SNPview: SNPs, SSLPs, Alleles and Haplotypes

Wiltshire T, Pletcher MT, Batalov S, Barnes W, Tarantino LM, Cooke MP, Wu H, Smylie K, Santrosyan A, Copeland NG, Jenkins NA, Kalush F, Mural RJ, Glynne RJ, Kay SA, Adams MD, and Fletcher CF. Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse ( Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6): 3380-5.)

The new 10,990 SNP collection page provides the supplementary materials for the article:

Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, Mural RJ, Paigen B, and Wiltshire T. Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS Biol. 2004 Nov 9; 2(12): e393.

The viewer allows comparing the distribution of the SNPs and SSLPs, alleles and derived haplotype blocks in different regions of the mouse genome. Several different views are available for each chromosome: a chromatogram-style view of validated SNPs, major and minor alleles, haplotypes, and combinations of the above. The data for the selected strains is displayed at the full chromosomes (or user-defined intervals), along with the interrogated SNP loci, the reference tracks of the EntrezGene loci, publicly available SSLP markers, and the subset of SSLP markers informative for the two selected strains. Additionally, Celera SNP density is displayed for chr.16 and three strains only. The choice of the Celera or Ensembl genomic coordinates is available.

Data deposition: The SNP data have been deposited in the dbSNP, www.ncbi.nlm.nih.gov/SNP/ (dbSNP ID nos. 6313904-6395786) and Mouse Genome Informatics database, www.jax.org/phenome/ ( ID no. MPD:133).

Select a genomic interval:
Select position: from to Mb or leave empty for a full chromosome
Select applet size: x Locus Zoom x
Dendrogram bootstrap x Missing data:
Window size for the statistics sheet:

Select
strains
for SNPs,
alleles:

additionally,
two or three strains
for SSLP/SNP
comparison:

to view the genomic
region with focus on

Major allele:

GNF SymAtlas
GNF Gene Expression Atlas
GFACT

Examples: dendrogram of strains based on all SNPs:

C57BL/6J
BALB/cByJ
C3H/HeJ
DBA/2J
A/J
129S1/SvImJ
CAST/Ei
SPRET/Ei
AKR/J
BUB/BnJ
C57BL/10J
C58/J
CBA/J
FVB/NJ
KK/HlJ
LG/J
LP/J
MOLF/Ei
NON/LtJ
NZB/BlNJ
RF/J
SJL/J
SM/J
SWR/J