Table 2.
ENCODE project regions and genotyping
| Available SNPs
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Region name |
Chromosome band |
Genomic interval (NCBI) (base numbers)† |
Gene density (%)‡ |
Conservation score (%)§ |
Pedigree-based recombination rate (cM Mb−1)|| |
Population-based recombination rate (cM Mb−1)¶ |
G+C content# |
dbSNP⋆ | Sequence** | Total | Successfully genotyped SNPs†† |
Sequencing centre/genotyping centre(s)‡‡ |
| ENr112 | 2p16.3 | 51,633,239–52,133,238 | 0 | 3.8 | 0.8 | 0.9 | 0.35 | 1,570 | 1,762 | 3,332 | 2,275 | Broad/McGill- GQIC |
| ENr131 | 2q37.1 | 234,778,639–235,278,638 | 4.6 | 1.3 | 2.2 | 2.5 | 0.43 | 1,736 | 1,259 | 2,995 | 1,910 | Broad/McGill- GQIC |
| ENr113 | 4q26 | 118,705,475–119,205,474 | 0 | 3.9 | 0.6 | 0.9 | 0.35 | 1,444 | 2,053 | 3,497 | 2,201 | Broad/Broad |
| ENm010 | 7p15.2 | 26,699,793–27,199,792 | 5.0 | 22.0 | 0.9 | 0.9 | 0.44 | 1,220 | 1,795 | 3,015 | 1,271 | Baylor/UCSF-WU, Broad |
| ENm013* | 7q21.13 | 89,395,718–89,895,717 | 5.5 | 4.4 | 0.4 | 0.5 | 0.38 | 1,394 | 1,917 | 3,311 | 1,807 | Broad/Broad |
| ENm014* | 7q31.33 | 126,135,436–126,632,577 | 2.9 | 11.2 | 0.4 | 0.9 | 0.39 | 1,320 | 1,664 | 2,984 | 1,966 | Broad/Broad |
| ENr321 | 8q24.11 | 118,769,628–119,269,627 | 3.2 | 11.4 | 0.6 | 1.1 | 0.41 | 1,430 | 1,508 | 2,938 | 1,758 | Baylor/Illumina |
| ENr232 | 9q34.11 | 127,061,347–127,561,346 | 5.9 | 8.3 | 2.7 | 2.6 | 0.52 | 1,444 | 1,523 | 2,967 | 1,324 | Baylor/Illumina |
| ENr123 | 12q12 | 38,626,477–39,126,476 | 3.1 | 1.7 | 0.3 | 0.8 | 0.36 | 1,877 | 1,379 | 3,256 | 1,792 | Baylor/Baylor |
| ENr213 | 18q12.1 | 23,717,221–24,217,220 | 0.9 | 7.4 | 1.2 | 0.9 | 0.37 | 1,330 | 1,459 | 2,789 | 1,640 | Baylor/Illumina |
| Total | – | – | – | – | – | – | – | 14,765 | 16,319 | 31,084 | 17,944 | – |
McGill-GQIC, McGill University and Génome Québec Innovation Centre.
These regions were truncated to 500 kb for resequencing.
Sequence build 34 coordinates.
Gene density is defined as the percentage of bases covered either by Ensembl genes or human mRNA best BLAT alignments in the UCSC Genome Browser database.
Non-exonic conservation with mouse sequence was measured by taking 125 base non-overlapping sub-windows inside the 500,000 base windows. Sub-windows with less than 75% of their bases in a mouse alignment were discarded. Of the remaining sub-windows, those with at least 80% base identity were used to calculate the conservation score. The mouse alignments in regions corresponding to the following were discarded: Ensembl genes, all GenBank mRNA Blastz alignments, FGenesh++ gene predictions, Twinscan gene predictions, spliced EST alignments, and repeats.
The pedigree-based sex-averaged recombination map is from deCODE Genetics48.
Recombination rate based on estimates from LDhat46.
G + C content calculated from the sequence of the stated coordinates from sequence build 34.
SNPs in dbSNP build 121 at the time the ENCODE resequencing began and SNPs added to dbSNP in builds 122–125 independent of the resequencing.
New SNPs discovered through the resequencing reported here (not found by other means in builds 122–125).
SNPs successfully genotyped in all analysis panels (YRI, CEU, CHB + JPT).
Perlegen genotyped a subset of SNPs in the CEU samples.