<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></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">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>