. Author manuscript; available in PMC: 2018 Oct 9.

Published in final edited form as: Nat Genet. 2018 Apr 9;50(4):559–571. doi: 10.1038/s41588-018-0084-1

Table 2.

Posterior probabilities for coding variants within 99% credible set across loci with annotation-informed and functionally-unweighted prior based on fine-mapping analysis performed using 50,160 T2D cases and 465,272 controls of European ancestry.

Locus	Variant	rs ID	Chr	Position	Posterior probability		Cumulative posterior probability attributed to coding variants
Locus	Variant	rs ID	Chr	Position	PPA	_aiPPA	PPA	_aiPPA
MACF1	MACF1 p.Ile39Val	rs16826069	1	39,797,055	0.012	0.240	0.032	0.628
	MACF1 p.Met1424Val	rs2296172	1	39,835,817	0.011	0.224
	MACF1 p.Lys1625Asn	rs41270807	1	39,801,815	0.008	0.163
FAM63A	FAM63A p.Tyr95Asn	rs140386498	1	150,972,959	0.005	0.129	0.012	0.303
GCKR	GCKR p. Pro 446Leu	rs1260326	2	27,730,940	0.773	0.995	0.773	0.995
THADA	THADA p.Cys845Tyr	rs35720761	2	43,519,977	<0.001	0.011	0.003	0.120
THADA	THADA p.Thr897Ala	rs7578597	2	43,732,823	0.003	0.107	0.003	0.120
CEP68	CEP68 p.Gly74Ser	rs7572857	2	65,296,798	<0.001	0.004	<0.001	0.004
GRB14	COBLL1 p.Asn901Asp	rs7607980	2	165,551,201	0.006	0.160	0.006	0.160
PPARG	PPARG p.Pro12Ala	rs1801282	3	12,393,125	0.023	0.410	0.024	0.410
KIF9	SETD2 p.Pro1962Lys	rs4082155	3	47,125,385	0.008	0.171	0.018	0.384
	NBEAL2 p.Arg511Gly	rs11720139	3	47,036,756	0.005	0.097
	KIF9 p.Arg638Trp	rs2276853	3	47,282,303	0.003	0.059
IGF2BP2	SENP2 p.Thr291Lys	rs6762208	3	185,331,165	<0.001	<0.001	<0.001	<0.001
WFS1	WFS1 p.Val333Ile	rs1801212	4	6,302,519	<0.001	0.001	<0.001	0.004
ANKH	ANKH p.Arg187Gln	rs146886108	5	14,751,305	0.459	0.972	0.447	0.972
POC5	POC5 p.His36Arg	rs2307111	5	75,003,678	0.697	0.954	0.702	0.986
PAM-PPIP5K2	PAM p.Asp336Gly	rs35658696	5	102,338,811	0.288	0.885	0.309	0.947
PAM-PPIP5K2	PPIP5K2 p.Ser1207Gly	rs36046591	5	102,537,285	0.020	0.063	0.309	0.947
RREB1 p.Asp1171Asn	RREB1 p.Asp1171Asn	rs9379084	6	7,231,843	0.920	0.997	0.920	0.997
RREB1 p.Ser1499Tyr	RREB1 p.Ser1499Tyr	rs35742417	6	7,247,344	<0.001	0.013	0.005	0.111
LPL	LPL p.Ser474*	rs328	8	19,819,724	0.023	0.832	0.023	0.832
SLC30A8	SLC30A8 p.Arg276Trp	rs13266634	8	118,184,783	0.295	0.823	0.295	0.823
GPSM1	GPSM1 p.Ser391Leu	rs60980157	9	139,235,415	0.031	0.557	0.031	0.557
KCNJ11-ABCC8	KCNJ11 p.Val250Ile	rs5215	11	17,408,630	0.208	0.412	0.481	0.951
	KCNJ11 p.Lys29Glu	rs5219	11	17,409,572	0.190	0.376
	ABCC8 p.Ala1369Ser	rs757110	11	17,418,477	0.083	0.163
PLCB3	PLCB3 p.Ser778Leu	rs35169799	11	64,031,241	0.113	0.720	0.130	0.830
TPCN2	TPCN2 p.Val219Ile	rs72928978	11	68,831,364	<0.001	0.004	0.006	0.140
CENTD2	ARAP1 p.Gln802Glu	rs56200889	11	72,408,055	<0.001	<0.001	<0.001	<0.001
KLHDC5	MRPS35 p.Gly43Arg	rs1127787	12	27,867,727	<0.001	<0.001	<0.001	<0.001
WSCD2	WSCD2 p.Thr113Ile	rs3764002	12	108,618,630	0.281	0.955	0.282	0.958
HNF1A p.Ile75Leu	HNF1A_Gly226Ala	rs56348580	12	121,432,117	0.358	0.894	0.358	0.894
HNF1A p.Ile75Leu	HNF1A p.Ile75Leu	rs1169288	12	121,416,650	<0.001	<0.001	0.358	0.894
HNF1A p.Ala146Val	HNF1A p.Ala146Val	rs1800574	12	121,416,864	0.269	0.867	0.280	0.902
MPHOSPH9	SBNO1 p.Ser729Asn	rs1060105	12	123,806,219	0.002	0.054	0.002	0.057
ZZEF1	ZZEF1 p.Ile402Val	rs781831	17	3,947,644	<0.001	0.001	<0.001	0.018
MLX	MLX p.Gln139Arg	rs665268	17	40,722,029	0.002	0.038	0.002	0.039
TTLL6	TTLL6 p.Glu712Asp	rs2032844	17	46,847,364	<0.001	<0.001	0.016	0.305
	CALCOCO2 p.Pro347Ala	rs10278	17	46,939,658	0.0100	0.187
	SNF8 p.Arg155His	rs57901004	17	47,011,897	0.005	0.092
C17orf58	C17orf58 p.Ile92Val	rs9891146	17	65,988,049	<0.001	0.009	<0.001	0.009
CILP2	TM6SF2 p.Glu167Lys	rs58542926	19	19,379,549	0.211	0.732	0.263	0.913
CILP2	TM6SF2 p.Leu156Pro	rs187429064	19	19,380,513	0.049	0.172	0.263	0.913
GIPR	GIPR p.Glu318Gln	rs1800437	19	46,181,392	0.169	0.901	0.169	0.901
ZHX3	ZHX3 p.Asn310Ser	rs17265513	20	39,832,628	<0.001	0.003	0.003	0.110
HNF4A	HNF4A p.Thr139Ile	rs1800961	20	43,042,364	1.000	1.000	1.00	1.000
MTMR3-ASCC2	ASCC2 p.Asp407His	rs28265	22	30,200,761	0.011	0.192	0.028	0.481
	ASCC2 p.Pro423Ser	rs36571	22	30,200,713	0.007	0.116
	ASCC2 p.Val123Ile	rs11549795	22	30,221,120	0.006	0.107
	MTMR3 p.Asn960Ser	rs41278853	22	30,416,527	0.004	0.065
PNPLA3	PNPLA3 p.Ile148Met	rs738409	22	44,324,727	0.112	0.691	0.130	0.806
PNPLA3	PARVB p.Trp37Arg	rs1007863	22	44,395,451	0.017	0.103	0.130	0.806
PIM3	IL17REL p.Leu333Pro	rs5771069	22	50,435,480	0.041	0.419	0.047	0.475
	IL17REL p.Gly70Arg	rs9617090	22	50,439,194	0.005	0.054
	PIM3 p.Val300Ala	rs4077129	22	50,356,693	<0.001	0.002

Chr: chromosome. Pos: Position build 37. PPA: functionally-unweighted prior; aiPPA: annotation informed prior. Index coding variants are highlighted in bold.