<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi<br>
<br>
For <a class="moz-txt-link-freetext" href="http://feb2014.archive.ensembl.org">http://feb2014.archive.ensembl.org</a>, variants with phenotypes
with non-significant associations, are not shown on the website. <br>
<br>
The non-significant phenotype associations are available through
the Ensembl BioMart for this release.</p>
<p>In BioMart you can filter and display Phenotype significance [0
non significant, 1 significant]<br>
</p>
<p>For later releases we stopped using this filtering. <br>
<br>
If possible, using more recent data from a later release would be
beneficial. <br>
</p>
<p>Regards<br>
Helen<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 02/11/2020 13:05, Türküler Özgümüş
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20201102130623.A68D962A52F_FA0044FB@hh-mx3.ebi.ac.uk">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>I am using the below code to map some SNP IDs to the
following attributes. I have a problem with
phenotype_description. Some of the SNPs match phenotypes such
as BMI, fasting plasma glucose and fasting insulin whereas
there is no such information on the webpage for the same SNPs
on ensembl or gwas catalog (For example, rs546206 and
rs11877729). Is this a problem with the database? If it is not
where is this information coming from?</div>
<div><br>
</div>
<div>Thank you for your help.<br>
</div>
<div><br>
</div>
<div>Best,</div>
<div>Turkuler<br>
</div>
<div><span
style="color:rgb(230,225,220);font-family:"DejaVu
Sans","Lucida Grande","Segoe
UI",Verdana,Helvetica,sans-serif;font-size:11px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:nowrap;word-spacing:0px;background-color:rgb(22,22,22);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none"><span
style="color:rgb(230,225,220);font-family:"DejaVu
Sans","Lucida Grande","Segoe
UI",Verdana,Helvetica,sans-serif;font-size:11px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:nowrap;word-spacing:0px;background-color:rgb(22,22,22);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none"></span></span></div>
<div><br>
</div>
<div>-------------------------------------------------------------------------------------------------------------------</div>
<div><b>code:</b><br>
</div>
<div>snp_mart <- useMart("ENSEMBL_MART_SNP",
dataset="hsapiens_snp", host = "<a
href="http://feb2014.archive.ensembl.org" target="_blank"
moz-do-not-send="true">http://feb2014.archive.ensembl.org</a>")</div>
snp_ids <- df_FDR005$SNP<br>
snp_attributes <- c("refsnp_id", "chr_name", "chrom_start",
"clinical_significance", <br>
"associated_gene", "phenotype_description",
"ensembl_gene_stable_id",<br>
"ensembl_transcript_stable_id",
"consequence_type_tv",<br>
"polyphen_prediction", "polyphen_score",
"sift_prediction", "sift_score",<br>
"consequence_types_20126")<br>
snp_locations <- getBM(attributes=snp_attributes,
filters="snp_filter", <br>
<div> values=snp_ids, mart=snp_mart)</div>
<div><br>
</div>
<div><b>sessionInfo()</b><br>
R version 4.0.3 (2020-10-10)<br>
Platform: x86_64-apple-darwin17.0 (64-bit)<br>
Running under: macOS Catalina 10.15.7<br>
<br>
Matrix products: default<br>
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib<br>
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib<br>
<br>
locale:<br>
[1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8<br>
<br>
attached base packages:<br>
[1] stats graphics grDevices utils datasets methods
base <br>
<br>
other attached packages:<br>
[1] biomaRt_2.44.1 forcats_0.5.0 stringr_1.4.0
dplyr_1.0.1 purrr_0.3.4 readr_1.3.1 tidyr_1.1.1
<br>
[8] tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0<br>
<br>
loaded via a namespace (and not attached):<br>
[1] Biobase_2.48.0 httr_1.4.2 bit64_4.0.2
jsonlite_1.7.0 modelr_0.1.8 <br>
[6] assertthat_0.2.1 askpass_1.1 stats4_4.0.3
BiocFileCache_1.12.1 blob_1.2.1 <br>
[11] cellranger_1.1.0 yaml_2.2.1 progress_1.2.2
pillar_1.4.6 RSQLite_2.2.0 <br>
[16] backports_1.1.8 glue_1.4.1 digest_0.6.25
rvest_0.3.6 snakecase_0.11.0 <br>
[21] colorspace_1.4-1 htmltools_0.5.0 XML_3.99-0.5
pkgconfig_2.0.3 broom_0.7.0 <br>
[26] haven_2.3.1 scales_1.1.1 openssl_1.4.2
generics_0.0.2 IRanges_2.22.2 <br>
[31] ellipsis_0.3.1 withr_2.2.0 janitor_2.0.1
BiocGenerics_0.34.0 cli_2.0.2 <br>
[36] magrittr_1.5 crayon_1.3.4 readxl_1.3.1
memoise_1.1.0 evaluate_0.14 <br>
[41] fs_1.5.0 fansi_0.4.1 xml2_1.3.2
tools_4.0.3 prettyunits_1.1.1 <br>
[46] hms_0.5.3 lifecycle_0.2.0
S4Vectors_0.26.1 munsell_0.5.0 reprex_0.3.0
<br>
[51] AnnotationDbi_1.50.3 compiler_4.0.3 rlang_0.4.7
grid_4.0.3 rstudioapi_0.11 <br>
[56] rappdirs_0.3.1 rmarkdown_2.3 gtable_0.3.0
DBI_1.1.0 curl_4.3 <br>
[61] R6_2.4.1 lubridate_1.7.9 knitr_1.29
bit_4.0.4 utf8_1.1.4 <br>
[66] stringi_1.4.6 parallel_4.0.3 Rcpp_1.0.5
vctrs_0.3.2 dbplyr_1.4.4 <br>
[71] tidyselect_1.1.0 xfun_0.16 <br>
</div>
<div>-----------------------------------------------------------------------------------------------------------</div>
<div><br>
</div>
<div>Turkuler Ozgumus<br>
Postdoctoral researcher<br>
Department of Clinical Science (K2)<br>
University of Bergen<br>
Bergen, Norway</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">
</pre>
</body>
</html>