Identification of a Novel Risk Locus for Progressive Supranuclear Palsy by a Pooled Genomewide Scan of 500,288 Single-Nucleotide Polymorphisms

Abstract

To date, only the H1 MAPT haplotype has been consistently associated with risk of developing the neurodegenerative disease progressive supranuclear palsy (PSP). We hypothesized that additional genetic loci may be involved in conferring risk of PSP that could be identified through a pooling-based genomewide association study of >500,000 SNPs. Candidate SNPs with large differences in allelic frequency were identified by ranking all SNPs by their probe-intensity difference between cohorts. The MAPT H1 haplotype was strongly detected by this methodology, as was a second major locus on chromosome 11p12-p11 that showed evidence of association at allelic (P<.001), genotypic (P<.001), and haplotypic (P<.001) levels and was narrowed to a single haplotype block containing the DNA damage-binding protein 2 (DDB2) and lysosomal acid phosphatase 2 (ACP2) genes. Since DNA damage and lysosomal dysfunction have been implicated in aging and neurodegenerative processes, both genes are viable candidates for conferring risk of disease.

Progressive supranuclear palsy (PSP [MIM 601104]) is the second-most-common form of parkinsonism, with a population prevalence rate of 6–6.4 per 100,000.^1,2 Clinical features include vertical-gaze palsy and postural instability.^3,4 PSP is characterized neuropathologically by neuronal and glial inclusions composed of aggregated microtubule associated protein tau (MAPT) in the basal ganglia and brain stem.^5,6 Mutations in the MAPT (MIM 157140) gene have been identified in patients with a clinical presentation of PSP.^7–14 A recent report also described linkage to chromosome 1q31.1 in a family with autosomal dominant PSP.¹⁵ However, only the MAPT locus has been consistently associated with increased risk for idiopathic PSP.^16–20 The MAPT locus exists as two major haplotype groups, termed “H1” and “H2”¹⁶ in European populations, with the H2 haplotype defined by >100 SNPs that are inherited in strong linkage disequilibrium (LD) with each other, reflecting the total absence of H1-H2 recombination.²¹ Inheritance of two copies of the H1 haplotype (H1/H1) is a major genetic risk factor for PSP.¹⁶ A large collection of pathologically confirmed PSP samples was used recently to fine map PSP risk on H1 chromosomes in PSP cases and controls. ^22,23 PSP risk was associated with an extended subhaplotype, and narrowing the region for PSP risk to a 22-kb region in intron 0 of MAPT was accomplished by examining younger patients with, presumably, a larger genetic component to their disease.^22,23 The most likely explanation of the association with the MAPT H1 haplotype and PSP is that variants in the H1 (and H2) haplotypes confer risk of (protect against) disease by altering expression at the locus, with the risky H1 haplotypes expressing higher levels of MAPT.^22–26

Calculations of population-attributable risk suggest that only ∼68% of the risk of PSP can be accounted for by the MAPT H1 haplotype, suggesting there may be additional risk genes involved in PSP. We hypothesized that additional genetic loci involved in conferring risk of PSP could be identified through genomewide association (GWA) methods. The cost of performing an association study that involved individual genotyping of thousands of SNPs for a series this size was prohibitive, so, instead, we used a pooled-DNA approach to identify additional risk factors. Whereas a pooling-based genomewide scan of thousands of SNPs has been proposed in principle, in large part, these studies have not been used for the discovery of genes predisposing to complex diseases,^27,28 likely because of technical concerns or lack of technology and analysis tools.

The patients used in the initial pooling study, the “original” series, were largely derived from pathologically confirmed subjects collected by the PSP Society and sent to D.W.D. for brain autopsy. As described elsewhere, the patient samples in this brain bank were donated from the United States and Canada.²⁹ The patient series is similar to the one that we employed in previous studies to fine map the H1 genetic risk,²² with 288 subjects with a primary pathological diagnosis of PSP used to create the pool of PSP-affected patients. A total of 344 age- and sex-matched cognitively normal control individuals were obtained through the Normal and Pathological Aging protocol at the Mayo Clinic (Scottsdale),^30,31 to create the pool of control individuals. All patient and control individuals were white from the United States and Canada, and institutional review board (IRB)–approved protocols were used in the collection of all samples.

Replicate pools of patients with PSP and control individuals were created as described elsewhere.³² Samples were genotyped on 20 replicate Affymetrix 500K arrays and 20 Affymetrix 100K, in accordance with the Affymetrix protocols, whereby each of the five replicate pools was genotyped on two replicate arrays. This design therefore yielded probe-intensity data for both platforms on 10 replicate arrays per cohort. Data were analyzed using GenePool software (TGen Bioinformatics Research Unit).³² In brief, probe-intensity data were directly read from cell-intensity (CEL) files, and relative allele signal (RAS) values were calculated for each quartet. These values yield independent measures of different hybridization events and are consequently treated as individual data points. We used a silhouette statistic to rank all genotyped SNPs,³³ because it avoids introducing unnecessary variance by averaging probe-intensity data from probes with different hybridization properties. Silhouette scores range from 1, where significant separation between data points has been achieved and cluster assignment can be made with confidence, to −1, where differences in allelic frequencies are less reliable. Poorly performing SNPs were identified by Affymetrix as unreliable in the transition to Mendel3 libraries or exhibited high variance between replicate arrays and were removed from the analysis; 428,867 SNPs remained. SNPs were ranked on the basis of silhouette score, whereby the SNP with the highest score was ranked 1 and the SNP with the lowest score was ranked 428,867, with use of Affymetrix’s Mendel3 libraries for the Affymetrix 500K arrays and HindIII and XbaI libraries for the Affymetrix 100K arrays, then were sorted by chromosome and physical position. With this ranking, it is assumed that SNPs approaching a rank of 1 will have larger differences in allelic frequency. With each sample ranked by silhouette score, we calculated a sliding-window statistic of the mean rank for consecutively neighboring SNPs across a fixed window size. Window sizes from 2 to 31 were used.

Since the MAPT H1 haplotype is associated with disease with a haplotypic odds ratio (OR) of ∼3–4,^16,22,23,34 it served as an internal positive control for the study. For analysis, we used the 500K data to identify chromosomal regions of interest (i.e., those with small mean-rank scores). The 100K data were then used to confirm that a region identified in the 500K analysis contained SNPs with large allelic frequency differences. The SNP with the single best statistical rank on the 500K chip was rs901746 on chromosome 11p12, and the second-best SNP was rs17662235, near MAPT. The top 1,000 SNPs, based on individual statistical rank, are given in table 1. Multimarker statistics also identified both chromosome 11p12 and chromosome 17q21 (MAPT) regions with sliding windows of multiple sizes. Although we recognize that this type of statistic is biased because of genomewide LD, it allowed us to identify clusters of high-ranking SNPs that neighbor one another, which reduced the possibility of technical errors influencing the results. Shown in figure 1A, the MAPT locus, labeled as having the #2 SNP overall, showed the greatest evidence of differences between case and control pools with use of the sliding-window analysis, largely because of 38 SNPs within the top 1,000 SNPs overall and a total of 75 SNPs in the region with a rank score of <10,000 (fig. 1B and table 1). Examination of the individual SNPs with high rank scores over this locus showed SNPs that were derived from a region covering the full extent of the MAPT H1 haplotype, spanning nearly 1 Mb (fig. 1B).³⁶ All of the 75 SNPs with genotype-frequency data in the database resembled MAPT H2 variants (which differentiate between H1 and H2 MAPT haplotypes) rather than H1 variants (which differentiate between H1 subhaplotypes); this is because, in white populations, the SNP minor-allele frequency was ∼0.2, whereas the minor allele of the SNP was absent or rare in Asian populations and African populations.^36,37 In addition, two of the SNPs with low rank scores (rs12150111 and rs807072) were identified definitively as MAPT H2 variants from prior MAPT genomic sequencing efforts.²²

Table 1. .

Predicted Allelic Frequencies for the Top 1,000 SNPs

				Frequencyc (SD) of Predicted Allele
SNP Ranka	dbSNP Number	Chromosome	Positionb	Case	Control
1	rs901746	11	47216895	61.3 (.042)	81.1 (.027)
2	rs17662235	17	41589553	2.7 (.019)	15.3 (.028)
3	rs2699808	7	26175747	60.5 (.039)	45.2 (.043)
4	rs17662853	17	41604625	26.7 (.068)	14.0 (.039)
5	rs11898241	2	115847267	75.6 (.057)	61.0 (.042)
6	rs17563501	17	41157478	96.4 (.050)	79.9 (.021)
7	rs2141299	17	41596763	94.7 (.035)	77.7 (.023)
8	rs17574228	17	41460355	12.4 (.016)	24.8 (.035)
9	rs2732706	17	41707463	8.5 (.036)	22.1 (.044)
10	rs7139545	13	24677429	74.2 (.022)	85.7 (.039)
11	rs6450530	5	59095265	30.6 (.047)	51.3 (.041)
12	rs2668695	17	41647903	13.3 (.034)	27.3 (.038)
13	rs3759297	12	32029119	63.6 (.033)	80.0 (.030)
14	rs10798036	1	182784619	45.0 (.045)	61.1 (.046)
15	rs10213502	4	11624923	93.7 (.023)	79.4 (.039)
16	rs7700506	5	56032355	65.5 (.029)	85.5 (.031)
17	rs7198242	16	68205996	24.0 (.083)	5.9 (.048)
18	rs2532286	17	41597441	96.6 (.045)	89.6 (.048)
19	rs7534271	1	47406001	55.7 (.035)	68.6 (.051)
20	rs9649052	7	134311099	49.4 (.012)	58.6 (.034)
21	rs17604700	15	29922129	51.6 (.053)	34.6 (.078)
22	rs11623728	14	96882409	27.6 (.019)	18.6 (.018)
23	rs1557996	7	7430544	93.4 (.039)	77.9 (.054)
24	rs2202445	5	7381176	57.7 (.047)	74.5 (.056)
25	rs1527036	23	3215185	50.3 (.035)	63.7 (.039)
26	rs2035515	8	107825837	92.1 (.025)	82.4 (.019)
27	rs11745421	5	168123644	11.8 (.044)	0.7 (.017)
28	rs429988	3	41081069	63.2 (.033)	74.0 (.028)
29	rs10838681	11	47231640	67.6 (.030)	80.8 (.041)
30	rs10517938	4	168729149	77.6 (.044)	84.9 (.028)
31	rs12918956	16	70781836	42.0 (.070)	57.0 (.059)
32	rs9567416	13	43806741	36.3 (.100)	15.2 (.044)
33	rs2107699	7	49367808	19.6 (.082)	45.4 (.182)
34	rs4794984	17	29333048	66.1 (.037)	78.8 (.037)
35	rs8088596	18	72620941	65.2 (.032)	50.1 (.049)
36	rs2116457	8	129876983	53.9 (.039)	67.3 (.029)
37	rs762038	14	20304608	71.0 (.028)	83.3 (.035)
38	rs1336433	10	113348065	32.8 (.038)	46.2 (.039)
39	rs7620394	3	55206368	36.1 (.035)	23.8 (.039)
40	rs6590039	11	123446989	72.7 (.029)	57.0 (.040)
41	rs10824896	10	51463093	81.7 (.046)	89.2 (.018)
42	rs354636	1	91184514	86.2 (.044)	95.7 (.051)
43	rs13020820	2	33892179	48.8 (.042)	59.9 (.039)
44	rs520605	1	181527436	68.8 (.021)	84.7 (.058)
45	rs11926691	3	83064778	64.6 (.027)	55.1 (.011)
46	rs16936441	9	18201655	70.9 (.068)	88.7 (.045)
47	rs8036777	15	48208710	46.8 (.060)	66.3 (.030)
48	rs1299704	3	108688432	32.0 (.022)	42.7 (.047)
49	rs1550532	2	234046848	58.4 (.042)	69.4 (.038)
50	rs9394550	6	38960939	56.3 (.059)	41.7 (.035)
51	rs12717171	6	112800652	53.2 (.027)	62.0 (.032)
52	rs2548879	16	77200307	54.7 (.081)	27.9 (.077)
53	rs10256927	7	125167859	71.8 (.021)	79.4 (.022)
54	rs7407281	18	55756601	67.4 (.045)	82.4 (.032)
55	rs1122452	3	144910038	77.7 (.039)	63.4 (.029)
56	rs12962651	18	56476045	47.9 (.052)	61.0 (.040)
57	rs2070929	1	47395627	30.0 (.045)	17.0 (.028)
58	rs2036535	17	28775126	47.9 (.046)	38.8 (.022)
59	rs11211670	2	1346042	42.7 (.041)	29.4 (.024)
60	rs4372225	1	211830838	75.3 (.070)	92.3 (.048)
61	rs17660065	17	41518102	97.2 (.045)	82.1 (.081)
62	rs1725604	7	101507570	51.8 (.035)	41.7 (.017)
63	rs2194711	5	154994268	17.8 (.043)	7.2 (.044)
64	rs6753459	2	190890259	25.0 (.041)	14.2 (.039)
65	rs1041834	21	41841892	40.9 (.034)	31.7 (.012)
66	rs6847349	4	13717192	27.6 (.040)	45.2 (.061)
67	rs6101206	20	59050033	59.8 (.040)	41.0 (.032)
68	rs2732675	17	41635965	1.6 (.048)	16.9 (.046)
69	rs7396713	11	88020266	39.0 (.073)	27.5 (.030)
70	rs11835314	12	106412032	75.3 (.034)	57.2 (.062)
71	rs1520961	15	35523947	85.5 (.056)	71.8 (.067)
72	rs4740919	9	7844892	38.0 (.042)	20.2 (.039)
73	rs8088963	18	57198294	48.5 (.057)	37.6 (.017)
74	rs695271	22	32327285	59.2 (.050)	47.9 (.057)
75	rs9377831	6	58761209	14.3 (.037)	6.3 (.013)
76	rs9955849	18	3052581	84.2 (.042)	70.0 (.027)
77	rs10791979	11	55916546	77.2 (.068)	55.7 (.079)
78	rs2805386	9	110761555	69.4 (.018)	56.6 (.072)
79	rs4845237	1	187114452	82.1 (.062)	61.3 (.061)
80	rs4440119	3	61936314	40.0 (.092)	60.2 (.080)
81	rs1289951	1	117625061	87.2 (.021)	76.5 (.061)
82	rs4669550	2	10273437	15.3 (.055)	7.2 (.016)
83	rs6712370	2	69766745	35.7 (.072)	20.3 (.057)
84	rs6469264	8	110594779	20.0 (.089)	6.4 (.041)
85	rs323376	8	30851071	15.5 (.071)	39.5 (.084)
86	rs916793	17	41310477	95.3 (.068)	78.9 (.027)
87	rs210069	20	52162352	62.5 (.022)	71.8 (.016)
88	rs1826763	4	177179201	27.1 (.059)	46.4 (.062)
89	rs12427267	12	90826440	49.4 (.079)	70.7 (.035)
90	rs2442497	8	6314156	11.5 (.052)	22.7 (.046)
91	rs2583513	4	116275788	71.1 (.023)	64.0 (.029)
92	rs2191265	7	12678307	42.2 (.039)	56.7 (.040)
93	rs2163385	18	38452575	8.5 (.021)	0.5 (.022)
94	rs11071075	15	29550901	68.0 (.042)	80.2 (.037)
95	rs12819116	12	12537788	59.2 (.036)	70.2 (.028)
96	rs7940239	11	55880498	19.4 (.056)	35.1 (.067)
97	rs1400174	3	52174	36.6 (.050)	23.4 (.048)
98	rs17563787	17	41169023	6.9 (.064)	22.4 (.022)
99	rs10829618	10	131380410	72.8 (.067)	89.9 (.064)
100	rs9710693	2	239504258	34.1 (.033)	20.7 (.040)
101	rs11157865	14	51436825	52.1 (.063)	67.9 (.041)
102	rs1678719	6	38901529	77.5 (.043)	95.5 (.033)
103	rs1692506	18	24511864	61.7 (.030)	73.5 (.037)
104	rs10928098	2	141715827	42.1 (.046)	23.8 (.046)
105	rs10975882	9	689065	43.1 (.034)	50.4 (.024)
106	rs578987	1	17948686	38.3 (.041)	25.2 (.042)
107	rs2274403	13	94645021	61.8 (.047)	48.4 (.024)
108	rs3807404	7	38325866	61.0 (.062)	77.7 (.036)
109	rs2532275	17	41602774	95.7 (.033)	84.0 (.048)
110	rs6920684	6	8306390	66.6 (.044)	56.3 (.054)
111	rs3911781	10	67516022	77.9 (.046)	89.6 (.036)
112	rs1304527	21	35459060	94.4 (.048)	77.0 (.067)
113	rs10021851	4	40209776	85.4 (.058)	58.0 (.109)
114	rs1445517	4	138159604	40.1 (.034)	48.7 (.056)
115	rs11119752	1	208064160	65.9 (.041)	54.1 (.015)
116	rs17577094	17	41543275	2.7 (.098)	28.7 (.093)
117	rs2532316	17	41569489	90.6 (.043)	80.2 (.021)
118	rs7177316	15	48209122	43.6 (.049)	58.8 (.059)
119	rs2696600	17	41572003	89.8 (.036)	79.7 (.031)
120	rs5751592	22	21822228	75.7 (.047)	91.0 (.019)
121	rs9354193	6	65733294	59.6 (.047)	47.7 (.041)
122	rs6581596	12	63670237	31.8 (.059)	46.1 (.037)
123	rs722979	10	83952201	66.8 (.051)	54.6 (.038)
124	rs4943389	13	36008899	36.4 (.049)	51.8 (.048)
125	rs10931378	2	189420130	29.9 (.049)	40.1 (.047)
126	rs919262	5	151246277	38.9 (.045)	26.1 (.044)
127	rs1399564	8	76646411	37.1 (.034)	49.7 (.052)
128	rs12043736	1	215866548	57.0 (.047)	72.5 (.057)
129	rs17353336	3	134155679	54.1 (.032)	39.8 (.024)
130	rs9371835	6	155327752	39.1 (.038)	48.7 (.030)
131	rs1635216	23	3214080	57.9 (.075)	80.9 (.053)
132	rs1159788	4	103664727	35.5 (.049)	25.0 (.030)
133	rs153518	5	142937957	46.4 (.021)	40.3 (.037)
134	rs17074118	13	29420217	17.8 (.026)	4.3 (.043)
135	rs206034	23	39291012	56.2 (.032)	74.3 (.066)
136	rs9287986	2	176312475	51.9 (.027)	36.9 (.046)
137	rs1562495	3	144910247	31.1 (.025)	43.8 (.051)
138	rs1993329	6	68992781	43.9 (.062)	28.3 (.068)
139	rs6060965	20	29869759	29.5 (.032)	18.1 (.030)
140	rs1957779	14	62739400	62.5 (.027)	43.1 (.059)
141	rs10745813	12	96767932	11.6 (.033)	24.0 (.055)
142	rs2064855	20	59058742	35.4 (.048)	16.9 (.045)
143	rs7321718	13	72257693	52.6 (.036)	66.2 (.025)
144	rs1220627	5	72906819	29.9 (.033)	20.0 (.029)
145	rs1952251	1	180714144	36.5 (.079)	23.8 (.040)
146	rs4420176	10	127666188	51.2 (.032)	40.7 (.061)
147	rs338565	1	181508758	22.5 (.112)	7.8 (.034)
148	rs776965	8	107768142	47.9 (.066)	30.1 (.052)
149	rs4132608	13	109898267	68.4 (.030)	80.8 (.021)
150	rs1841043	4	69889478	10.9 (.034)	30.4 (.058)
151	rs11259272	10	6586077	34.3 (.058)	61.5 (.106)
152	rs7901651	10	85617227	49.3 (.048)	63.1 (.057)
153	rs7999230	13	106749278	27.0 (.033)	39.2 (.039)
154	rs12144146	1	151338046	40.1 (.081)	22.3 (.038)
155	rs10842885	12	27291048	63.8 (.054)	47.7 (.056)
156	rs17173853	7	149243724	81.3 (.037)	93.4 (.026)
157	rs1547597	7	147404398	39.5 (.096)	2.3 (.064)
158	rs1549411	12	29684407	75.5 (.070)	92.6 (.070)
159	rs586457	10	6537428	41.6 (.042)	25.6 (.042)
160	rs10894846	11	133954025	23.6 (.074)	10.7 (.048)
161	rs10459826	16	5680786	87.5 (.070)	70.6 (.039)
162	rs256447	5	79375707	1.6 (.029)	9.7 (.064)
163	rs476906	3	177685396	68.6 (.040)	78.8 (.017)
164	rs4633144	9	32494294	52.3 (.058)	71.6 (.065)
165	rs694444	13	63372180	73.3 (.066)	83.3 (.018)
166	rs332735	2	119167473	79.3 (.056)	90.6 (.028)
167	rs12424367	12	90826168	55.4 (.079)	73.1 (.048)
168	rs12281742	11	68060205	30.8 (.050)	16.1 (.060)
169	rs2809658	1	42719489	35.8 (.047)	53.7 (.049)
170	rs1249426	2	141775551	67.9 (.039)	88.3 (.060)
171	rs2709733	7	20728610	56.7 (.052)	37.6 (.096)
172	rs1878248	10	113311751	32.1 (.060)	21.1 (.028)
173	rs4730720	7	115489186	34.1 (.048)	16.2 (.053)
174	rs9321395	6	133642955	8.3 (.057)	24.2 (.042)
175	rs2167287	12	61068734	85.2 (.040)	92.7 (.014)
176	rs973406	2	176935238	76.4 (.047)	63.9 (.041)
177	rs10795321	10	15901281	14.4 (.061)	30.4 (.044)
178	rs10832515	11	15725228	33.6 (.038)	24.8 (.034)
179	rs6538018	9	135465832	50.3 (.044)	75.4 (.095)
180	rs1692507	18	24511941	63.6 (.042)	75.2 (.027)
181	rs798544	7	2536343	32.9 (.048)	19.3 (.025)
182	rs11708068	3	63429650	68.9 (.055)	86.0 (.038)
183	rs2399547	10	10719044	62.2 (.055)	78.2 (.020)
184	rs2059741	2	218719965	26.2 (.067)	11.9 (.053)
185	rs7610580	3	179446096	59.9 (.017)	50.9 (.045)
186	rs4705890	5	130882899	28.3 (.071)	14.4 (.050)
187	rs6949651	7	68983791	82.2 (.045)	72.1 (.070)
188	rs10944721	6	94937693	91.5 (.051)	80.5 (.062)
189	rs4865206	4	53047922	13.1 (.073)	26.6 (.026)
190	rs2532292	17	41592845	93.2 (.029)	81.3 (.078)
191	rs807339	14	98483425	21.4 (.057)	5.0 (.051)
192	rs2830191	21	26664758	1.8 (.049)	12.6 (.044)
193	rs980214	6	116996269	57.8 (.073)	77.1 (.057)
194	rs1868629	14	80117727	37.5 (.043)	16.1 (.045)
195	rs2589559	10	9101376	94.9 (.084)	76.3 (.081)
196	rs402642	1	18332121	56.8 (.038)	70.1 (.021)
197	rs10823706	10	72678863	40.6 (.028)	54.3 (.032)
198	rs2227072	22	33662312	47.3 (.054)	33.1 (.030)
199	rs1460167	8	80402202	33.9 (.054)	24.7 (.026)
200	rs6470355	8	126529717	74.1 (.032)	89.1 (.034)
201	rs4877253	9	83194004	58.2 (.050)	73.5 (.049)
202	rs17641413	5	177706306	65.7 (.025)	52.6 (.048)
203	rs11869264	17	28135096	45.7 (.035)	63.8 (.051)
204	rs17617724	8	40283622	74.0 (.029)	89.7 (.057)
205	rs4795653	17	27163735	6.8 (.043)	18.0 (.050)
206	rs2053844	4	64740967	61.3 (.056)	76.3 (.050)
207	rs7649638	3	61936012	40.5 (.094)	66.5 (.104)
208	rs2916755	8	6356758	80.3 (.069)	61.6 (.066)
209	rs1257669	14	98561945	52.6 (.026)	42.8 (.027)
210	rs1635217	23	3214104	32.7 (.077)	16.5 (.077)
211	rs11241644	5	121831417	73.1 (.034)	80.3 (.009)
212	rs594731	1	178226185	21.3 (.048)	13.5 (.028)
213	rs7750190	6	67325355	45.5 (.058)	33.6 (.028)
214	rs10826304	10	60940671	43.3 (.035)	55.1 (.038)
215	rs13419861	2	139837545	23.0 (.031)	14.0 (.018)
216	rs12936006	17	2628917	71.8 (.026)	61.9 (.035)
217	rs12434898	14	100831794	15.1 (.018)	22.0 (.031)
218	rs17100010	14	62022876	18.6 (.068)	37.0 (.031)
219	rs307022	4	124375261	38.0 (.105)	15.6 (.080)
220	rs4945261	11	77667908	21.9 (.042)	8.0 (.042)
221	rs11609955	12	641938	73.5 (.024)	79.4 (.047)
222	rs7270791	20	42558543	86.3 (.028)	94.3 (.025)
223	rs228832	20	49493555	69.5 (.047)	78.2 (.044)
224	rs5770111	22	47957002	74.2 (.036)	84.2 (.030)
225	rs11596456	10	120562236	20.4 (.041)	5.1 (.040)
226	rs796459	3	119980825	42.9 (.073)	28.7 (.036)
227	rs4537652	1	213626581	37.4 (.047)	46.2 (.055)
228	rs5755439	22	33662286	51.1 (.031)	38.7 (.029)
229	rs741245	12	4097509	44.2 (.082)	28.3 (.028)
230	rs2128404	3	65075198	65.9 (.058)	48.0 (.042)
231	rs4276705	8	131631298	6.7 (.030)	19.9 (.048)
232	rs2532276	17	41602401	4.9 (.059)	19.9 (.029)
233	rs17098942	1	76590177	24.5 (.034)	16.6 (.048)
234	rs9320784	6	121334748	95.9 (.021)	89.2 (.028)
235	rs17650063	17	41358383	95.8 (.032)	82.3 (.051)
236	rs17659881	17	41513416	89.8 (.038)	77.4 (.035)
237	rs9296268	6	39007463	76.1 (.029)	64.8 (.025)
238	rs12708283	9	107956429	35.2 (.057)	20.8 (.054)
239	rs9372465	6	116968576	56.5 (.034)	69.4 (.036)
240	rs11043827	12	18109374	87.7 (.103)	68.4 (.072)
241	rs1760931	14	20017108	71.5 (.046)	54.8 (.068)
242	rs2037276	15	60349273	70.2 (.047)	80.5 (.033)
243	rs1178355	7	17978051	67.7 (.055)	82.2 (.044)
244	rs10892044	11	116272109	15.6 (.069)	5.5 (.031)
245	rs1356266	12	37689848	56.0 (.051)	40.0 (.040)
246	rs4358170	2	42027555	62.3 (.061)	77.4 (.060)
247	rs241212	1	4541639	39.2 (.053)	26.7 (.026)
248	rs1902408	10	33913367	20.5 (.059)	8.1 (.047)
249	rs17040424	3	14882981	16.7 (.046)	3.3 (.055)
250	rs7491764	13	113618608	49.0 (.041)	38.0 (.034)
251	rs7849137	9	18132898	36.9 (.126)	9.2 (.067)
252	rs5934262	23	15451678	50.1 (.037)	36.3 (.064)
253	rs11650055	17	11643618	45.2 (.055)	56.9 (.023)
254	rs13414618	2	31488285	23.4 (.052)	41.7 (.028)
255	rs9825224	3	181158256	78.8 (.039)	69.6 (.045)
256	rs9861677	3	29472993	45.5 (.051)	57.5 (.031)
257	rs6058847	20	30787796	17.9 (.039)	28.4 (.037)
258	rs386871	4	127938037	5.4 (.033)	15.0 (.033)
259	rs11835989	12	90827221	40.2 (.049)	27.5 (.037)
260	rs3865177	16	81127053	52.7 (.064)	69.4 (.046)
261	rs11598814	10	120562175	71.0 (.089)	93.6 (.068)
262	rs6746542	2	141692156	34.5 (.085)	18.6 (.042)
263	rs3924849	18	5422330	18.3 (.043)	31.5 (.057)
264	rs2501856	1	209245380	49.2 (.053)	57.1 (.022)
265	rs7748820	6	112048849	61.3 (.025)	66.3 (.020)
266	rs1347638	15	32729249	50.7 (.058)	63.2 (.053)
267	rs6548038	2	30949136	59.5 (.036)	71.8 (.037)
268	rs5993875	22	18289880	54.6 (.046)	41.8 (.056)
269	rs2483535	10	116303825	27.3 (.025)	18.7 (.033)
270	rs2292006	3	172341108	68.8 (.062)	81.5 (.039)
271	rs2696425	17	41022689	10.5 (.054)	22.6 (.027)
272	rs10242225	7	67089936	38.0 (.081)	14.8 (.061)
273	rs11895224	2	226748363	70.9 (.027)	81.0 (.026)
274	rs11080702	18	13933768	91.2 (.045)	78.4 (.106)
275	rs258619	5	75429046	72.0 (.050)	84.0 (.040)
276	rs721010	6	16680699	46.4 (.044)	60.8 (.065)
277	rs2321743	3	158491298	61.8 (.054)	46.5 (.053)
278	rs1458246	4	69998842	0.6 (.037)	11.8 (.037)
279	rs9929519	16	77365884	45.0 (.041)	28.6 (.074)
280	rs968027	17	41137033	96.1 (.025)	85.3 (.034)
281	rs4732082	7	134175660	58.5 (.063)	43.2 (.040)
282	rs12454115	18	55731532	69.2 (.025)	57.3 (.055)
283	rs475444	7	54325257	31.6 (.045)	17.0 (.048)
284	rs17330110	2	36021585	24.1 (.047)	16.5 (.031)
285	rs11761356	7	21016758	39.3 (.036)	23.8 (.046)
286	rs2241392	19	6636983	28.8 (.025)	41.7 (.046)
287	rs10175397	2	154779198	74.9 (.050)	85.6 (.051)
288	rs3777994	6	116846716	63.3 (.059)	80.4 (.034)
289	rs1229718	5	136771691	37.7 (.049)	23.1 (.028)
290	rs7690944	4	44765392	84.4 (.043)	99.1 (.032)
291	rs2765315	13	100470046	82.0 (.035)	89.0 (.021)
292	rs2511775	11	130709025	47.7 (.124)	70.4 (.059)
293	rs11846959	14	93916069	64.2 (.038)	77.1 (.046)
294	rs7116710	11	15218897	44.6 (.038)	36.8 (.039)
295	rs6468953	8	88748007	24.5 (.115)	41.2 (.049)
296	rs1558226	17	9747805	61.9 (.022)	55.1 (.026)
297	rs1965805	8	73818016	89.8 (.024)	74.9 (.036)
298	rs9836282	3	168225293	37.7 (.037)	52.8 (.056)
299	rs4965458	15	96496047	76.3 (.039)	82.4 (.026)
300	rs6740906	2	213658228	76.4 (.031)	67.7 (.062)
301	rs206942	6	34363454	12.6 (.045)	23.5 (.063)
302	rs166812	3	194908758	65.3 (.070)	43.5 (.089)
303	rs199436	17	42144468	9.8 (.052)	23.5 (.046)
304	rs6078524	20	12268155	4.0 (.067)	26.1 (.071)
305	rs12620374	2	162024500	63.4 (.065)	76.3 (.049)
306	rs6918297	6	19507476	30.3 (.053)	48.1 (.067)
307	rs1232487	20	11827248	66.4 (.058)	52.9 (.052)
308	rs1583758	2	209886318	21.7 (.052)	38.7 (.053)
309	rs282802	15	77859875	63.7 (.055)	78.2 (.015)
310	rs241301	1	225269162	26.4 (.040)	45.4 (.048)
311	rs892535	13	104007916	62.8 (.044)	73.8 (.038)
312	rs10817882	9	116225295	71.2 (.040)	81.7 (.034)
313	rs2766542	6	35815668	58.6 (.049)	42.4 (.035)
314	rs10038760	5	134924732	18.5 (.060)	10.2 (.025)
315	rs10043237	5	24890906	81.7 (.018)	87.3 (.021)
316	rs223185	1	18330326	51.3 (.095)	67.6 (.034)
317	rs11863694	16	12561363	38.0 (.161)	13.5 (.034)
318	rs305039	15	67873370	69.5 (.076)	87.6 (.041)
319	rs9525291	13	113962630	83.6 (.064)	93.8 (.027)
320	No rs numberd	17	41472085	9.2 (.076)	25.5 (.029)
321	rs241031	17	41090087	4.1 (.033)	14.9 (.040)
322	rs3127572	6	160652629	14.6 (.067)	4.1 (.016)
323	rs10420904	19	34394929	30.7 (.050)	42.1 (.041)
324	rs10777224	12	89010777	89.4 (.030)	75.1 (.061)
325	rs6418604	23	28557998	49.4 (.045)	60.7 (.032)
326	rs4245562	7	54178194	65.2 (.035)	76.4 (.053)
327	rs6670619	1	204831917	57.9 (.067)	78.8 (.080)
328	rs9806222	15	66671258	53.6 (.027)	47.0 (.024)
329	rs6797081	3	24973727	50.9 (.064)	38.0 (.043)
330	rs7181055	15	97852959	21.7 (.041)	9.0 (.033)
331	rs12485961	3	163179791	30.4 (.032)	22.6 (.024)
332	rs237744	20	47336183	36.7 (.036)	27.2 (.035)
333	rs10956287	8	127256564	34.4 (.066)	23.3 (.049)
334	rs1635135	12	111917616	74.8 (.023)	81.7 (.028)
335	rs13313479	15	55959003	58.7 (.086)	30.8 (.077)
336	rs6803992	3	10597941	64.8 (.067)	52.8 (.051)
337	rs1289745	3	109408948	22.2 (.042)	11.5 (.019)
338	rs1343657	6	127305227	69.3 (.062)	52.8 (.067)
339	rs7136648	12	48911089	60.5 (.058)	48.7 (.033)
340	rs4426313	15	77590382	37.7 (.057)	53.1 (.053)
341	rs2013867	11	47216848	74.1 (.066)	96.6 (.053)
342	rs1158811	6	69090289	67.2 (.032)	75.3 (.032)
343	rs10853854	19	57923940	17.1 (.079)	33.0 (.034)
344	rs12273933	11	78628220	53.8 (.067)	68.8 (.031)
345	rs5920468	23	144018371	47.9 (.061)	61.0 (.023)
346	rs1247487	10	77676143	49.8 (.045)	63.6 (.047)
347	rs9831276	3	142995721	82.1 (.051)	70.5 (.026)
348	rs10932486	2	214210418	69.1 (.037)	53.2 (.076)
349	rs10203659	2	152777095	91.1 (.029)	80.0 (.044)
350	rs1482108	4	52968985	17.0 (.037)	30.5 (.031)
351	rs6998348	8	122706022	33.9 (.046)	22.2 (.055)
352	rs12612116	2	227618234	37.1 (.063)	47.7 (.036)
353	rs10507428	13	35274755	96.5 (.108)	65.0 (.111)
354	rs2248161	10	13056534	51.7 (.043)	62.2 (.054)
355	rs12607476	18	26841275	73.5 (.040)	87.6 (.025)
356	rs10922273	1	194457030	88.3 (.055)	77.8 (.045)
357	rs2024266	7	150825612	55.1 (.053)	40.9 (.064)
358	rs10276128	7	8632452	53.9 (.051)	66.0 (.064)
359	rs6000790	22	20740851	33.9 (.062)	21.7 (.016)
360	rs4701563	5	22072008	15.2 (.028)	28.1 (.021)
361	rs11695415	2	217963990	75.0 (.053)	87.5 (.030)
362	rs3743761	16	75785385	69.3 (.062)	58.6 (.033)
363	rs12546080	8	137129495	60.6 (.054)	48.6 (.045)
364	rs7776346	6	111968058	71.9 (.038)	83.6 (.049)
365	rs11005115	10	57357276	42.5 (.054)	30.1 (.033)
366	rs6560011	9	87486191	68.5 (.035)	58.2 (.055)
367	rs9859834	3	143589049	57.4 (.037)	74.4 (.041)
368	rs1564117	8	107688729	99.5 (.035)	87.7 (.047)
369	rs9398069	6	106707858	69.5 (.052)	50.7 (.078)
370	rs10461198	4	116786149	71.6 (.066)	55.3 (.059)
371	rs9309981	3	85588634	88.5 (.049)	75.7 (.076)
372	rs1656400	2	233253288	27.1 (.040)	7.5 (.066)
373	rs16845213	2	141641328	29.4 (.054)	15.1 (.053)
374	rs3946526	17	40897439	86.3 (.075)	76.5 (.082)
375	rs11799420	1	168384635	23.4 (.039)	15.5 (.030)
376	rs12570751	10	5480932	26.0 (.058)	10.1 (.053)
377	rs660465	10	78855117	64.8 (.060)	52.5 (.074)
378	rs659670	18	30903493	12.9 (.031)	19.0 (.025)
379	rs318931	10	131967734	61.2 (.031)	48.7 (.042)
380	rs6134031	20	10700610	15.9 (.044)	29.4 (.035)
381	No rs numberd	2	36099185	83.0 (.024)	91.4 (.023)
382	rs1506929	12	59784657	74.9 (.046)	64.1 (.036)
383	rs9803850	1	85782465	70.6 (.041)	79.3 (.047)
384	rs12730116	1	117845272	20.8 (.100)	12.4 (.022)
385	rs11078927	17	35317931	48.4 (.030)	58.0 (.039)
386	rs11199686	10	122728541	52.2 (.042)	43.3 (.060)
387	rs5958390	23	122976032	60.4 (.081)	77.0 (.046)
388	rs10215677	7	140538698	87.7 (.056)	72.1 (.063)
389	rs17135662	7	100838409	74.1 (.072)	85.6 (.033)
390	rs7037570	9	132325895	29.1 (.035)	19.7 (.024)
391	rs10815701	9	7861163	33.8 (.044)	18.3 (.029)
392	rs4796017	17	23099118	33.2 (.038)	46.8 (.069)
393	rs601962	8	29306465	66.1 (.059)	79.1 (.038)
394	rs2069278	1	66347392	65.3 (.045)	74.4 (.028)
395	rs2566970	3	114944813	36.8 (.028)	24.7 (.054)
396	rs840600	2	187985256	75.1 (.040)	62.9 (.053)
397	rs8034444	15	56323687	46.7 (.047)	29.0 (.063)
398	rs17167930	7	13961171	93.7 (.028)	87.5 (.039)
399	rs9564057	13	62927711	19.7 (.034)	31.3 (.049)
400	rs6895344	5	55607343	73.7 (.060)	56.7 (.085)
401	rs7219245	17	60547161	7.5 (.074)	24.0 (.753)
402	rs17379636	4	154764283	67.1 (.040)	56.8 (.039)
403	rs4931243	12	30072654	61.1 (.057)	48.5 (.030)
404	rs2018971	17	26896751	55.6 (.044)	67.8 (.036)
405	rs1002007	15	69369104	67.7 (.082)	85.2 (.076)
406	rs2673559	8	133548347	48.2 (.152)	15.7 (.055)
407	rs12230555	12	4289045	46.7 (.050)	34.4 (.058)
408	rs2878802	7	158027122	15.9 (.056)	5.8 (.025)
409	rs11639949	16	12561909	69.6 (.093)	85.2 (.032)
410	rs2075425	1	210514249	32.0 (.042)	43.2 (.046)
411	rs2469564	15	74277010	86.4 (.060)	98.3 (.044)
412	rs6999868	8	5502341	18.9 (.057)	12.1 (.018)
413	rs9388860	6	131215145	71.8 (.124)	83.3 (.025)
414	rs2977070	8	75275324	35.4 (.118)	24.5 (.027)
415	No rs numberd	7	90549644	79.5 (.120)	96.3 (.045)
416	rs12711664	2	124517464	59.7 (.034)	70.0 (.025)
417	rs1331574	6	115747405	47.4 (.039)	34.5 (.032)
418	rs2838571	21	44722797	43.2 (.069)	57.9 (.034)
419	rs4382714	1	234742585	48.8 (.058)	34.6 (.038)
420	No rs numberd	4	4652651	73.3 (.060)	83.7 (.042)
421	rs1886543	13	51599783	37.2 (.044)	19.1 (.056)
422	rs879278	10	72671959	57.4 (.039)	51.9 (.027)
423	rs1038990	2	238329392	39.6 (.068)	30.0 (.055)
424	rs1496483	18	24511520	32.3 (.048)	20.8 (.041)
425	rs696851	3	155586013	83.0 (.028)	92.9 (.012)
426	rs17053864	9	88033026	88.2 (.075)	99.0 (.026)
427	rs4585704	8	27766421	38.2 (.054)	48.8 (.052)
428	rs17306695	10	87333513	13.2 (.037)	20.1 (.022)
429	rs884329	4	106281075	29.4 (.079)	49.4 (.047)
430	rs2071967	1	4606465	8.1 (.052)	22.8 (.118)
431	rs13423714	2	227722157	35.4 (.045)	48.4 (.016)
432	rs10977527	9	9134115	65.1 (.029)	80.6 (.088)
433	rs10875641	5	148273115	30.6 (.062)	42.4 (.054)
434	rs285753	15	91019081	26.6 (.022)	16.7 (.026)
435	rs190034	5	95043287	51.2 (.040)	36.6 (.039)
436	rs17085569	6	155030335	12.1 (.110)	34.9 (.056)
437	rs2676419	8	33475428	14.2 (.098)	45.0 (.092)
438	no rs#	17	41492888	91.2 (.061)	82.3 (.063)
439	rs6659522	1	204587495	56.7 (.033)	66.4 (.014)
440	rs17192114	12	88673906	86.3 (.042)	74.1 (.035)
441	rs7442929	5	24262649	27.6 (.047)	17.0 (.041)
442	rs10769846	11	7860814	91.9 (.054)	75.8 (.050)
443	rs780331	8	127129712	75.5 (.042)	63.7 (.055)
444	rs872411	5	116089281	57.1 (.027)	63.8 (.036)
445	rs5909876	23	120947783	59.4 (.074)	77.4 (.041)
446	rs11764997	7	115242171	37.2 (.022)	51.1 (.034)
447	rs2191057	17	29915167	26.9 (.063)	13.5 (.042)
448	rs6050164	20	24863295	26.7 (.109)	6.4 (.050)
449	rs12265750	10	130742160	42.1 (.094)	27.5 (.058)
450	rs10950297	7	71018779	73.2 (.023)	82.0 (.034)
451	rs205737	7	130118083	53.2 (.085)	65.4 (.064)
452	rs10501321	11	47251202	60.7 (.041)	71.7 (.045)
453	rs16910869	8	140616426	53.0 (.055)	36.0 (.036)
454	No rs numberd	7	19368364	55.5 (.061)	71.6 (.047)
455	rs2426936	20	58909276	36.1 (.027)	22.7 (.062)
456	rs9261489	6	30217461	73.0 (.056)	85.5 (.047)
457	rs17784515	11	44831086	62.6 (.063)	71.1 (.027)
458	rs4943770	13	39808388	39.9 (.034)	50.3 (.024)
459	rs17637161	8	138940595	26.6 (.049)	16.1 (.056)
460	rs11170782	12	37796650	10.5 (.043)	29.2 (.046)
461	rs11006702	10	19066613	83.7 (.043)	73.2 (.064)
462	rs419097	9	111791298	71.6 (.095)	45.7 (.044)
463	rs4880568	10	303504	29.4 (.041)	41.5 (.060)
464	rs10894157	11	99289243	80.1 (.042)	69.8 (.056)
465	rs6495126	15	72962079	92.3 (.107)	73.0 (.075)
466	rs2495408	1	184528663	61.0 (.084)	43.1 (.066)
467	rs2402057	7	115491047	28.2 (.019)	12.5 (.049)
468	rs17649553	17	41350476	87.8 (.074)	75.7 (.091)
469	rs9403813	6	147112198	72.6 (.071)	89.0 (.034)
470	rs2244284	20	24696432	66.0 (.053)	47.9 (.030)
471	rs477233	23	23464832	49.8 (.029)	60.0 (.056)
472	rs11695811	2	234997133	46.7 (.028)	59.9 (.037)
473	rs1266734	23	107257424	25.7 (.042)	11.4 (.054)
474	rs6450023	5	68561819	74.3 (.027)	84.4 (.030)
475	rs10492331	12	113026864	81.9 (.062)	89.9 (.024)
476	rs12487	15	72923747	33.5 (.031)	43.9 (.066)
477	rs41295	7	28439876	65.2 (.044)	53.4 (.026)
478	rs234440	14	96892646	30.4 (.062)	12.4 (.036)
479	rs5916245	23	5521272	81.2 (.056)	67.2 (.050)
480	rs743444	21	38978129	37.8 (.078)	24.6 (.051)
481	rs2040920	7	147228429	29.4 (.045)	21.8 (.021)
482	rs1862175	5	121560760	69.8 (.026)	63.2 (.022)
483	rs7701573	5	59053652	52.2 (.049)	39.0 (.042)
484	rs2986425	11	34872332	75.4 (.068)	61.1 (.080)
485	rs4264335	15	59000266	55.1 (.043)	67.3 (.031)
486	rs1911573	3	102336872	59.5 (.022)	70.8 (.053)
487	rs273981	7	137076530	59.5 (.061)	44.8 (.057)
488	rs2240737	17	9731884	19.4 (.062)	10.4 (.039)
489	rs492125	11	125949932	51.0 (.044)	59.9 (.059)
490	rs4420962	4	120378074	73.4 (.048)	61.1 (.071)
491	rs12605509	18	52998303	36.9 (.039)	26.6 (.031)
492	rs764180	1	168531993	59.9 (.098)	43.4 (.087)
493	rs11640077	16	19432372	34.6 (.043)	21.4 (.046)
494	rs1152472	14	55840960	48.2 (.031)	34.6 (.063)
495	No rs numberd	2	203333169	73.9 (.081)	53.3 (.133)
496	rs1975634	16	54756806	63.5 (.082)	45.9 (.085)
497	rs6817763	4	139567306	35.6 (.119)	66.3 (.072)
498	rs10893347	11	124568317	61.6 (.086)	86.4 (.112)
499	rs4973285	2	230871448	79.6 (.033)	69.0 (.033)
500	rs5971587	23	31450636	24.9 (.047)	39.0 (.074)
501	rs9484261	6	139686988	78.3 (.048)	65.4 (.039)
502	rs1934534	6	150125146	71.4 (.041)	58.6 (.070)
503	rs9504093	6	4371770	43.6 (.024)	31.2 (.047)
504	rs2394807	10	72971347	50.6 (.065)	32.6 (.037)
505	rs4122017	6	148347645	62.1 (.054)	47.8 (.035)
506	rs11587621	1	208056795	11.6 (.035)	36.0 (.116)
507	rs17363368	1	160090491	9.0 (.064)	0.7 (.023)
508	rs4119152	2	18599315	83.7 (.078)	63.4 (.039)
509	rs6907995	6	127304781	41.5 (.047)	52.1 (.042)
510	rs1448871	2	6893288	68.6 (.058)	53.1 (.048)
511	rs1356951	12	117486021	52.9 (.056)	61.8 (.021)
512	rs1049296	3	134977052	73.4 (.217)	83.7 (.117)
513	rs2405783	1	221333402	53.3 (.032)	61.5 (.035)
514	rs10917825	1	160431297	50.2 (.057)	37.7 (.022)
515	rs1884014	14	53934713	27.0 (.041)	12.5 (.051)
516	rs4685846	3	538399	69.5 (.091)	43.1 (.044)
517	rs7141809	14	49630695	72.8 (.034)	58.5 (.057)
518	rs12925573	16	76662867	56.4 (.086)	73.3 (.070)
519	rs2836531	21	38870860	57.1 (.038)	64.9 (.050)
520	rs7763880	6	152894411	47.8 (.074)	65.5 (.049)
521	rs1414491	10	43632364	79.9 (.030)	90.7 (.062)
522	rs4675490	2	205768066	56.8 (.045)	70.6 (.025)
523	rs1437933	2	211862181	29.9 (.046)	43.7 (.075)
524	rs1699001	6	38714589	30.6 (.038)	37.2 (.077)
525	rs12432184	14	55753214	37.8 (.060)	49.3 (.057)
526	rs4740904	9	7672860	44.7 (.054)	29.5 (.052)
527	rs469326	5	102192017	41.9 (.068)	28.1 (.043)
528	rs17783630	14	92025138	53.8 (.049)	43.5 (.044)
529	rs6463270	7	45040529	24.1 (.046)	10.3 (.046)
530	rs4759061	12	52024481	66.6 (.055)	77.5 (.053)
531	rs5017082	12	37600831	49.2 (.058)	40.2 (.035)
532	rs2694874	12	124527344	67.1 (.033)	73.8 (.048)
533	rs17684894	8	138604979	78.5 (.083)	90.7 (.038)
534	rs1588706	4	69795828	3.3 (.057)	19.0 (.033)
535	rs7706831	5	116087496	60.8 (.078)	75.1 (.050)
536	rs379643	14	87719507	69.3 (.020)	59.7 (.029)
537	rs17005517	1	215992848	26.2 (.040)	16.7 (.048)
538	rs17040460	3	14889969	71.0 (.103)	86.0 (.043)
539	rs2504458	1	107939403	54.8 (.042)	70.4 (.055)
540	rs10503818	8	27731666	48.0 (.100)	31.0 (.087)
541	rs2016459	8	82067869	76.3 (.050)	59.4 (.064)
542	rs7068699	10	129132012	49.5 (.044)	58.0 (.046)
543	rs8019096	14	47033221	5.1 (.065)	26.5 (.056)
544	rs12865636	13	109097925	8.8 (.070)	27.3 (.116)
545	rs13022222	2	226573182	18.7 (.035)	12.8 (.028)
546	rs6035539	20	19987506	63.9 (.060)	80.1 (.061)
547	rs2878722	18	38437616	78.9 (.020)	86.6 (.028)
548	rs12701769	7	39626870	9.9 (.054)	21.3 (.059)
549	rs6701341	1	150787694	56.4 (.037)	68.8 (.043)
550	rs6462825	7	38067354	26.3 (.045)	36.9 (.095)
551	rs2280884	8	27670057	50.1 (.033)	59.6 (.028)
552	rs7357405	8	79183255	49.8 (.065)	30.0 (.093)
553	rs9826951	3	132921144	82.5 (.057)	94.2 (.024)
554	rs1408575	6	147264593	75.0 (.055)	62.5 (.051)
555	rs2283792	22	20455679	57.8 (.082)	44.6 (.061)
556	rs2316640	13	54542925	84.8 (.043)	71.0 (.062)
557	rs16858997	1	229811908	54.6 (.073)	69.4 (.040)
558	rs8070993	17	39109982	49.5 (.031)	34.9 (.013)
559	rs7836489	8	21460484	42.0 (.043)	51.3 (.040)
560	rs9381307	6	44361369	27.8 (.048)	17.9 (.028)
561	rs12942155	17	46608140	41.2 (.049)	25.2 (.042)
562	rs588933	9	2527815	82.3 (.029)	73.0 (.028)
563	rs10785334	12	40906644	38.3 (.045)	27.0 (.043)
564	rs7084059	10	93828325	42.3 (.022)	32.8 (.044)
565	rs6473008	8	78185065	39.3 (.047)	57.6 (.057)
566	rs7424879	2	181884034	55.7 (.058)	43.3 (.058)
567	rs459162	6	1161376	41.2 (.045)	26.0 (.046)
568	rs4629541	4	142381927	70.2 (.061)	80.7 (.031)
569	rs2056411	4	83859712	58.8 (.046)	72.7 (.056)
570	rs13427835	2	23142654	21.8 (.089)	12.1 (.019)
571	No rs numberd	4	25764488	39.2 (.048)	54.5 (.051)
572	rs503897	9	37372099	59.9 (.049)	74.5 (.037)
573	rs7795573	7	12693015	33.1 (.112)	4.7 (.122)
574	rs1564274	1	34351855	71.3 (.065)	81.1 (.043)
575	rs10822753	10	67648865	33.3 (.036)	48.2 (.055)
576	rs2254535	10	72207879	88.7 (.035)	96.8 (.016)
577	rs7926553	11	76470079	47.6 (.040)	33.6 (.022)
578	rs17805522	20	59174920	29.5 (.088)	17.3 (.016)
579	rs17361077	7	75083414	64.5 (.045)	73.7 (.064)
580	rs308901	2	86758147	62.8 (.037)	70.1 (.030)
581	rs260454	19	63458980	49.4 (.058)	66.7 (.054)
582	rs13184396	5	149669366	63.3 (.037)	77.5 (.022)
583	rs11558511	1	164745508	79.4 (.026)	74.2 (.037)
584	rs6563655	13	38433775	74.8 (.031)	93.0 (.060)
585	rs2179593	20	42093700	64.6 (.086)	81.6 (.067)
586	rs9385717	6	135500116	75.2 (.033)	79.0 (.035)
587	rs10000203	4	78633738	80.2 (.086)	93.1 (.024)
588	rs11034770	11	38459187	48.9 (.063)	78.9 (.111)
589	rs265619	12	128636559	61.0 (.030)	69.5 (.030)
590	rs6470418	8	127311456	70.5 (.065)	82.9 (.048)
591	rs7327426	13	60510741	63.3 (.040)	73.1 (.035)
592	rs10800485	1	166578804	59.8 (.064)	74.6 (.058)
593	rs10167944	2	115857630	15.0 (.081)	28.7 (.077)
594	rs11685401	2	100435203	42.4 (.046)	52.7 (.048)
595	rs1389709	3	86572955	23.6 (.038)	39.8 (.069)
596	rs4730470	7	110202088	59.5 (.064)	74.6 (.055)
597	rs1899384	18	49357887	91.5 (.040)	80.3 (.046)
598	rs10467913	15	45505944	25.5 (.037)	8.6 (.057)
599	rs1703975	8	8614749	86.7 (.036)	96.4 (.024)
600	rs9378540	6	8280374	14.3 (.045)	30.2 (.067)
601	No rs numberd	1	176703994	86.8 (.047)	79.5 (.050)
602	rs11803410	1	107853520	33.6 (.063)	46.4 (.033)
603	rs10149991	14	46638818	51.6 (.036)	63.3 (.046)
604	rs981579	4	28221496	79.4 (.056)	67.6 (.040)
605	rs573301	6	24030685	40.7 (.045)	56.5 (.055)
606	rs1918788	17	41623394	6.4 (.023)	16.0 (.027)
607	rs2081748	12	113780260	99.7% (1.982)	89.4 (.066)
608	rs16978462	18	41551134	26.0 (.058)	9.6 (.044)
609	rs10518973	15	56438872	72.7 (.079)	80.5 (.035)
610	rs12288391	11	124629292	32.1 (.064)	21.9 (.040)
611	rs7774349	6	137517551	58.1 (.058)	49.0 (.043)
612	rs2972284	16	5008153	60.8 (.110)	79.6 (.032)
613	rs10885211	10	113314292	58.4 (.031)	50.4 (.028)
614	rs11124178	2	239700789	35.9 (.070)	26.6 (.029)
615	rs10491524	9	119336808	65.3 (.156)	87.2 (.050)
616	rs890067	2	60089993	47.6 (.050)	37.0 (.058)
617	rs12980971	19	56872738	51.6 (.072)	63.2 (.071)
618	rs17283761	3	152070880	36.7 (.047)	45.4 (.054)
619	rs1220620	5	72813638	33.1 (.036)	22.8 (.058)
620	rs1944761	9	18178242	70.9 (.049)	85.7 (.039)
621	rs1397148	16	54655880	46.3 (.043)	60.2 (.053)
622	rs5958281	23	122515806	44.3 (.099)	25.3 (.033)
623	rs17363814	19	4795633	35.3 (.072)	29.2 (.024)
624	rs9372118	6	106708048	65.8 (.058)	49.1 (.063)
625	rs10935960	3	155136125	78.8 (.050)	71.2 (.050)
626	rs13120622	4	139911721	44.0 (.052)	31.1 (.063)
627	rs7769478	6	103393153	73.2 (.097)	49.6 (.054)
628	rs600702	11	124569824	14.2 (.056)	29.3 (.064)
629	rs2136531	11	108406015	83.2 (.069)	97.1 (.036)
630	rs11832772	12	41145855	60.0 (.046)	50.3 (.038)
631	rs16990692	4	34868232	79.2 (.032)	69.4 (.042)
632	rs2434245	5	175139805	24.2 (.066)	9.1 (.056)
633	rs8007728	14	81242457	15.7 (.042)	31.4 (.059)
634	rs404801	3	83534051	62.6 (.063)	50.4 (.032)
635	rs2350811	6	115984204	88.5 (.044)	71.9 (.063)
636	rs7655209	4	158408990	91.2 (.036)	78.1 (.054)
637	rs9852802	3	8116722	46.3 (.033)	31.7 (.029)
638	rs3784678	15	34733595	47.0 (.060)	60.7 (.086)
639	rs1711004	3	189348121	53.0 (.034)	37.3 (.043)
640	rs1363530	5	147324564	15.4 (.047)	29.4 (.059)
641	rs7799704	7	92874191	38.3 (.065)	52.3 (.047)
642	rs1922185	2	52353433	38.9 (.057)	23.3 (.074)
643	rs6473164	8	80567257	58.2 (.040)	41.1 (.032)
644	rs734489	15	55435304	71.9 (.040)	57.0 (.040)
645	rs2607924	12	570936	71.1 (.043)	81.9 (.058)
646	rs925111	15	78872538	21.8 (.028)	34.5 (.018)
647	rs1483198	1	4627764	29.2 (.070)	11.8 (.060)
648	rs13424077	2	35455013	76.4 (.056)	68.9 (.033)
649	rs6069892	20	54820158	53.3 (.038)	43.3 (.060)
650	rs10992674	9	93042669	59.1 (.047)	72.4 (.058)
651	rs1790318	11	70777862	36.1 (.032)	48.4 (.041)
652	rs4316515	11	68065416	31.9 (.070)	17.8 (.038)
653	rs4747385	10	7096022	53.3 (.038)	65.1 (.073)
654	rs207078	6	66826775	39.1 (.056)	52.3 (.042)
655	rs7221595	17	3954343	26.1 (.042)	14.4 (.045)
656	rs7241635	18	31568422	69.1 (.071)	54.6 (.042)
657	rs917500	17	29884677	69.3 (.035)	77.5 (.035)
658	rs2274201	14	30716992	53.7 (.055)	71.5 (.044)
659	rs10113968	9	2445202	51.2 (.059)	39.4 (.038)
660	rs4714890	6	46003658	58.7 (.059)	73.7 (.035)
661	rs6469756	8	119625611	26.7 (.050)	18.6 (.053)
662	rs10979211	9	107950576	59.8 (.036)	75.7 (.052)
663	rs12716267	5	170356139	60.1 (.069)	69.6 (.034)
664	rs3913972	6	87217610	50.3 (.057)	40.1 (.025)
665	rs252811	5	106764256	78.7 (.156)	95.0 (.088)
666	rs11136949	8	5792133	44.1 (.043)	56.3 (.034)
667	rs9380791	6	38938388	51.1 (.052)	28.9 (.036)
668	rs6486303	11	16593899	31.8 (.097)	13.0 (.051)
669	rs11103117	9	135753858	16.3 (.089)	32.4 (.098)
670	rs4706205	6	85241292	47.0 (.030)	56.8 (.036)
671	rs7048135	9	1776681	78.3 (.064)	97.4 (.049)
672	rs12551465	9	4565673	65.5 (.023)	55.3 (.023)
673	rs3910449	16	5750350	28.4 (.037)	41.7 (.067)
674	rs433395	7	23175195	55.0 (.054)	65.4 (.049)
675	rs4446347	4	62889346	53.2 (.060)	42.1 (.057)
676	rs4641528	12	70673609	44.9 (.077)	56.5 (.034)
677	rs17651822	3	28695130	20.5 (.035)	11.2 (.017)
678	rs4939008	11	55446947	43.8 (.056)	34.1 (.021)
679	rs3741755	12	68358746	30.1 (.098)	43.6 (.060)
680	rs169173	21	30926217	62.3 (.036)	69.4 (.016)
681	rs1893854	11	105574558	91.7 (.059)	80.4 (.040)
682	rs1996537	11	36707703	8.4 (.135)	3.6 (.042)
683	rs1159929	5	77804576	84.0 (.051)	75.5 (.035)
684	rs2256143	4	166903785	72.8 (.067)	56.8 (.042)
685	rs1550099	2	233253652	70.5 (.045)	87.0 (.029)
686	rs1454535	2	221055427	50.6 (.020)	41.9 (.041)
687	rs17753780	7	4275526	62.7 (.034)	73.7 (.052)
688	rs697550	5	14125453	7.9 (.070)	21.0 (.047)
689	rs3777995	6	116846696	61.9 (.065)	78.4 (.042)
690	rs11613448	12	37811416	48.7 (.048)	33.2 (.060)
691	rs3737880	1	199778332	81.6 (.054)	91.4 (.033)
692	rs11787001	8	25654515	67.2 (.024)	76.4 (.035)
693	rs7656178	4	173829976	33.0 (.108)	21.2 (.067)
694	rs9990848	4	32885412	8.9 (.045)	17.9 (.029)
695	rs685478	11	112182092	49.1 (.060)	32.9 (.031)
696	rs7213273	17	40511440	59.2 (.067)	71.9 (.030)
697	rs201480	7	101341010	56.8 (.025)	70.3 (.058)
698	rs7649496	3	61936045	56.0 (.070)	40.9 (.080)
699	rs17673165	2	9385739	32.9 (.021)	25.5 (.024)
700	rs17284017	7	26356960	26.8 (.065)	46.8 (.105)
701	rs6089071	20	29842045	79.9 (.038)	70.0 (.059)
702	rs7944870	11	68065684	64.1 (.098)	82.3 (.051)
703	rs10751296	11	77954925	73.8 (.041)	81.8 (.059)
704	rs7791862	7	47516496	88.2 (.034)	75.7 (.036)
705	rs4373552	8	139055105	43.6 (.046)	64.0 (.060)
706	rs570549	3	173541823	17.5 (.024)	24.8 (.024)
707	rs3784131	14	68032257	17.8 (.028)	10.4 (.024)
708	rs142167	17	42150418	22.8 (.057)	36.0 (.070)
709	rs10236767	7	7385089	89.9 (.069)	71.0 (.118)
710	rs7636734	3	37721855	61.5 (.067)	50.2 (.073)
711	rs1457623	12	13432691	15.8 (.036)	6.9 (.048)
712	rs2848519	11	97618389	33.0 (.037)	22.6 (.048)
713	rs4677106	3	72296777	71.9 (.054)	82.5 (.040)
714	rs10095813	8	78201617	69.4 (.041)	56.4 (.039)
715	rs3106653	2	155401068	84.6 (.044)	73.0 (.038)
716	rs17544750	4	170548087	27.0 (.021)	18.6 (.031)
717	rs1250388	18	36833774	36.4 (.051)	25.8 (.061)
718	rs7860079	9	2096237	24.3 (.039)	17.1 (.025)
719	rs10895266	11	101533105	45.7 (.090)	24.7 (.071)
720	rs10899285	11	76191470	38.9 (.081)	4.6 (.047)
721	rs17762565	14	87726574	26.2 (.050)	15.9 (.056)
722	rs4629211	2	139112236	95.0 (.045)	85.7 (.065)
723	rs10445581	19	56275540	45.3 (.039)	30.6 (.033)
724	rs1437539	15	59173372	55.3 (.032)	66.3 (.034)
725	rs11844114	14	93530282	48.5 (.027)	36.1 (.032)
726	rs7143971	14	89650542	35.8 (.060)	20.8 (.073)
727	rs7211982	17	15335097	54.4 (.084)	35.0 (.069)
728	rs11639621	16	81545373	49.0 (.049)	42.2 (.027)
729	rs7938161	11	5169852	51.9 (.093)	23.5 (.091)
730	rs10754052	1	189871903	66.0 (.035)	76.5 (.032)
731	rs6929790	6	99152470	73.7 (.080)	89.9 (.033)
732	rs7727239	5	124084840	23.2 (.074)	16.1 (.023)
733	rs11961994	6	127691043	61.9 (.025)	74.4 (.039)
734	rs10979500	9	108641021	18.4 (.081)	6.5 (.023)
735	rs7113069	11	55939582	51.4 (.039)	36.0 (.024)
736	rs798601	3	119995613	38.9 (.055)	29.6 (.031)
737	rs2836365	21	38690144	39.8 (.029)	29.2 (.022)
738	rs7006032	8	140328379	55.8 (.028)	66.4 (.046)
739	rs831791	5	56385520	67.5 (.029)	57.7 (.048)
740	rs6425430	1	174229105	38.5 (.050)	50.5 (.059)
741	rs1078671	8	142140160	35.7 (.053)	24.1 (.053)
742	rs4644762	13	85511389	50.2 (.028)	65.8 (.066)
743	rs4981220	14	33669097	38.5 (.045)	26.0 (.035)
744	rs6898765	5	50910013	44.6 (.065)	29.4 (.043)
745	rs4734037	8	102740588	7.3 (.061)	21.0 (.016)
746	rs870992	5	52228994	7.0 (.055)	1.3 (.018)
747	rs12189287	5	148286759	27.4 (.040)	36.0 (.037)
748	rs1588705	4	69795733	16.0 (.050)	28.4 (.035)
749	rs3824070	7	1348618	58.9 (.046)	69.5 (.025)
750	rs10806221	6	82133833	81.8 (.079)	64.6 (.107)
751	rs4628676	11	68238806	61.1 (.023)	71.3 (.040)
752	rs17450420	13	103837147	95.5 (.021)	88.3 (.026)
753	rs777574	6	166426507	11.1 (.027)	19.4 (.041)
754	rs4130337	3	107848773	2.8 (.037)	10.8 (.035)
755	rs2491649	9	126108064	56.9 (.079)	70.5 (.077)
756	rs6995156	8	82494218	68.8 (.059)	54.6 (.055)
757	rs6472348	8	68945433	31.6 (.043)	43.9 (.053)
758	rs4448276	8	10092338	47.4 (.058)	36.0 (.053)
759	rs7582215	2	33139818	67.0 (.088)	49.0 (.061)
760	rs7201414	16	76762567	11.7 (.066)	21.9 (.076)
761	rs12947718	17	40848884	1.7 (.086)	17.3 (.067)
762	rs1468995	2	154842933	86.4 (.049)	78.7 (.038)
763	rs2532259	17	41609141	14.2 (.030)	24.7 (.027)
764	rs17439526	2	154656842	23.1 (.026)	35.9 (.067)
765	rs16841426	2	157942808	95.4 (.034)	84.3 (.053)
766	rs2272789	22	34004505	64.9 (.039)	74.9 (.047)
767	rs878815	14	65561860	58.7 (.024)	71.9 (.062)
768	rs3885957	5	75884149	67.2 (.046)	75.8 (.029)
769	rs11599418	10	113408949	19.2 (.054)	39.5 (.082)
770	rs7441878	4	118680094	11.9 (.074)	5.3 (.031)
771	rs360234	2	126757785	25.7 (.026)	15.9 (.026)
772	rs2696640	17	41007016	44.5 (.048)	54.3 (.053)
773	rs963666	1	230165486	26.9 (.021)	31.9 (.025)
774	rs16869658	8	103702938	65.7 (.099)	81.0 (.053)
775	rs17836505	16	86279192	59.3 (.065)	48.8 (.039)
776	rs4873584	8	52802297	89.6 (.061)	78.5 (.064)
777	rs13095558	3	77827384	36.2 (.037)	54.9 (.052)
778	rs11742145	5	166764657	37.6 (.064)	58.7 (.077)
779	rs8181728	12	115462617	23.6 (.066)	7.2 (.051)
780	rs4806891	19	2898152	77.0 (.061)	90.1 (.049)
781	rs6543297	2	105529677	68.1 (.030)	57.9 (.032)
782	rs16936517	10	37773387	15.0 (.032)	7.8 (.023)
783	rs2245201	16	77092871	68.4 (.105)	83.7 (.020)
784	rs9524017	13	92803806	23.1 (.022)	31.2 (.035)
785	rs7803877	7	146543556	33.9 (.091)	21.6 (.044)
786	rs4815812	20	5352526	34.6 (.113)	13.4 (.073)
787	rs10926796	1	239122055	23.6 (.117)	7.0 (.036)
788	rs430306	1	112364061	17.5 (.028)	27.0 (.028)
789	rs3749237	3	49745036	60.9 (.073)	75.6 (.048)
790	rs16927557	9	1315179	84.3 (.058)	95.7 (.034)
791	rs10808523	8	123579918	60.4 (.051)	52.6 (.040)
792	rs10933144	2	227088913	21.7 (.061)	7.4 (.042)
793	rs17182039	13	105595620	87.0 (.069)	95.5 (.036)
794	rs6051846	20	3351824	34.8 (.049)	21.5 (.044)
795	rs9923322	16	77401370	75.3 (.034)	80.2 (.040)
796	rs8007849	14	84494886	10.2 (.049)	18.7 (.035)
797	rs10787472	10	114771287	54.8 (.038)	46.7 (.028)
798	rs13016130	2	217799783	52.8 (.031)	42.5 (.038)
799	rs12408987	1	42721564	99.9 (.033)	88.7 (.038)
800	rs4837264	9	128281449	33.6 (.038)	15.1 (.046)
801	rs10898503	11	85970170	58.9 (.060)	40.6 (.088)
802	rs16867195	2	9940040	64.6 (.148)	96.1 (.103)
803	rs7811301	7	66876971	31.0 (.053)	19.0 (.026)
804	rs9366215	6	170591998	34.1 (.027)	25.5 (.025)
805	rs330609	2	150811273	44.0 (.056)	57.3 (.047)
806	rs4749580	10	31014180	70.1 (.049)	51.9 (.096)
807	rs2639974	18	71057723	55.5 (.035)	68.8 (.041)
808	rs265632	12	128600215	73.3 (.035)	59.8 (.027)
809	rs4236335	7	32840370	82.9 (.044)	71.3 (.057)
810	rs7367380	1	243492784	35.8 (.043)	24.0 (.063)
811	rs10858925	12	88649902	77.4 (.052)	67.5 (.055)
812	rs4302660	6	38953337	41.2 (.048)	55.0 (.044)
813	rs852102	20	17102385	15.2 (.055)	4.2 (.036)
814	rs792106	2	5482130	40.9 (.067)	52.4 (.069)
815	rs12885270	14	86242583	62.7 (.049)	76.4 (.060)
816	rs711635	3	4465513	66.5 (.047)	60.8 (.069)
817	rs2554830	18	72256690	47.9 (.035)	34.8 (.040)
818	rs7703173	5	51796987	92.6 (.056)	76.1 (.029)
819	rs12614495	2	172902347	17.7 (.074)	34.0 (.089)
820	rs6945478	7	149862999	98.3 (.034)	89.5 (.060)
821	rs34872	3	10483495	53.8 (.058)	44.9 (.025)
822	rs4796420	17	7320341	79.8 (.063)	93.1 (.035)
823	rs9646322	16	77722352	27.4 (.043)	17.1 (.027)
824	rs11924195	3	109409208	18.7 (.064)	11.1 (.023)
825	rs2814064	1	223996368	39.4 (.075)	26.9 (.035)
826	rs7810044	7	25718910	29.1 (.029)	38.3 (.037)
827	rs12418302	11	102844087	93.7 (.015)	88.4 (.027)
828	rs9573193	13	72902025	29.8 (.030)	21.5 (.057)
829	rs1188445	1	30832969	70.3 (.099)	94.0 (.055)
830	rs6089195	20	30194984	77.3 (.144)	99.9 (.071)
831	rs7406828	17	77229631	54.9 (.060)	38.0 (.027)
832	rs2065914	1	236496837	48.8 (.048)	62.1 (.041)
833	rs597566	15	31671915	26.3 (.031)	33.9 (.048)
834	rs1346173	12	107137927	44.9 (.040)	32.0 (.026)
835	rs7598978	2	66074063	84.4 (.038)	73.8 (.040)
836	rs748005	16	53882623	38.8 (.050)	33.3 (.043)
837	rs11173732	12	59750049	73.7 (.041)	54.1 (.039)
838	rs927297	6	91081015	58.3 (.026)	69.9 (.049)
839	rs36059	3	136215430	37.1 (.057)	25.8 (.035)
840	rs1793220	11	130414497	27.7 (.041)	16.9 (.027)
841	rs4397372	8	95061743	58.7 (.045)	45.2 (.050)
842	rs6703991	1	231011001	63.7 (.078)	72.9 (.045)
843	rs1005478	22	35802754	45.1 (.040)	36.1 (.037)
844	rs11846868	14	48857807	58.7 (.042)	65.3 (.047)
845	rs9905258	17	5847985	53.0 (.064)	40.5 (.044)
846	rs1156154	8	72646537	37.4 (.055)	28.0 (.027)
847	rs508521	6	116853934	62.5 (.042)	75.3 (.054)
848	rs2075520	16	21130173	40.1 (.077)	22.3 (.056)
849	rs2033050	7	134391023	39.2 (.065)	29.4 (.040)
850	rs10893032	11	122751364	73.9 (.073)	60.4 (.062)
851	rs6852460	4	183245512	52.2 (.059)	65.4 (.075)
852	rs16954586	13	97306879	79.8 (.048)	91.2 (.065)
853	rs11199884	10	123053164	81.8 (.120)	63.6 (.145)
854	rs7073611	10	126225492	41.2 (.117)	20.7 (.049)
855	rs545735	3	29093778	94.0 (.027)	89.5 (.056)
856	rs13419175	2	168813446	22.0 (.078)	9.2 (.050)
857	rs340989	11	22452794	70.6 (.027)	59.5 (.039)
858	rs10033498	4	31038208	50.9 (.084)	69.6 (.046)
859	rs348901	5	83457623	79.7 (.054)	67.4 (.058)
860	rs2693371	17	41011471	42.8 (.101)	59.2 (.066)
861	rs6791314	3	179505092	54.6 (.049)	38.7 (.078)
862	rs11579848	1	204517250	65.8 (.073)	86.8 (.084)
863	rs274946	9	23575350	68.3 (.121)	42.7 (.097)
864	rs4888846	16	77363264	68.2 (.069)	91.4 (.058)
865	rs10763586	10	60181765	66.2 (.028)	78.3 (.084)
866	rs1440355	8	73798241	74.1 (.033)	64.4 (.027)
867	rs10075995	5	148273622	33.1 (.063)	49.5 (.016)
868	rs12100904	14	35554731	42.9 (.032)	32.3 (.020)
869	rs1023497	22	40665008	95.2 (.037)	81.3 (.078)
870	rs10975412	9	6039547	99.3 (.062)	75.6 (.061)
871	rs184556	15	62100208	19.2 (.062)	0.4 (.034)
872	rs2973869	5	91133551	60.3 (.040)	73.0 (.049)
873	rs17814201	11	36225647	18.1 (.098)	5.2 (.043)
874	rs13204990	6	122731099	51.6 (.054)	65.9 (.052)
875	rs6065533	20	40828800	72.4 (.144)	97.6 (.033)
876	rs1549622	5	151246242	68.3 (.051)	74.9 (.028)
877	rs7096546	10	115234052	16.1 (.050)	4.5 (.027)
878	rs357758	2	71276935	34.5 (.060)	27.9 (.043)
879	rs1501605	3	172449118	22.8 (.044)	16.6 (.040)
880	rs4810113	20	56010505	78.1 (.063)	87.5 (.029)
881	rs1870419	12	68653898	66.8 (.095)	74.9 (.031)
882	rs344540	19	6638768	45.8 (.083)	27.7 (.055)
883	rs6864641	5	14803251	32.5 (.124)	8.9 (.076)
884	rs2804386	23	68759939	68.3 (.041)	58.0 (.055)
885	rs11938968	4	112100356	51.3 (.069)	77.2 (.111)
886	rs7869905	9	132680938	39.1 (.030)	30.9 (.022)
887	rs864643	3	39530584	74.4 (.043)	81.4 (.019)
888	rs2074948	22	28232404	71.6 (.057)	78.8 (.045)
889	rs2172712	1	161819150	34.6 (.046)	45.2 (.041)
890	rs8030411	15	74486910	72.2 (.062)	52.9 (.070)
891	rs1707956	3	39498520	25.5 (.059)	18.0 (.021)
892	rs1461349	11	37157502	45.2 (.044)	30.3 (.033)
893	rs4364968	10	6543737	55.8 (.075)	71.7 (.097)
894	rs16830611	2	135019123	27.5 (.093)	15.9 (.034)
895	rs557373	6	44366302	70.1 (.037)	81.9 (.032)
896	rs13440446	9	28241541	20.9 (.065)	30.7 (.050)
897	rs11059856	12	127735009	38.6 (.049)	46.2 (.026)
898	rs17727982	18	45689548	81.7 (.026)	89.8 (.038)
899	rs2722683	19	49610498	10.2 (.054)	23.7 (.103)
900	rs9309783	3	78033636	82.2 (.052)	73.1 (.039)
901	rs788216	10	27550340	84.2 (.074)	62.1 (.068)
902	rs10911886	1	183269248	95.3 (.018)	87.4 (.050)
903	rs3748538	1	237020043	25.5 (.055)	35.8 (.029)
904	rs6529924	23	5978160	23.6 (.023)	39.3 (.032)
905	rs13263328	8	21396041	33.6 (.046)	45.6 (.046)
906	rs7560229	2	214274149	73.7 (.036)	55.6 (.084)
907	rs10814831	9	4073863	60.8 (.087)	77.8 (.059)
908	rs1949807	2	227717366	95.5 (.084)	64.3 (.044)
909	rs17118133	8	13848795	3.1 (.051)	20.6 (.057)
910	rs10845852	12	13918404	88.0 (.082)	75.2 (.060)
911	rs6428237	1	191155604	35.3 (.096)	46.7 (.065)
912	rs4689558	4	7038538	54.5 (.052)	41.2 (.040)
913	rs10513456	9	125799403	67.8 (.040)	80.8 (.024)
914	rs1035695	7	134301230	48.0 (.055)	28.5 (.115)
915	rs2099821	5	3276744	83.3 (.046)	98.2 (.052)
916	rs9590631	13	41197653	80.5 (.047)	67.7 (.078)
917	rs9321570	6	137137372	60.5 (.040)	69.0 (.028)
918	rs925848	2	115802862	85.4 (.075)	66.7 (.064)
919	rs6954522	7	141300966	62.9 (.053)	46.1 (.112)
920	rs3936080	6	120900452	39.8 (.031)	48.7 (.031)
921	rs11969564	6	52889519	72.5 (.055)	86.8 (.021)
922	rs12989577	2	107656407	27.8 (.031)	43.3 (.061)
923	rs7808122	7	22571320	34.2 (.048)	46.1 (.041)
924	rs7757213	6	67053332	80.3 (.032)	88.8 (.038)
925	rs3766396	1	27905696	42.9 (.046)	27.2 (.051)
926	rs10053917	5	56858271	34.7 (.137)	8.2 (.059)
927	rs17790217	18	63944299	38.3 (.056)	50.0 (.047)
928	rs10052199	5	130544267	17.4 (.054)	7.0 (.032)
929	rs4072865	16	10931606	45.2 (.052)	55.3 (.058)
930	rs12477582	2	125980163	66.1 (.078)	76.3 (.036)
931	rs4681577	3	151316687	87.2 (.030)	92.0 (.030)
932	rs942703	1	197824636	36.9 (.079)	21.6 (.037)
933	rs12037277	1	79983359	56.4 (.022)	69.1 (.031)
934	rs8104146	19	34220766	47.2 (.047)	58.1 (.030)
935	rs4837082	9	126267377	26.1 (.060)	14.6 (.048)
936	rs2280732	2	28730018	78.8 (.042)	88.1 (.037)
937	rs7233739	18	6718488	37.7 (.046)	50.9 (.033)
938	rs11131719	4	68357286	41.1 (.043)	17.8 (.061)
939	rs7994224	13	49450185	18.2 (.076)	4.5 (.042)
940	rs1446893	2	72731680	88.0 (.040)	99.1 (.024)
941	rs7401404	14	62684209	29.0 (.028)	35.6 (.036)
942	rs4851854	2	105842256	51.5 (.027)	44.8 (.041)
943	rs1467616	10	102631681	38.6 (.050)	26.6 (.045)
944	rs9822959	3	185681145	37.8 (.051)	26.9 (.022)
945	rs8021814	14	46735752	50.6 (.032)	61.6 (.039)
946	rs12921623	16	16003634	87.8 (.070)	63.2 (.073)
947	rs4961688	9	16252191	46.7 (.062)	33.8 (.041)
948	rs2837297	21	40225051	23.3 (.038)	13.0 (.037)
949	rs4309752	3	136416314	49.3 (.055)	38.2 (.046)
950	rs500586	1	40744302	59.7 (.030)	70.6 (.047)
951	rs2577001	15	94555158	75.9 (.099)	88.3 (.026)
952	rs2662389	5	58162103	50.4 (.021)	40.5 (.021)
953	rs264705	3	65839896	34.2 (.047)	27.6 (.053)
954	rs275838	19	53558026	28.6 (.033)	21.0 (.033)
955	rs17345528	3	102777520	35.3 (.071)	14.2 (.072)
956	rs7541193	1	150485320	34.6 (.079)	53.0 (.064)
957	rs960537	2	124629747	14.6 (.077)	5.6 (.023)
958	rs1332011	6	39016289	25.1 (.052)	15.6 (.033)
959	rs875964	14	95802744	77.8 (.135)	95.1 (.087)
960	rs10016578	4	17742615	22.7 (.048)	3.3 (.041)
961	rs6056754	20	9540598	45.5 (.035)	36.9 (.015)
962	rs2480490	9	89387779	44.2 (.052)	32.3 (.034)
963	rs3857501	6	92348639	63.8 (.057)	74.3 (.033)
964	rs2084414	8	481735	72.6 (.034)	85.2 (.039)
965	rs2909824	5	116091320	69.2 (.087)	86.7 (.063)
966	rs1954916	6	162418023	91.1 (.055)	78.6 (.061)
967	rs17755177	2	187794592	71.0 (.054)	79.9 (.043)
968	rs7965234	12	126595604	62.1 (.086)	78.7 (.034)
969	rs6131684	20	15572156	56.2 (.062)	46.6 (.057)
970	rs17712923	11	39149865	16.6 (.172)	52.6 (.158)
971	rs2252550	6	38649462	29.2 (.040)	39.6 (.046)
972	rs6908475	6	22680777	67.1 (.032)	58.8 (.041)
973	rs11176031	12	64763239	71.5 (.132)	53.3 (.146)
974	rs3770536	2	216664326	69.7 (.029)	57.4 (.052)
975	rs10027488	4	187482998	29.2 (.059)	44.7 (.048)
976	rs2218248	3	179591920	64.5 (.091)	79.3 (.090)
977	rs17077348	5	173699036	71.0 (.044)	87.0 (.061)
978	rs974491	14	24835423	76.1 (.040)	62.1 (.070)
979	rs7751500	6	37697775	32.3 (.078)	14.7 (.060)
980	rs11127608	3	78033812	82.2 (.044)	68.6 (.042)
981	rs975974	2	43851917	15.4 (.048)	26.6 (.040)
982	rs3845948	3	37798704	75.6 (.043)	85.5 (.034)
983	rs611052	7	68601918	70.2 (.031)	62.0 (.039)
984	rs7930841	11	38466276	56.0 (.053)	68.9 (.039)
985	rs12433343	14	46617494	7.7 (.036)	17.8 (.023)
986	rs1281978	6	153565346	38.5 (.051)	51.1 (.047)
987	rs7077548	10	113350071	76.6 (.083)	58.8 (.036)
988	rs7127507	11	27671460	25.2 (.059)	38.3 (.076)
989	rs4971342	2	926687	88.8 (.076)	67.8 (.056)
990	rs1683119	14	96572498	33.5 (.040)	22.5 (.041)
991	rs2482527	9	25554648	81.6 (.057)	72.5 (.054)
992	rs6894312	5	18712040	13.7 (.044)	24.3 (.030)
993	rs4716908	7	155060486	77.2 (.054)	96.5 (.039)
994	rs1900455	10	55266508	50.5 (.043)	62.9 (.060)
995	rs2391870	7	30314272	77.4 (.102)	58.3 (.079)
996	rs771443	6	83452859	72.3 (.055)	57.4 (.090)
997	rs3091260	7	76475046	22.9 (.032)	34.4 (.053)
998	rs10878366	12	64708641	79.6 (.055)	68.7 (.112)
999	rs255026	5	178717241	48.6 (.035)	56.2 (.039)
1,000	rs5750373	22	35749531	73.5 (.064)	59.6 (.036)

^aThe rank order of the SNPs is based on a silhouette-test statistic calculated on probe intensity measures from replicate arrays, implemented in GenePool 0.81 (TGen Bioinformatics Research Unit). Only SNPs for which allelic frequencies could be calculated using the k-correction method³⁵ from a training database of 1,000 individually genotyped samples are included.

^bChromosomal positions for each SNP are based on National Center for Biotechnology Information build 35.1.

^cFrequencies are expressed as percentages. Predicted allelic frequencies are the median frequency of all replicate arrays and refer to the A allele as defined by Affymetrix 500K. The median value is used, since an extreme outlier is occasionally observed.

^dSNP has no rs number, only an Affymetrix identification number.

Figure 1. .

Two loci showing strong support for association by pooled analysis. A, Genomewide plot of the mean rank of five consecutive SNPs, calculated to identify clusters of high-ranking SNPs. The single best region was on chromosome 17, neighboring MAPT, and the second best region was on chromosome 11p12. Chromosome 11p12 also harbored the SNP that ranked #1 overall by single-marker statistics. B, Single-marker rank statistics for SNPs over the MAPT (left) and DDB2/ACP2 (right) loci. SNPs deemed less reliable or showing high variability among replicates were removed, and the remaining SNPs were ranked in order from 1 (showing the greatest difference between cases and controls) to 428,867 (showing the least difference between cases and controls) with use of a silhouette-test statistic in GenePool software (TGen Bioinformatics Research Unit). Rank scores are plotted versus chromosomal position. Genes within the plotted chromosomal region are shown below. SNPs on the Affymetrix 500K platform are shown above, and SNPs on the Affymetrix 100K platform are shown below. EA = Early Access.

The chromosome 11p12 region that showed the highest rank SNP by single-marker statistics and multimarker sliding-window analysis was a novel locus and therefore was examined in greater detail (fig. 1B). The top overall ranked SNP, rs901746, a SNP in intron 9 of the DNA damage-binding protein 2 (DDB2 [MIM 600811]) gene, was chosen for follow-up in the individual samples comprising the pooled DNA. A significant increase of 10% in the G allele frequency was seen in cases versus controls (P=.0002) (table 2). The SNP was then genotyped in a second U.S. series to confirm the association. This “replication” sample (n=161) was made up of both pathologically confirmed (n=97) and clinically defined PSP case individuals (n=64), as described in Rademakers et al.²² A total of 165 age- and sex-matched cognitively normal control individuals were obtained from the Normal and Pathological Aging Protocol at the Mayo Clinic (Scottsdale).^30,31 In addition, for the rs901746 and rs2167079 analysis, additional pathologically confirmed cases (n=41) and clinically defined PSP case indivuals (n=22) were genotyped, and 252 age- and sex-matched cognitively normal control individuals collected at Mayo Clinic Jacksonville were used as a second source of controls.²² All case and control individuals in this set were white from the United States and Canada, and IRB-approved protocols were used in the collection of all samples.

Table 2. .

Association Analysis of rs901746 in Original and Replication Series

		No. (%) of
		Alleles		Genotypes			GG versus AG and AA
Population	n	A	G	AA	AG	GG	OR	95% CI	P
Control combined	735	1,011 (75)	335 (25)	377 (56)	257 (38)	39 (6)	…	…	…
Control original	344	438 (78)	126 (22)	166 (58)	106 (37)	10 (4)	…	…	…
Control replication	391	573 (73)	209 (27)	211 (54)	151 (39)	29 (7)	…	…	…
PSP combined	501	661 (68)	317 (32)	231 (47)	199(41)	59 (12)	2.2	1.5–3.4	.0001
PSP original	288	374 (68)	178 (32)	131 (47)	112 (41)	33 (12)	4.0	1.9–8.3	.0001
PSP replication	213	287 (67)	139 (33)	100 (47)	87 (41)	26 (12)	1.7	1.0–3.0	.05

When allele frequencies at rs901746 were examined in the replication sample set, a 6% increase in the frequency of the G allele in subjects with PSP was observed; however, because of the smaller sample size, this allele frequency difference is borderline significant (P=.05). When genotype distributions were examined in both PSP case-control series, the frequencies were very similar, with an increase from 4% to 12% in the GG genotype in the original population and an increase from 7% to 12% in the replication set. The allelic frequency difference in both series is explained by an apparent doubling of the GG frequency in subjects with PSP compared with controls, suggesting that risk at this locus acts in a recessive manner. We explicitly tested dominant, recessive, and additive models at this locus, and the model that best fit the data was a recessive one (P<.0001). The OR for harboring an rs901746 GG genotype versus all other genotypes in the original series was 3.7 (95% CI 1.2–3.9) and was 1.7 (95% CI 1.0–3.0) for the replication series. When these individuals in both of these series were combined and analyzed, the combined OR for the GG genotype compared with all other genotypes in the series was 2.2 (95% CI 1.4–3.4). To confirm that the rs901746 association observed is not a control frequency artifact, we examined allele frequencies for rs901746 in 250 cognitively normal controls recently published in a Parkinson disease (PD [MIM 168600]) GWA study.³⁸ We found that the frequency of the rs901746 G allele in this independent control series was 0.27, consistent with our observed control frequencies (0.22 and 0.27).

The genomic context near rs901746 was examined by downloading the CEPH-from-Utah SNP genotypes for 100 kb around rs901746 from the HapMap genome browser and by examining the LD patterns and haplotype-block structure of the region with use of the Haploview software.³⁹ rs901746 lies in the middle of a haplotype block encompassing at least two genes—the DDB2 gene and the lysosomal acid phosphatase 2 (ACP2 [MIM 171650]) gene—and can extend into the 3′ of another gene, nuclear receptor subfamily 1, group H, member 3 (NR1H3 [MIM 602423]), depending on the type of haplotype-block definition used.³⁹ Variation in this 100-kb region could be fully described by 16 additional tag SNPs. These tag SNPs were genotyped in all PSP series, and both single and multimarker analysis was performed on the combined series (table 3). Single-marker analysis showed that nine tag SNPs showed significant allelic association. Of these, five tag SNP associations were highly significant (P values ⩽.003), with rs10501320 showing the greatest association after rs901746 (P<.0001).

Table 3. .

Single-Marker Analysis of Tag SNPs in the Combined Series and in Both Young and Old Patient Populations^[Note]

		All Cases(n=448)		Youngb Cases(n=162)		Oldb Cases(n=182)
tagIDa (SNP), and Allele	No. (%) of Alleles in Controls (n=532)	No. (%) of Alleles	P	No. (%) of Alleles	P	No. (%) of Alleles	P
1 (rs11039130):			.003		.02		.25
C	600 (69)	614 (75)		224 (76)		245 (72)
T	274 (31)	202 (25)		72 (24)		95 (28)
2 (rs4647709):			.5		.57		.88
C	806 (91)	787 (90)		292 (90)		331 (91)
T	78 (9)	85 (10)		32 (10)		31 (9)
3 (rs2291120):			.0004		.003		.006
T	781 (92)	859 (87)		280 (86)		317 (87)
C	67 (8)	115 (13)		44 (14)		47 (13)
4 (rs10742797):			.81		.72		.98
A	591 (81)	572 (81)		212 (82)		243 (80)
T	143 (19)	134 (19)		48 (18)		59 (20)
5 (rs1685404):			.72		.97		.96
G	598 (68)	560 (67)		213 (68)		237 (68)
C	282 (32)	274 (33)		101 (32)		111 (32)
6 (rs7395581):			.03		.02		.07
A	378 (71)	437 (65)		157 (63)		180 (65)
G	152 (29)	233 (35)		93 (37)		96 (35)
7 (rs11039138):			.01		.02		.37
G	470 (56)	442 (62)		168 (64)		173 (59)
A	372 (44)	268 (38)		94 (36)		121 (41)
8 (rs2957873):			.22		.52		.28
A	728 (83)	679 (81)		257 (81)		281 (80)
G	150 (17)	163 (19)		59 (19)		69 (20)
9 (rs4647736):			.03		.04		.12
C	807 (91)	736 (88)		273 (88)		305 (89)
T	75 (9)	98 (12)		39 (13)		39 (11)
10 (rs2013867):			.004		.006		.02
T	657 (74)	549 (66)		206 (66)		236 (67)
C	229 (26)	279 (34)		106 (34)		114 (33)
11 (rs901746):			<.0001		.003		.004
A	659 (76)	570 (67)		204 (65)		242 (68)
G	213 (24)	282 (33)		110 (35)		116 (32)
12 (rs1050244):			.53		.89		.44
C	851 (97)	823 (96)		307 (97)		343 (96)
T	29 (3)	33 (4)		11 (3)		15 (4)
13 (rs11039143):			.87		.64		.52
T	830 (98)	782 (98)		293 (98)		319 (98)
G	18 (2)	16 (2)		5 (2)		5 (2)
14 (rs7118396):			.16		.27		.13
C	741 (86)	688 (84)		253 (84)		287 (83)
T	117 (14)	132 (16)		49 (16)		59 (17)
15 (rs12577530):			.0009		.005		.04
G	784 (88)	701 (82)		260 (82)		296 (84)
C	106 (12)	149 (18)		58 (18)		58 (16)
16 (rs7114704):			.01		.3		.0006
C	813 (93)	803 (96)		288 (95)		343 (98)
T	61 (7)	35 (4)		16 (5)		7 (2)
17 (rs10501320):			<.0001		.003		.16
G	609 (70)	641 (78)		230 (79)		255 (74)
C	265 (30)	179 (22)		62 (21)		91 (26)

Note.— Significant P values are shown in bold.

^aTag SNPs were chosen on the basis of the tagging algorithm in Haploview v3.32 software,³⁹ with the “Pairwise Tagging Only” option selected and the r² threshold set at .8.

^bSubjects aged <76 years were classified as “young”; subjects aged ⩾76 were classified as “old.”

We examined the DDB2/ACP2 tag SNP data set in different age groups in our combined series of cases and controls to see whether looking at younger cases might help further refine the associated region, as it had for the MAPT locus, where younger cases show a stronger association with the H1/H1 genotype.²² Pathologically confirmed cases were divided into “young” and “old” groups on the basis of median age at death (75 years), and single-marker allelic association statistics were calculated using 2×2 contingency tables and were examined using χ² tests. On the whole, all of the SNPs that show significant association in the combined PSP case set also show significant association (P<.05) with the younger case subset, whereas there is less-significant association observed for the older cases.

To refine the disease-associated region, we performed haplotype-inference analysis in the young cases versus all controls, using a sliding-window approach.⁴⁰ As described elsewhere, this type of approach was key in refining the associated region on the MAPT H1 haplotype.²² However, as figure 2 displays, when data from all the tag SNPs were included in the analysis, there was no obvious resolution of the associated region when the young cases were considered separately. This may reflect the fact that the contribution to the overall signal of the association at this locus was not as great with the younger cases as had been seen with the MAPT locus; therefore, the sample size and/or the number of informative SNPs was inadequate to detect a smaller associated region.

Figure 2. .

Haplotype sliding window–analysis results. The haplotype score–based method of Schaid et al.⁴⁰ was used to investigate evidence of association of haplotypes with case-control status. Only haplotypes with an estimated overall frequency of ⩾5% were considered for these analyses. Reported P values are based on asymptotic assumptions but were verified by simulating P values derived from 1,000 permutations of case and control labels and were found to be consistent. Global P values for each 4-marker haplotype are denoted as lines at the −log₁₀P. Only young pathologically confirmed PSP cases (death at age <76 years) were used for the analysis. All individuals in the control group were used in all analyses, since no single SNP showed significantly different allelic frequency distribution in controls when stratified by age. Global P=.01 is denoted by a dashed line. SNP numbers are as noted in table 3.

Since a haplotype-inference approach was unsuccessful in narrowing the associated region, we decided to identify additional novel SNPs that may represent functional variant(s) accounting for increased risk of disease by sequencing a series of 18 subjects with PSP who had the various genotypes at rs901746, the majority of whom carried the risky GG genotype (n=11 GG, n=5 AG, and n=2 AA) (table 4). Primers were designed to fully sequence coding exons of both DDB2 and ACP2. Only one SNP, found 63 bp downstream of exon 3 in ACP2, was not already in the dbSNP database; however, this SNP appeared to be in near-complete LD with nearby rs10838677 in exon 5 of ACP2, encoding a silent change (L165L). Interestingly, a number of SNPs identified through sequencing appeared to be in near-complete LD with rs901746, including rs2167079, a coding SNP in ACP2 in which the minor allele changes the amino acid at position 29 from an arginine to a glutamine (R29Q). This converts the protein sequence to the mouse amino acid residue at the equivalent position. Interestingly, this position in ACP2 is predicted to encode the signal peptidase cleavage site,⁴¹ suggesting that carriers of the minor allele encoding glutamine at position 29 may have altered cleavage of the signal peptide compared with those encoding arginine at that position. Since this SNP could affect function of the protein, we genotyped it through the combined series. Results from this analysis are shown in table 5. Overall, the LD between rs901746 and rs2167079 was high (cases r²=0.97; controls r²=0.94). As expected, significant allelic association was observed with rs2167079 (P=.002); however, this was not any greater than the association observed with rs901746, suggesting that rs2167079 is unlikely to fully explain the association at the DDB2/ACP2 locus. We tested the R29Q variant for dominant, recessive, and additive models, and the additive model best fit the data (P<.0001).

Table 4. .

SNP Discovery Results from Sequencing DDB2 and ACP2 in 18 Subjects with PSP

	Genotype at DDB25′→3′			Genotype at ACP23′→5′
	Intron 8	Intron 9	3′ UTR	Intron 6		Exon 5	Intron 3		Exon 1
Sample	rs326222	rs901746	rs1050244	rs11039146	rs2242261	rs10838677a	ss68362654b	rs4752973	rs2167079c
1	GG	GG	CT	CT	AA	AG	AG	AG	AA
2	GG	GG	CC	CC	AA	GG	GG	AA	AA
3	GG	GG	CC	CC	CC	GG	GG	GG	AA
4	GG	GG	CC	CC	AC	GG	GG	AG	AA
5	GG	GG	CC	CC	AC	GG	GG	AG	AA
6	GG	GG	CC	CC	CC	GG	GG	GG	AA
7	GG	GG	CC	CC	AA	GG	GG	AA	AA
8	GG	GG	CT	CT	AA	AG	AG	AG	AA
9	AG	AG	CC	CC	AA	GG	GG	AA	AG
10	GG	GG	CC	CC	AC	GG	GG	AG	AA
11	GG	GG	CC	CC	AC	GG	GG	AG	AA
12	GG	GG	CC	CC	AC	GG	GG	AG	AA
13	AG	AG	CC	CC	AA	GG	GG	AA	AG
14	AG	AG	CC	CC	AA	GG	GG	AA	GG
15	AG	AG	CC	CC	AA	GG	GG	AA	AG
16	AG	AG	CC	CC	AA	GG	GG	AA	AG
17	AA	AA	CC	CC	AA	GG	GG	AA	GG
18	AA	AA	CC	CC	AA	GG	GG	AA	GG

^aEncodes synonymous change L165L.

^bNo rs number; submitted to dbSNP.

^cEncodes nonsynonymous change R29Q.

Table 5. .

Association Analysis of rs2167079 in the Combined Series^[Note]

	No. (%) of Alleles
SNP and Allele	All Controls (n=735)	All Patients (n=501)	P
rs901746:			<.0001
A	1,011 (75)	661 (68)
G	335 (25)	317 (32)
rs2167079:			.002
G	918 (73)	598 (67)
A	332 (27)	292 (33)

Note.— Results include the additional cases and controls used in the replication series.

In an alternative method for determining the gene responsible for disease risk at this locus, expression analysis was performed on the DDB2 and ACP2 genes. Analysis was performed, using real-time Taqman expression assays (Applied Biosystems), on mRNA extracted from the cerebella of 20 rs901746 AA and 20 rs901746 GG genotype carriers, to determine whether risk variants at the DDB2/ACP2 locus have a direct effect on gene expression. Unfortunately, although DDB2 transcript levels are slightly increased in cases with a GG genotype, no significant differences were observed between the cases with AA and GG genotypes for either DDB2 or ACP2 mRNA levels (for DDB2, P=.29; for ACP2, P=.48) (fig. 3).

Figure 3. .

Relative mRNA expression with TATA-binding protein as an endogenous control. Plotted are relative levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH); tyrosine 3-monooxygenase/tryptophan 5-mono-oxygenase activation protein, zeta polypeptide (YWHAZ); ACP2 (assay Hs00155636_m1 [Applied Biosystems]); and DDB2 (assay Hs00172068_m1 [Applied Biosystems]) for 20 carriers of the rs901746 AA (neutral) genotype and 20 carriers of the rs901746 GG (risky) genotype. SE is denoted by the error bars. None of the comparisons between AA and GG carriers reach the level of statistical significance (P values noted below each graph). Similar results are seen when GAPDH or YWHAZ was used as the endogenous control (data not shown). RQ = relative quantity.

GWA studies are appealing because of their lack of bias, in that they represent a model-free approach for identification of new and novel genes that are involved in a disease process that may never be identified using other methodologies. However, even now, individually genotyping hundreds of individuals to perform a “traditional” GWA is not feasible for many rarer diseases, including PSP, because of the lack of available funding. Therefore, this type of pooled genomewide approach potentially represents a fast and economical initial solution to this problem. Pooling methods lack the analytical flexibility inherent in a traditional genomewide study because it is not possible to reanalyze the data with use of subgroups of cases or controls or to perform true haplotype-scanning analyses. However, there is still some uncertainty about how best to analyze the large amounts of individual genotype data used in GWA studies. An early GWA study of the PD showed problems in replication of results, potentially because of problems in study design.^42–47

Although pooling methods clearly have limitations, the analysis procedures we used in the GenePool software (TGen Bioinformatics Research Unit) were developed using individual genotype data from samples that were also pooled, thereby allowing the algorithms to be adjusted until they predicted SNP ranks on the basis of what was known from the individual genotype data.³² In the present analysis, we had prior knowledge that the MAPT H1 haplotype is associated with disease, so it could serve as a positive control for the genomewide analysis.

The identification of a new risk locus for PSP on chromosome 11 from the pooled genomewide approach was confirmed in a second U.S. PSP case-control series, with similar allele and genotype frequencies. Closer examination of this locus by dense SNP genotyping suggests that the association spans the entire haplotype block containing the DDB2 and ACP2 genes. Examination of potential functional variants yielded no definitive explanation for the observed association.

Both ACP2 and DDB2 are reasonable candidate genes that highlight previously implicated pathways for neurodegenerative disease. There are many lines of evidence suggesting a role for lysosomes and autophagic processes in neurodegeneration. Autophagy has been implicated in the clearance of protein aggregates, a common feature of many neurodegenerative disorders.^48,49 Interestingly, patients with lysosomal-storage disorders often exhibit neurological phenotypes with pathology similar to that seen in PSP.^50–52 Two lines of evidence implicate ACP2 in neurodegeneration. First, it has been reported that, in brains of subjects with Alzheimer disease (AD [MIM 104300]), microglia surrounding the amyloid plaques stain strongly for ACP2.⁵³ In addition, cerebrospinal fluid from half of the examined subjects with AD showed evidence of ACP2 activity, whereas patients not affected with AD showed no activity.⁵³ These results leave open the question of whether ACP2 in AD is just a secondary marker of neurodegeneration or perhaps plays a more active role in the neurodegenerative process. Second, knockouts and mutations of Acp2 in mice have neurological phenotypes.^54,55 Neuropathology of Acp2^−/− tissue showed increased lysosomal staining (as detected by lamp-1 and cathepsin D immunoreactivity), primarily in glial cells. Interestingly, ∼7% of these Acp2^−/− mice presented with generalized seizures after age 8 wk, and it has been suggested that this phenotype may be correlated with the defective lysosomal storage observed in glial cells.⁵⁴ The observation that loss of Acp2 causes deficits in glial lysosomal storage in the Acp2^−/− mice may also be significant, given that, in PSP, there is abundant MAPT-inclusion pathology within glia (astrocytes and olgodendroglia), as well as in neurons.⁵⁶

Mutations in the DDB2 gene are responsible for xeroderma pigmentosum (XP) complementation group E (XPE [MIM 278740]). Interestingly, some mutations in the nucleotide excision–repair pathway that cause the diseases XP and Cockayne syndrome (MIM 216400) present with neurological phenotypes; however, XPE does not seem to be one of them.^57,58 DDB2 forms a ubiquitin E3-ligase complex, with DNA damage-binding protein 1 (DDB1 [MIM 600045]) and Cullin 4a (CUL4A [MIM 603137]), that binds damaged DNA. Both histone H2A (H2AA [MIM 603137]) and XP complementation group C (XPC [MIM 278720]) proteins have been implicated as substrates for the DDB1/DDB2/CUL4A complex upon activation.^59,60 Ubiquitination of histone H2A may change local chromatin configuration at the damage site, thereby allowing access to other DNA-repair proteins farther down the pathway.⁶⁰ The accumulation of damaged DNA in aging brain suggests that DNA-repair capacity is reduced as we age and appears to be selective to genes important in learning and memory. Interestingly, there is evidence of brain-specific alternatively spliced forms of DDB2 that splice out either exons 4–7 or exons 4 and 6 alone.⁶¹ The proteins encoded by these alternatively spliced transcripts act as dominant negative inhibitors of DNA repair, when tested in an in vitro system.⁶¹ It will be interesting to tease apart which gene or genes at this locus are involved in conferring risk of PSP, but functional studies, rather than genetic ones, will probably be required to address these issues.

Given the size of the association seen at the DDB2/ACP2 locus, the fact that the described PSP series represents the largest collection of PSP-affected subjects worldwide, and the fact that our U.S. replication series is underpowered to detect changes with an OR <2.0, we may be at the limit of what can be consistently detected and confirmed using the case-control populations available. Six additional weaker loci were identified in the genomewide screen that still need to be analyzed in detail, and it will be interesting to examine this potential power issue in closer detail. This genomewide analysis has identified a novel second locus implicated in PSP risk, accelerating research and the hope of identifying effective therapeutics for this devastating disease.