Information on the CNV project and CNV data can be found at at the FAQ

Browse Data by Individual

Individual NA06985 NA06991 NA06993 NA06994 NA07000 NA07019 NA07022 NA07029 NA07034 NA07048 NA07055 NA07056 NA07345 NA07348 NA07357 NA10830 NA10831 NA10835 NA10838 NA10839 NA10846 NA10847 NA10854 NA10855 NA10856 NA10857 NA10859 NA10860 NA10861 NA10863 NA11829 NA11830 NA11831 NA11832 NA11839 NA11840 NA11881 NA11882 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12056 NA12057 NA12144 NA12145 NA12146 NA12154 NA12155 NA12156 NA12234 NA12236 NA12239 NA12248 NA12249 NA12264 NA12707 NA12716 NA12717 NA12740 NA12750 NA12751 NA12752 NA12753 NA12760 NA12761 NA12762 NA12763 NA12801 NA12802 NA12812 NA12813 NA12814 NA12815 NA12864 NA12865 NA12872 NA12873 NA12874 NA12875 NA12878 NA12891 NA12892 NA18500 NA18501 NA18502 NA18503 NA18504 NA18505 NA18506 NA18507 NA18508 NA18515 NA18516 NA18517 NA18521 NA18522 NA18523 NA18524 NA18526 NA18529 NA18532 NA18537 NA18540 NA18542 NA18545 NA18547 NA18550 NA18552 NA18555 NA18558 NA18561 NA18562 NA18563 NA18564 NA18566 NA18570 NA18571 NA18572 NA18573 NA18576 NA18577 NA18579 NA18582 NA18592 NA18593 NA18594 NA18603 NA18605 NA18608 NA18609 NA18611 NA18612 NA18620 NA18621 NA18622 NA18623 NA18624 NA18632 NA18633 NA18635 NA18636 NA18637 NA18852 NA18853 NA18854 NA18855 NA18856 NA18857 NA18858 NA18859 NA18860 NA18861 NA18862 NA18863 NA18870 NA18871 NA18872 NA18912 NA18913 NA18914 NA18940 NA18942 NA18943 NA18944 NA18945 NA18947 NA18948 NA18949 NA18951 NA18952 NA18953 NA18956 NA18959 NA18960 NA18961 NA18964 NA18965 NA18966 NA18967 NA18968 NA18969 NA18970 NA18971 NA18972 NA18973 NA18974 NA18975 NA18976 NA18978 NA18980 NA18981 NA18987 NA18990 NA18991 NA18992 NA18994 NA18995 NA18997 NA18998 NA18999 NA19000 NA19003 NA19005 NA19007 NA19012 NA19092 NA19093 NA19094 NA19098 NA19099 NA19100 NA19101 NA19102 NA19103 NA19116 NA19119 NA19120 NA19127 NA19128 NA19129 NA19130 NA19131 NA19132 NA19137 NA19138 NA19139 NA19140 NA19141 NA19142 NA19143 NA19144 NA19145 NA19152 NA19153 NA19154 NA19159 NA19160 NA19161 NA19171 NA19172 NA19173 NA19192 NA19193 NA19194 NA19200 NA19201 NA19202 NA19203 NA19204 NA19205 NA19206 NA19207 NA19208 NA19209 NA19210 NA19211 NA19221 NA19222 NA19223 NA19238 NA19239 NA19240 chromosome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y genome assembly NCBI35 NCBI36 browser UCSC Ensembl

( alternatively click here to browse all Samples ( merged CNVs) in a browser )

How to browse a sample :

Choose the sample , the chromosome, the genome assembly and the browser that you would like to use, then click on "Browse".
This will redirect you to the first 1Mb of the chosen chromosome.

UCSC

The UCSC browser will show up to four tracks:

1. The clones on the WGTP array (Track "Sanger_WGTP_clones" )
   
2. The log2ratio of copy number at each clone (Track "DyeSwap Ratios for ...")
   
3. The clones called as losses relative to the reference DNA (Track "Loss calls ...")
   
4. The clones called as gains relative to the reference DNA (Track "Gain calls ...")
   

The distribution of log2ratios across all 270 HapMap samples can be visualised for each clone on the array by clicking on the desired clone in the track "Sanger_WGTP_Clones" to show the details page for that clone and then clicking on the link entitled "Outside Link".

Some illustrations can be found here.
For help about the UCSC browser use, please visit UCSC help

Ensembl

Choosing to display the CNVs for an individual in the Ensembl browser will show four tracks. These will be :

1. The clones on the WGTP array (Track "Sanger_WGTP_clones" )
2. A histogram track of the probe/clone intensity log2ratios.
3. The clones called as losses relative to the reference DNA (Track "cnvs_loss_NAxxxxx")
4. The clones called as gains relative to the reference DNA (Track "cnvs_gain_NAxxxxxx")

By clicking on any of the clone features in the Sanger_WGTP_clones you can follow a link (click 'details') to view a distribution of the log2ratio scores for each clone across the whole dataset of 270 HapMap individuals.

Note that due to software issues with the Ensembl website, when viewing CNVs on the NCBI35 assembly the histogram track of log2ratios will appear as a track of vertical bars. When you mouse over these the log2ratio will be displayed as a tool tip. Ideally, use the NCBI36 assembly display as it is much more illustrative.

For help about the Ensembl browser use, please visit Ensembl help

Browse Copy Number Variable regions identified within the 270 HapMap samples

Hapmap CNVs WGTP_CNVs 500KEA_CNVs Redon_CNVs genome assembly NCBI35 NCBI36 browser UCSC Ensembl

( alternatively click here to browse a single sample in a browser )

• WGTP_CNVs - CNV identified using the WGTP array among all 270 HapMap samples
  
• 500KEA_CNVs - CNV identified using the Affymetrix 500k GeneChip Early Access arrays among all 270 HapMap samples
  
• Redon_CNVs - merged CNVs from both 500KEA and WGTP platforms for the 270 HapMap Samples
  

Please see FTP_README ( section V - CNVS PREDICTED using CNVfinder ) for additional details on the different datasets.

Back to WGTP Array data

Information on the CNV project and CNV data can be found at at the FAQ