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<p><font face="Arial">Dear all</font></p>
<p><br>
<font face="Arial">I was hoping you might be able to help me with
something to do with the incorporation of dbSNP 132 into ensembl</font></p>
<p><font face="Arial">I was looking at rs43469576 a few weeks ago
in dbSNP and I am 99% positive it said on the webpage in big red
letters that this snp mapped to 3 genome locations. I checked
what ensembl does about this and i have code showing how ensembl
too maps it to 3 genome locations<span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">
<ul style="margin: 16px 0px; padding: 0px 3em; font-size:
11px; line-height: 13pt; list-style-type: disc;">
<li style="font-size: 11px; line-height: 13pt; margin:
0px; padding: 0px;">chr7(65859978), chr7(91674598),
chr6(86134792)</li>
</ul>
Now when i look at dbSNP it says this variation isn't mapped
to any assembly. </span></span></font><font face="Arial"><span
class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: 'Times New Roman';
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">If i search dbsnp for one of those
genome locations (e.g. </span></span><span
class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: 'Times New Roman';
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">chr7(65859978)) rs43469576 </span></span>is
no longer in the results</font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;"></span></span></font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">Now i appreciate that I am a
fallible human being and could have got confused but it
looks to me as if dbSNP has changed and now doesn't seem to
show snps as mapping to multiple locations. </span></span>I
looked on their build release notes and schema revisions etc but
there is no mention of this. So perhaps i am mistaken. It often
happens :)</font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;"></span></span></font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">But regardless of whether i am
mistaken or not there still exists a difference between the
info in ensembl and dbsnp and I would like to know what to
expect from ensembl in the january release. Will i still see
a variation like </span></span>rs43469576 mapped to
multiple genome locations or will it be mapped to no assembly.<br>
</font></p>
<p><font face="Arial">Which then leads to the next question, what
will you get for a variation feature start/end/chromosome if it
isn't mapped. As i said at present ensembl seems to map the rs
entries in dbSNP that are unmapped so I've not come across it.<br>
</font></p>
<p><font face="Arial">thanks a lot<br>
</font></p>
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