[ensembl-dev] phenotype description for SNPs

[Türküler Özgümüş]

Hi,

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?

Thank you for your help.

Best,
Turkuler

-------------------------------------------------------------------------------------------------------------------
*code:*
snp_mart <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host = "
http://feb2014.archive.ensembl.org")
snp_ids <- df_FDR005$SNP
snp_attributes <- c("refsnp_id", "chr_name", "chrom_start",
"clinical_significance",
                    "associated_gene", "phenotype_description",
"ensembl_gene_stable_id",
                    "ensembl_transcript_stable_id", "consequence_type_tv",
                    "polyphen_prediction", "polyphen_score",
"sift_prediction", "sift_score",
                    "consequence_types_20126")
snp_locations <- getBM(attributes=snp_attributes, filters="snp_filter",
                      values=snp_ids, mart=snp_mart)

*sessionInfo()*
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [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
 [8] tibble_3.0.3    ggplot2_3.3.2   tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] Biobase_2.48.0       httr_1.4.2           bit64_4.0.2
 jsonlite_1.7.0       modelr_0.1.8
 [6] assertthat_0.2.1     askpass_1.1          stats4_4.0.3
BiocFileCache_1.12.1 blob_1.2.1
[11] cellranger_1.1.0     yaml_2.2.1           progress_1.2.2
pillar_1.4.6         RSQLite_2.2.0
[16] backports_1.1.8      glue_1.4.1           digest_0.6.25
 rvest_0.3.6          snakecase_0.11.0
[21] colorspace_1.4-1     htmltools_0.5.0      XML_3.99-0.5
pkgconfig_2.0.3      broom_0.7.0
[26] haven_2.3.1          scales_1.1.1         openssl_1.4.2
 generics_0.0.2       IRanges_2.22.2
[31] ellipsis_0.3.1       withr_2.2.0          janitor_2.0.1
 BiocGenerics_0.34.0  cli_2.0.2
[36] magrittr_1.5         crayon_1.3.4         readxl_1.3.1
memoise_1.1.0        evaluate_0.14
[41] fs_1.5.0             fansi_0.4.1          xml2_1.3.2
tools_4.0.3          prettyunits_1.1.1
[46] hms_0.5.3            lifecycle_0.2.0      S4Vectors_0.26.1
munsell_0.5.0        reprex_0.3.0
[51] AnnotationDbi_1.50.3 compiler_4.0.3       rlang_0.4.7
 grid_4.0.3           rstudioapi_0.11
[56] rappdirs_0.3.1       rmarkdown_2.3        gtable_0.3.0
DBI_1.1.0            curl_4.3
[61] R6_2.4.1             lubridate_1.7.9      knitr_1.29
bit_4.0.4            utf8_1.1.4
[66] stringi_1.4.6        parallel_4.0.3       Rcpp_1.0.5
vctrs_0.3.2          dbplyr_1.4.4
[71] tidyselect_1.1.0     xfun_0.16
-----------------------------------------------------------------------------------------------------------

Turkuler Ozgumus
Postdoctoral researcher
Department of Clinical Science (K2)
University of Bergen
Bergen, Norway
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