Welcome to the CEPH Genotype database

All genotypes contributed to the CEPH database are available on the anonymous FTP server.
V10.0 genotypes, marker descriptions and pairwise lod scores may be downloaded from the FTP server. In addition, the server contains databases for published CEPH consortium maps and for recombinant breakpoint maps.

In order to submit data, please contact


The Foundation Jean Dausset-Centre d'Etude du Polymorphisme Humain (CEPH) maintains a database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping (Genomics 6: 575-577, 1990; Science 265: 2049-2054, 1994).

The present version of the database (V10.0 - November 2004) contains genotypes for 32,356 genetic markers. These include data for a total of 21,480 bi-allelic markers, of which 17,512 may be assigned to dbSNP by rs or ss numbers. V10 also contains more than 9,900 microsatellite markers (often identified by AFM%, afm%, Mfd%, GATA%, GGAA%, and GGAT%, in the Probe field of the V10 chromosome files). The mean observed heterozygote frequency of all the loci in V10.0 is 0.438, and for identifiable microsatellite loci 0.698, of which 56% are highly polymorphic (obs.het. ≥ 0.70). The CEPH database now manages 6,081,570 genotypes.

Reference family-based genotypes for dbSNP clusters were sent to CEPH from The SNP Consortium (TSC) database by Drs. G. A. Thorisson and L. D. Stein. Markers known to be included in dbSNP are identified in V10 chromosome files by ss numbers or by typing TSC%, and WIAF% in the Probe field and by rs or ss numbers in the Entrez link field. A subset of the genotypes for 2821 of these SNPs were used to construct the CEPH family-based SNP linkage map of the human genome by Matisse et al. (Am J Hum Genetics 73:271-284, 2003).

We have computed 25,924,717 lod scores between all pairs of syntenic marker loci on each pair of segregating chromosomes. Of the 32,356 markers in V10, only 333 (all reported as SNPs) could not be localized by linkage to other mapped markers in the database (lod score ≥ 3.0). These unlocalized markers may be reviewed in the Chr. 0 file with the CEPH database browser, available on this web page, by taking the search option. The column entitled NCBI Entrez link permits linking a chosen marker to the NCBI Entrez home page where clicking on the SNP option allows entry into the current build of dbSNP that provides a summary of genome information for SNP markers including their chromosome assignments and their positions in the chromosome sequence. All of the markers in the Chr 0 file are potential SNPs, most of these each show a single unique chromosome assignment, and some are validated with allele and genotype frequency information. These markers will be assigned to the appropriate chromosome file in the next version of the CEPH genotype database. Other markers, estimated to account for less than 20% of SNPs in the Chr. 0 file, show several chromosome assignments.

CEPH collaborators and others who have genotyped CEPH families can submit data for markers directly by interacting with the CEPH WEB server (see Marker Submission or SNP submission). Marker submissions require a submitter password, available on request. File submission is also available after consultation with CEPH (please, see contact addresses below).


Your requests, suggestions for improvements and corrections are welcome. Send mail to:


For more information, please contact the
Last update : 2008-07-22