Worldwide population differentiation at disease-associated SNPs

Myles, Sean; Davison, Dan; Barrett, Jeffrey; Stoneking, Mark; Timpson, Nic

doi:10.1186/1755-8794-1-22

BMC Medical Genomics

Table 1 Worldwide risk allele frequencies and global Fst for 25 disease-associated SNPs typed in the CEPH-HGDP panel.

From: Worldwide population differentiation at disease-associated SNPs

									Risk allele frequency
SNP¹	Disease²	Replication	Chr	Position³	Gene⁴	Global Fst	P	P _cor	Global	Africa	Middle East	Europe	Central South Asia	East Asia	America	Oceania
rs10077785	CD	[30]	5	131829057		0.062	0.642	0.511	0.82	0.975	0.809	0.812	0.716	0.898	0.688	0.75
rs10210302	CD	[30]	2	233940839	ATG16L1	0.117	0.315	0.323	0.393	0.268	0.459	0.539	0.541	0.31	0.066	0.018
rs10761659	CD	[30]	10	64115570		0.251	0.036	0.046	0.542	0.015	0.427	0.507	0.631	0.759	0.811	0.269
rs10811661	T2D	[27]	9	22124094	CDKN2A/2B	0.126	0.278	0.224	0.782	0.97	0.805	0.833	0.876	0.584	0.836	0.518
rs10883365	CD	[29]	10	101277754		0.04	0.8	0.65	0.459	0.48	0.541	0.497	0.43	0.449	0.161	0.643
rs10946398	T2D	[27, 31]	6	20769013	CDKAL1	0.028	0.901	0.697	0.328	0.47	0.338	0.286	0.243	0.382	0.242	0.321
rs1111875	T2D	[27, 28]	1	218111919		0.179	0.131	0.183	0.525	0.828	0.664	0.588	0.487	0.232	0.685	0.554
rs11171739	T1D	[32]	12	54756892		0.221	0.063	0.049	0.367	0.884	0.343	0.438	0.318	0.219	0.056	0.481
rs11805303	CD	[33]	1	67387537	IL23	0.085	0.483	0.492	0.421	0.27	0.456	0.303	0.513	0.547	0.121	0.446
rs12708716	T1D	[32]	16	11087374	KIAA0350	0.071	0.57	0.398	0.648	0.411	0.592	0.611	0.645	0.773	0.849	0.571
rs13266634	T2D	[27, 28]	8	114748339	SLC30A8	0.07	0.575	0.365	0.74	0.941	0.803	0.721	0.756	0.593	0.703	0.911
rs1333049	CAD	[34, 35, 36]	9	22115503		0.079	0.516	0.464	0.483	0.157	0.54	0.569	0.536	0.52	0.5	0.161
rs17234657	CD	[37]	5	40437266		0.112	0.334	0.192	0.07	0.243	0.099	0.126	0.021	0.002	0.008	0
rs17696736	T1D	[32]	12	110949538	C12orf30	0.237	0.049	0.113	0.165	0	0.37	0.413	0.13	0.011	0.04	0
rs1801282	T2D	[27, 38, 39]	3	12368125	PPARG	0.021	0.943	0.581	0.923	1	0.938	0.91	0.877	0.923	0.897	1
rs2542151	T1D/CD	[29]	18	12769947		0.008	0.991	0.77	0.153	0.183	0.127	0.144	0.179	0.154	0.172	0.018
rs4402960	T2D	[27]	3	186994389	IGF2BP2	0.077	0.53	0.612	0.371	0.693	0.302	0.354	0.378	0.306	0.218	0.536
rs5215	T2D	[27, 38, 39]	11	17365206	KCNJ11	0.057	0.671	0.697	0.319	0.056	0.268	0.418	0.34	0.377	0.312	0.393
rs564398	T2D	[27]	9	22019547	CDKN2A/2B	0.113	0.332	0.246	0.818	1	0.848	0.706	0.753	0.862	0.937	0.34
rs6679677	T1D/RA	[40, 41]	1	114015850	RSBN1	0.019	0.95	0.875	0.016	0	0.019	0.055	0.013	0.004	0	0
rs6887695	CD	[29]	5	158755223		0.028	0.898	0.741	0.362	0.381	0.383	0.281	0.299	0.409	0.371	0.643
rs7901695	T2D	[27, 28, 31]	10	114744078	TCF7L2	0.213	0.073	0.08	0.281	0.629	0.438	0.325	0.321	0.044	0.087	0.054
rs9858542	CD	[29]	3	49676987	BSN	0.094	0.432	0.318	0.222	0.23	0.301	0.317	0.331	0.077	0.016	0.143
rs9939609	T2D/OB	[27, 42]	16	52378028	FTO	0.101	0.391	0.446	0.315	0.471	0.41	0.426	0.348	0.157	0.048	0.25

¹ All SNPs were initially obtained from the WTCCC [26], except rs13266634 which was not well tagged by the Affymetrix GeneChip Human Mapping 500 K platform but was reported elsewhere as a T2D candidate [27, 28].
² CD = Crohn's disease; T2D = type 2 diabetes; T1D = type 1 diabetes; CAD = coronary artery disease; RA = rheumatoid arthritis; OB = obesity.
³ Positions refer to NCBI Build 35 coordinates.
⁴ Blank cells indicate that the SNP does not fall within or near a known coding gene.

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ISSN: 1755-8794

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