G>A - IntronicSNV - 11/13
11-47292237-A-G MADD c.-89+440A>G - intron_variant - 1/32
1-55523802-A-G PCSK9 c.1274A>G p.Asn425Ser Missense 8/12 -
11-116653296-C-G ZPR1 c.1093-336G>C - IntronicSNV - 11/13
1-230265677-T-G GALNT2 c.127-48287T>G - IntronicSNV - 1/15
19-45405062-A-G TOMM40 c.946+495A>G - IntronicSNV - 9/9
11-116652207-C-T ZPR1 c.1179+667G>A - IntronicSNV - 12/13
16-67997920-T-C SLC12A4 c.116-458A>G - IntronicSNV - 1/23
17-38026585-C-T ZPBP2 c.53-362C>T - IntronicSNV - 1/6
19-19454013-C-T MAU2 c.973+338C>T - IntronicSNV - 9/18
20-39729884-A-G TOP1 c.1199A>G p.Lys400Arg Missense 13/21 -
1-109698281-A-G KIAA1324 c.154-6235A>G - IntronicSNV - 1/21
11-126278458-C-A ST3GAL4 c.615+67C>A - IntronicSNV - 8/10
4-87980066-C-T AFF1 c.1038+11320C>T - IntronicSNV - 3/19
1-55512222-C-G PCSK9 c.426C>G p.Tyr142* Nonsense 3/12 -
16-72054984-G-T DHODH c.518-39G>T - IntronicSNV - 4/8
5-156479572-A-G HAVCR1 c.473T>C p.Met158Thr Missense 3/8 -
19-45398264-C-T TOMM40 c.643+941C>T - IntronicSNV - 6/9
4-87980066-C-G AFF1 c.1038+11320C>G - IntronicSNV - 3/19
20-44534909-G-A PLTP c.703C>T p.Arg235Trp Missense 8/16 -
2-44091083-A-G ABCG8 c.965-8032A>G - IntronicSNV - 6/12
17-66875294-C-G ABCA8 c.3919-1474G>C - IntronicSNV - 30/37
20-39992997-C-T EMILIN3 c.291-496G>A - IntronicSNV - 2/3
19-45410548-A-G APOE c.44-469A>G - IntronicSNV - 2/3
12-109947905-C-T UBE3B c.1742-244C>T - IntronicSNV - 16/27
8-19813529-A-G LPL c.953A>G p.Asn318Ser Missense 6/10 -
15-42681199-G-A CAPN3 c.706G>A p.Ala236Thr Missense 5/24 -
2-165577434-G-A COBLL1 c.996+1151C>T - IntronicSNV - 6/13
2-165540800-T-C COBLL1 c.*1656A>G - 3-UTRSNV 14/14 -
16-56997353-A-C CETP c.233+317A>C - IntronicSNV - 2/15
1-55518467-A-G PCSK9 c.799+3A>G - IntronicSNV - 5/11
15-42642677-A-G GANC c.2532-850A>G - IntronicSNV - 22/23
11-116651115-C-G ZPR1 c.1180-562G>C - IntronicSNV - 12/13
9-15304782-C-A TTC39B c.240+2300G>T - IntronicSNV - 1/19
13-74561549-T-A KLF12 c.33+7578A>T - IntronicSNV - 2/7
2-27743215-A-G GCKR c.1572+1411A>G - IntronicSNV - 17/18
19-45401666-A-G TOMM40 c.644-2321A>G - IntronicSNV - 6/9
16-57006590-C-G CETP c.750+595C>G - IntronicSNV - 8/15
16-57006590-C-T CETP c.750+595C>T - IntronicSNV - 8/15
6-160520768-C-T IGF2R c.6843-2783C>T - IntronicSNV - 45/47
1-230295789-A-G GALNT2 c.127-18175A>G - IntronicSNV - 1/15
16-57007353-C-T CETP c.861C>T p.Phe287Phe Synonymous 9/16 -
2-21257697-A-C APOB c.895T>G p.Phe299Val Missense 8/29 -
17-37475104-A-C FBXL20 c.105-15212T>G - IntronicSNV - 2/14
13-74565500-A-G KLF12 c.33+3627T>C - IntronicSNV - 2/7
1-109698281-A-C KIAA1324 c.154-6235A>C - IntronicSNV - 1/21
2-21252534-G-A APOB c.1594C>T p.Arg532Trp Missense 12/29 -
9-136437378-A-C ADAMTSL2 c.2593-1587A>C - IntronicSNV - 17/18
1-55518093-G-A PCSK9 c.657+9G>A - IntronicSNV - 4/11
9-107588033-C-T ABCA1 c.2473G>A p.Val825Ile Missense 17/50 -
19-45412040-C-T APOE c.487C>T p.Arg163Cys Missense 4/4 -
11-116662407-G-A APOA5 c.56C>T p.Ser19Leu Missense 3/4 -
12-125266172-C-T SCARB1 c.*1057G>A - IntronicSNV - 12/12
13-74588747-G-C KLF12 c.1-19588C>G - IntronicSNV - 1/7
13-74588747-G-A KLF12 c.1-19588C>T - IntronicSNV - 1/7
15-42632915-A-G GANC c.2115A>G p.Glu705Glu Synonymous 18/24 -
2-21231524-G-A APOB c.8216C>T p.Pro2739Leu Missense 26/29 -
15-42652059-CC-GG CAPN3 c.56_57delCCinsGG p.Ser19Trp Missense 1/24 -
17-38025417-G-A ZPBP2 c.52+758G>A - IntronicSNV - 1/6
11-126260864-A-G ST3GAL4 c.1-15187A>G - IntronicSNV - 1/10
16-72054984-G-C DHODH c.518-39G>C - IntronicSNV - 4/8
11-126243952-G-A ST3GAL4 c.-61+17755G>A - intron_variant - 1/10
1-230265677-T-A GALNT2 c.127-48287T>A - IntronicSNV - 1/15
17-37813856-G-C STARD3 c.298-172G>C - IntronicSNV - 3/14
8-19805708-G-C LPL c.106G>C p.Asp36His Missense 2/10 -
8-19805708-G-A LPL c.106G>A p.Asp36Asn Missense 2/10 -
16-67977382-T-C LCAT c.155-267A>G - IntronicSNV - 1/5
2-44075483-T-C ABCG8 c.322+2033T>C - IntronicSNV - 3/12
6-16132409-C-T MYLIP c.278+1431C>T - IntronicSNV - 2/6
7-72129667-C-T TYW1B c.1506+30010G>A - intron_variant - 12/14
16-72101525-C-G HPR c.5+4366C>G - IntronicSNV - 1/4
9-136141870-C-T ABO c.29-4299G>A - IntronicSNV - 1/7
8-10654168-T-G PINX1 c.471+23535A>C - IntronicSNV - 6/6
19-19456917-C-T MAU2 c.1221+739C>T - IntronicSNV - 12/18
16-67976622-G-A LCAT c.475C>T p.Arg159Trp Missense 4/6 -
7-72070325-T-G TYW1B c.1785+11332A>C - intron_variant - 14/14
7-72070325-T-C TYW1B c.1785+11332A>G - intron_variant - 14/14
11-47259668-T-C DDB2 c.1189-21T>C - IntronicSNV - 8/9
1-230295307-C-A GALNT2 c.127-18657C>A - IntronicSNV - 1/15
1-230295307-C-G GALNT2 c.127-18657C>G - IntronicSNV - 1/15
19-19558306-A-G GATAD2A c.1-17849A>G - IntronicSNV - 1/11
12-57828863-G-A INHBC c.194G>A p.Arg65His Missense 1/2 -
7-73027450-C-A MLXIPL c.400+2951G>T - IntronicSNV - 2/16
7-73027450-C-G MLXIPL c.400+2951G>C - IntronicSNV - 2/16
1-55523865-C-T PCSK9 c.1337C>T p.Pro446Leu Missense 8/12 -
1-25669829-G-A TMEM50A c.206+265G>A - IntronicSNV - 3/6
7-73020676-G-A MLXIPL c.619-235C>T - IntronicSNV - 5/16
11-116651115-C-T ZPR1 c.1180-562G>A - IntronicSNV - 12/13
11-116635282-C-T BUD13 c.322+796G>A - IntronicSNV - 3/9
2-44099433-C-A ABCG8 c.1199C>A p.Thr400Lys Missense 8/13 -
1-55529215-C-A PCSK9 c.2037C>A p.Cys679* Nonsense 12/12 -
19-11227602-C-T LDLR c.1773C>T p.Asn591Asn Synonymous 12/18 -
7-73020676-G-T MLXIPL c.619-235C>A - IntronicSNV - 5/16
15-42740369-C-T ZNF106 c.2967G>A p.Ala989Ala Synonymous 3/19 -
9-107620835-G-A ABCA1 c.688C>T p.Arg230Cys Missense 7/50 -
7-73020676-G-C MLXIPL c.619-235C>G - IntronicSNV - 5/16
5-156479572-A-T HAVCR1 c.473T>A p.Met158Lys Missense 3/8 -
8-19823674-C-G LPL c.*853C>G - 3-UTRSNV 10/10 -
16-68156085-T-C NFATC3 c.299T>C p.Leu100Ser Missense 2/11 -
1-55518422-C-T PCSK9 c.757C>T p.Leu253Phe Missense 5/12 -
7-72130213-T-C TYW1B c.1506+29464A>G - intron_variant - 12/14
8-10683929-G-C PINX1 c.302-175C>G - IntronicSNV - 4/6
8-10683929-G-T PINX1 c.302-175C>A - IntronicSNV - 4/6
12-57707295-C-T R3HDM2 c.1-3084G>A - IntergenicSNV - 1/23
8-19823674-C-T LPL c.*853C>T - 3-UTRSNV 10/10 -
13-74574178-C-T KLF12 c.1-5019G>A - IntronicSNV - 1/7
11-126278458-C-T ST3GAL4 c.615+67C>T - IntronicSNV - 8/10
1-55523855-G-A PCSK9 c.1327G>A p.Ala443Thr Missense 8/12 -
6-160520745-G-A IGF2R c.6843-2806G>A - IntronicSNV - 45/47
20-43052570-T-C HNF4A c.893-88T>C - IntronicSNV - 7/9
15-42740369-C-A ZNF106 c.2967G>T p.Ala989Ala Synonymous 3/19 -
1-62957030-G-A DOCK7 c.5268+1345C>T - IntronicSNV - 40/48
2-21226560-A-G APOB c.12088-354T>C - IntronicSNV - 28/28
1-230295789-A-T GALNT2 c.127-18175A>T - IntronicSNV - 1/15
12-125266432-T-C SCARB1 c.*797A>G - IntronicSNV - 12/12
1-63057136-T-C DOCK7 c.1683-4841A>G - IntronicSNV - 14/48
1-63057136-T-A DOCK7 c.1683-4841A>T - IntronicSNV - 14/48
7-72992350-C-T TBL2 c.130+400G>A - IntronicSNV - 1/6
16-57006378-A-G CETP c.750+383A>G - IntronicSNV - 8/15