**Description of the CEPH files**

The files are named as follows:

Gene(s) \_ File set \_File type\_ Reference date

**Genes**: Usually a single gene symbol. Occasionally, two gene symbols
when two genes are in close proximity in the same chromosomal region
(e.g. HSD3B1-HSD3B2).

**File set**:

Two file sets are provided:

[- CEPH set]{.underline}

The CEPH file set contains information on SNPs that were observed in the
SNP discovery phase of BPC3. The corresponding SNPs were typed on more
than 80 CEPH trios and an additional 100 unrelated European CEPH
individuals. The files are based exclusively on data generated at CEPH.
The SNP locations were derived from NCBI build 36, the latest build
available at the time the files were generated. These files provide
reliable linkage disequilibrium values and are relevant for the
monitoring of the critical regions explored in the SNP discovery phase:
the exons and 5' promoter region.

[- HapMap set]{.underline}

The HapMap file set is based on information combining genotypes
generated at CEPH and genotypes downloaded from the HapMap consortium
FTP site. For each gene/region, the number of SNPs is larger than in the
CEPH set. The genotypes of the SNPs that were considered for the TagSNP
selection were generated on a small population, usually 25 CEPH trios.
These 25 trios are included in the 80 CEPH trios used for the CEPH file
set. The SNP positions, downloaded from the HapMap website, correspond
to NCBI build 35. These files are relevant for the monitoring of the
large intronic regions and the 20Kb upstream and 10 Kb downstream
regions of each gene.

**File type:**

There are six different File-types. On rare occasions, the data was too
large to be accommodated into a single file, so the files were split
into two or three files. In these cases the position of the first and
last SNP contained in a split file is indicated.

[- Marker]{.underline}:

These files contain 11 columns and correspond to an output of Haploview.

> Column 1: SNP position
>
> Column 2: rs number
>
> Column 3: coordinate in build 35 or 36
>
> Column 4: observed heterozygozity
>
> Column 5: expected heterozygozity under the expectation of
> Hardy-Weinberg equilibrium
>
> Column 6: p-value for Hardy-Weinberg equilibrium
>
> Column 7: call rate for the SNP in the population considered
>
> Column 8: number of informative CEPH trios
>
> Column 9: number of observed Mendelian errors
>
> Column 10: minor allele frequency
>
> Column 11: minor allele
>
> Column 12: Rating. A SNP is qualified BAD if:

-   not polymorphic

-   has a call rate lower than 75%

-   has a p value for Hardy-Weinberg proportion \< 10^-3^

-   has more than one Mendelian errors

[- Dprime:]{.underline}

Haploview plot for the linkage disequilibrium parameter D\'. The
coordinates are either in build 35 (HapMap set) or in build 36 (CEPH
set). The SNPs included in the BPC3 OPA are in green. Only SNPs with MAF
\> 0.05 are considered.

[- DprimeB]{.underline}

Same as Dprime with, in addition, the position of the haplotypes shown
in the Haplo file

[- Haplo]{.underline}

Representation of the Haplotypes defined by the four-gamete rule and
having a frequency greater than 1%.

[- Rsquared]{.underline}

Haploview plot for the linkage disequilibrium parameter r^2^. The
coordinates are in either build 35 (HapMap set) or build 36 (CEPH set).
The SNPs included in the BPC3 OPA are in green. Only SNPs with MAF\>
0.05 are considered

[- TagPair]{.underline}

These files provide for all SNPs of the Marker file with MAF\> 0.05 and
not qualified as \"BAD\", the highest pairwise r^2^ marker that can be
found with a SNP typed in the BPC3 OPA. No information is provided if
this value is lower than 0.8. The number preceding \"TagPair\" in the
filename is the number of Tag SNPs used to generate the file.

[- TagAgg]{.underline}

These files provide for all SNPs of the Marker file with MAF\> 0.05 and
not qualified as \"BAD\". The highest determination coefficient, which
is obtained by the use of one or two SNPs from the BPC3 OPA, is
indicated. No information is provided if this value is lower than 0.8.
The number preceding \"TagAgg\" in the filename is the number of Tag
SNPs used to generate the file

**Reference date:**

Date the file was created.

**Notes:**

-   For the HapMap set of data of HSD3B1_HSD3B2, the aggressive tagging
    option of the Tagger program failed to run with the specified number
    of Tag-SNPs.

-   For GHR: The D' and R2 files were divided into two parts

-   (markers 1 to 250 and markers 150 to 404). A compressed image is
    provided showing the entire region

-   For the HapMap set of data of HSD17B4, the aggressive tagging option
    of the Tagger program failed to run with the specified number of
    Tag-SNPs.

-   For IGFR1: The D' and R2 files were divided into three parts
    (markers 1 to 250, markers 150 to 400 and markers 250 to 510). A
    compressed image is provided showing the entire region.

-   For any of the PNG files, you might need to open the file in a
    graphic software program to zoom in on the details.