Table 2.

Alternate Loci for Haplotype Counting

Chromosome∗	Gene†	Start‡	Stop	Length (bp)	No. of SNPs	No. of haplotypes	CEU	JPT	YRI	Mean
1	—	238855189	238855428	240	9	7	0.63	0.46	0.63	0.57
1	—	238416454	238416673	220	9	11	0.39	0.46	0.43	0.43
2	—	106142506	106142791	286	10	8	0.63	0.61	0.66	0.63
2	VIT	36927840	36928071	232	9	6	0.58	0.59	0.61	0.59
3	ST6GAL1	186654745	186655022	278	9	12	0.72	0.67	0.73	0.70
3	—	97907092	97907374	283	10	13	0.58	0.42	0.64	0.55
4	SORCS2	7447136	7447434	299	9	16	0.60	0.46	0.65	0.57
4	—	66995978	66996254	277	9	8	0.63	0.45	0.60	0.56
5	—	125498526	125498753	228	10	19	0.67	0.58	0.67	0.64
5	—	178259629	178259892	264	13	23	0.69	0.56	0.64	0.63
6	HLA-DRB1	32551493	32551765	273	9	306	0.98	0.95	0.96	0.96
6	HLA-B	31319390	31319668	279	10	27	0.93	0.91	0.88	0.91
7	—	64895079	64895355	277	10	12	0.59	0.61	0.66	0.62
7	—	9111002	9111297	296	9	11	0.60	0.64	0.59	0.61
8	—	6160141	6160442	302	10	13	0.56	0.67	0.63	0.62
8	CSMD1	3478267	3478568	302	10	13	0.63	0.51	0.66	0.60
9	—	132197723	132197947	225	11	11	0.66	0.45	0.53	0.55
9	—	95691312	95691534	223	10	14	0.39	0.35	0.46	0.40
10	—	133376146	133376435	290	9	14	0.74	0.74	0.78	0.75
10	—	123095093	123095377	285	10	18	0.74	0.78	0.69	0.74
11	CNTN5	99491238	99491538	301	9	7	0.62	0.50	0.60	0.57
11	—	5078880	5079122	243	10	15	0.65	0.40	0.61	0.55
12	—	82460264	82460531	268	9	7	0.65	0.66	0.66	0.66
12	—	17884472	17884719	248	9	10	0.67	0.61	0.66	0.65
13	FARP1	99084002	99084259	258	9	17	0.63	0.70	0.71	0.68
13	—	33553507	33553784	278	9	29	0.68	0.45	0.65	0.59
14	—	107094021	107094317	297	10	25	0.53	0.51	0.66	0.57
14	TRA	22736235	22736521	287	9	11	0.51	0.57	0.61	0.56
15	—	34750054	34750330	277	9	8	0.51	0.57	0.61	0.56
15	—	25047393	25047681	289	10	25	0.51	0.44	0.55	0.50
16	—	56576389	56576687	299	11	46	0.76	0.82	0.80	0.79
16	—	84540653	84540932	280	9	16	0.69	0.66	0.74	0.70
17	TBCD	80804085	80804372	288	9	33	0.70	0.70	0.74	0.71
17	RBFOX3	77148074	77148367	294	10	15	0.38	0.60	0.52	0.50
18	—	76597079	76597332	254	9	14	0.40	0.40	0.40	0.40
18	CLUL1	631210	631400	191	9	12	0.35	0.27	0.38	0.33
19	CCDC61	46500080	46500360	281	9	14	0.41	0.38	0.43	0.41
19	—	57525179	57525424	246	13	10	0.37	0.39	0.41	0.39
20	PROKR2	5289890	5290161	272	9	7	0.64	0.51	0.59	0.58
20	SIRPA	1895467	1895674	208	11	24	0.49	0.58	0.56	0.54
21	—	20548907	20549196	290	9	6	0.44	0.35	0.42	0.40
21	UMODL1	43528819	43529079	261	9	10	0.33	0.38	0.39	0.36

—, No data.

^∗Chromosome 22 is absent because of the lack of good polymorphic loci. X and Y were excluded.

^†Gene, if present.

^‡Hg19 coordinates.