[Genome] Genome Browser Questions

[choi at cabm.rutgers.edu]

Dear colleague:

We are requesting help in attaining some bioinformatic information about
sequence surrounding two human SNPs, rs1861972, and rs1861973.  These SNPs
map to distal chromosome 7 in the intron of the ENGRAILED 2 (EN2) gene.

We have previously demonstrated that these 2 SNPs are significantly
associated with Autism Spectrum Disorder (Gharani et al. Mol Psychiatry.
2004 May;9(5):474-84, Benayed et al. Am J Hum Genet. 2005
Nov;77(5):851-68).

We are now preparing a manuscript that demonstrates these two SNPs are
functional, affecting the transcriptional regulation of EN2. A part of the
manuscript explores the evolutionary conservation of the area surrounding
these SNPs.

>From "17-Way Most Cons Track Settings" at genome.ucsc.edu, it is possible
to attain lod and score values for different portions of EN2 that are
evolutionarily conserved.  For example, there is one area of the intron
that is ~2kb 5’ of rs1861972 and rs1861973 that is highly conserved
between 11 mammalian species (chr7:154945604-154945685; score = 483;
lod=147).

We would like to attain similar values for the ~1.6kb chromosomal region
encompassing rs1861972 and rs1861973 (chr7:154945993-154947619).  Is this
possible?

Thank you for your time

Jiyeon Choi
Dr. Millonig lab, UMDNJ