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Background
This site provides an easy way to access and download supplementary results of a
comprehensive study of genetic variation in three diverse human populations.
Perlegen Sciences genotyped over 1.5 million unique
genetic variants, known as single nucleotide polymorphisms (SNPs), in 71 individuals
of European American, African American, or Han Chinese ancestry. In total, more
than 112 million individual genotypes were determined, with an average distance
between adjacent SNPs of 1871 base pairs. The genotypes were then phased and partitioned
into haplotype blocks using the phasing software
HAP. The full results
of this study, published by Hinds et al. in the Journal Science and available
for full text download on the Perlegen web site, indicate these SNPs capture
most common human genetic variation
as a result of linkage disequilibrium, the correlation among common SNP alleles.
Using the Site
The site contains the block partition and the haplotypes in each of the blocks. A map of where the genes are located relative to the positions on this site is available here. (See the README below for more information.) The The SNPs can
also be viewed graphically in the Perlegen Genotype Browser. The data can also be downloaded by following the link below.
Download Complete Data (README file for data).
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Chromosome Summaries
For each population (afr=African American, chn=Han Chinese, eur=European Americans), the number of SNPs, blocks and Tag SNPs are shown for each chromosomes. Click on the chromosome to obtain detailed information about each region in the genome.
| Pop |
Chrom |
Num SNPs |
Num Blocks |
Num Tag SNPs |
| afr |
1 |
126733 |
18325 |
44596 |
| afr |
2 |
141431 |
20748 |
50508 |
| afr |
3 |
99438 |
15043 |
36328 |
| afr |
4 |
113161 |
16202 |
39237 |
| afr |
5 |
106386 |
15476 |
37640 |
| afr |
6 |
96548 |
13499 |
33260 |
| afr |
7 |
86626 |
12643 |
30758 |
| afr |
8 |
97566 |
14192 |
34330 |
| afr |
9 |
58554 |
9347 |
22372 |
| afr |
10 |
77297 |
11137 |
27116 |
| afr |
11 |
73270 |
10993 |
26530 |
| afr |
12 |
69524 |
10225 |
24846 |
| afr |
13 |
68782 |
9763 |
23758 |
| afr |
14 |
55446 |
8413 |
20294 |
| afr |
15 |
46048 |
7473 |
17897 |
| afr |
16 |
42731 |
7158 |
17022 |
| afr |
17 |
34836 |
5688 |
13586 |
| afr |
18 |
52041 |
7786 |
18970 |
| afr |
19 |
18406 |
3077 |
7271 |
| afr |
20 |
35249 |
5506 |
13266 |
| afr |
21 |
27416 |
4070 |
9884 |
| afr |
22 |
20360 |
3382 |
8059 |
| afr |
X |
37294 |
5517 |
13358 |
| afr |
Y |
334 |
102 |
117 |
| chn |
1 |
126733 |
6822 |
16823 |
| chn |
2 |
141431 |
7176 |
17565 |
| chn |
3 |
99438 |
5758 |
14044 |
| chn |
4 |
113161 |
5712 |
14167 |
| chn |
5 |
106386 |
5619 |
13975 |
| chn |
6 |
96548 |
5327 |
13278 |
| chn |
7 |
86626 |
5122 |
12609 |
| chn |
8 |
97566 |
4975 |
12378 |
| chn |
9 |
58554 |
3922 |
9599 |
| chn |
10 |
77297 |
4592 |
11321 |
| chn |
11 |
73270 |
4053 |
10029 |
| chn |
12 |
69524 |
4171 |
10279 |
| chn |
13 |
68782 |
3533 |
8817 |
| chn |
14 |
55446 |
3117 |
7778 |
| chn |
15 |
46048 |
2995 |
7355 |
| chn |
16 |
42731 |
2999 |
7194 |
| chn |
17 |
34836 |
2408 |
5713 |
| chn |
18 |
52041 |
2890 |
7085 |
| chn |
19 |
18406 |
1531 |
3615 |
| chn |
20 |
35249 |
2199 |
5308 |
| chn |
21 |
27416 |
1547 |
3828 |
| chn |
22 |
20360 |
1476 |
3467 |
| chn |
X |
37294 |
2050 |
4582 |
| chn |
Y |
334 |
101 |
103 |
| eur |
1 |
126733 |
8257 |
20924 |
| eur |
2 |
141431 |
9069 |
22915 |
| eur |
3 |
99438 |
6968 |
17445 |
| eur |
4 |
113161 |
6971 |
17616 |
| eur |
5 |
106386 |
7250 |
18415 |
| eur |
6 |
96548 |
6715 |
17270 |
| eur |
7 |
86626 |
6062 |
15306 |
| eur |
8 |
97566 |
6377 |
16038 |
| eur |
9 |
58554 |
4650 |
11548 |
| eur |
10 |
77297 |
5416 |
13666 |
| eur |
11 |
73270 |
4975 |
12665 |
| eur |
12 |
69524 |
5052 |
12811 |
| eur |
13 |
68782 |
4608 |
11653 |
| eur |
14 |
55446 |
3921 |
9786 |
| eur |
15 |
46048 |
3434 |
8451 |
| eur |
16 |
42731 |
3560 |
8684 |
| eur |
17 |
34836 |
2816 |
6980 |
| eur |
18 |
52041 |
3472 |
8681 |
| eur |
19 |
18406 |
1760 |
4173 |
| eur |
20 |
35249 |
2660 |
6574 |
| eur |
21 |
27416 |
1836 |
4610 |
| eur |
22 |
20360 |
1682 |
4126 |
| eur |
X |
37294 |
2402 |
5623 |
| eur |
Y |
334 |
108 |
142 |
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