# Open Targets Genetics FAQs **URL:** https://community.opentargets.org/c/archive/ot-genetics-faqs/29.md [Latest](https://community.opentargets.org/latest.md) · [Categories](https://community.opentargets.org/categories.md) · [Tags](https://community.opentargets.org/tags.md) --- ## [About the Open Targets Genetics FAQs category](https://community.opentargets.org/t/about-the-open-targets-genetics-faqs-category/52)
**Author:** [@community\_manager](https://community.opentargets.org/u/community_manager)\ **Replies:** 0
FAQs specific to Open Targets Genetics. Note, this category is mainly intended for use by the Open Targets team. --- ## [What is the best way to query pheWAS traits for multiple variants?](https://community.opentargets.org/t/what-is-the-best-way-to-query-phewas-traits-for-multiple-variants/466)
**Author:** [@slifong08](https://community.opentargets.org/u/slifong08)\ **Replies:** 5\ **Last updated:** [10 August 2023 07:42 UTC](https://community.opentargets.org/t/what-is-the-best-way-to-query-phewas-traits-for-multiple-variants/466 "2023-08-10T07:42:51Z")
Hi Open Target Team, I’d like to query multiple genetic variants (100s) for pheWAS trait associations using UKBB, FinnGen, and GWAS catalog. Is it best to use an API approach or download the entire dataset from the Open… --- ## [Why does Open Targets Genetics display partial L2G scores on Locus pages when there is no evidence of colocalization?](https://community.opentargets.org/t/why-does-open-targets-genetics-display-partial-l2g-scores-on-locus-pages-when-there-is-no-evidence-of-colocalization/397)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [3 November 2021 12:08 UTC](https://community.opentargets.org/t/why-does-open-targets-genetics-display-partial-l2g-scores-on-locus-pages-when-there-is-no-evidence-of-colocalization/397 "2021-11-03T12:08:47Z")
The Open Targets Genetics “Locus” page shows which genes are prioritised by our Locus-to-Gene (L2G) scoring model. In this table, you can see the L2G score from the full model as well as “Partial L2G scores” from models … --- ## [Why are beta and odds ratios not always displayed in Open Targets Genetics?](https://community.opentargets.org/t/why-are-beta-and-odds-ratios-not-always-displayed-in-open-targets-genetics/330)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [26 August 2021 16:23 UTC](https://community.opentargets.org/t/why-are-beta-and-odds-ratios-not-always-displayed-in-open-targets-genetics/330 "2021-08-26T16:23:42Z")
Where available, we show confidence intervals for the beta or odds ratio estimates of variant associations. In some cases, we may not show a value for beta or odds ratio when the variant is palindromic (A vs T SNPs, or … --- ## [In the “tag variants” section of variant summary pages in Open Targets Genetics, why do some SNPs have a posterior probability and others don’t?](https://community.opentargets.org/t/in-the-tag-variants-section-of-variant-summary-pages-in-open-targets-genetics-why-do-some-snps-have-a-posterior-probability-and-others-don-t/322)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [23 August 2021 09:41 UTC](https://community.opentargets.org/t/in-the-tag-variants-section-of-variant-summary-pages-in-open-targets-genetics-why-do-some-snps-have-a-posterior-probability-and-others-don-t/322 "2021-08-23T09:41:30Z")
Only variants that are in a 95% credible set (and have an absolute probability \> 0.1%) have their posterior probability shown in this table. Tag variants for 1\_55055436\_G\_A (rs693668) (Open Targets Genetics) showin… --- ## [How can I download data from Open Targets Genetics?](https://community.opentargets.org/t/how-can-i-download-data-from-open-targets-genetics/290)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [4 August 2021 09:33 UTC](https://community.opentargets.org/t/how-can-i-download-data-from-open-targets-genetics/290 "2021-08-04T09:33:39Z")
The downloads that are available are described here: Data Download - Open Targets Genetics Documentation You can also find a step-by-step guide to the data downloads on our blog, in the third part of our Crash Course in… --- ## [How often is Open Targets Genetics updated?](https://community.opentargets.org/t/how-often-is-open-targets-genetics-updated/284)
**Author:** [@hcornu](https://community.opentargets.org/u/hcornu)\ **Replies:** 0\ **Last updated:** [29 July 2021 10:25 UTC](https://community.opentargets.org/t/how-often-is-open-targets-genetics-updated/284 "2021-07-29T10:25:05Z")
Open Targets Genetics does not currently have a fixed update schedule. However, in the future we aim to have more frequent updates, with at least two releases a year. Sign up for the Community, follow us on social media,… --- ## [In Open Targets Genetics, what is the “credible set overlap”?](https://community.opentargets.org/t/in-open-targets-genetics-what-is-the-credible-set-overlap/272)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [22 July 2021 17:37 UTC](https://community.opentargets.org/t/in-open-targets-genetics-what-is-the-credible-set-overlap/272 "2021-07-22T17:37:03Z")
The credible is the set of genetic variants, selected by fine-mapping analyses, that have 95% probability of containing the causal variant for a given genetic signal (if the assumptions of the model are correct). For st… --- ## [How to interpret Variant-to-Gene (V2G) and Locus-to-Gene (L2G) scores in Open Targets Genetics](https://community.opentargets.org/t/how-to-interpret-variant-to-gene-v2g-and-locus-to-gene-l2g-scores-in-open-targets-genetics/266)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [19 July 2021 09:51 UTC](https://community.opentargets.org/t/how-to-interpret-variant-to-gene-v2g-and-locus-to-gene-l2g-scores-in-open-targets-genetics/266 "2021-07-19T09:51:16Z")
The V2G score The V2G score is a disease-agnostic score that we developed early on to assign likely causal genes for any given variant in gnomAD v2.1. The score aggregates across a range of datasets that overlap with t… --- ## [What fine-mapping and colocalisation software does Open Targets Genetics use?](https://community.opentargets.org/t/what-fine-mapping-and-colocalisation-software-does-open-targets-genetics-use/259)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [14 July 2021 11:08 UTC](https://community.opentargets.org/t/what-fine-mapping-and-colocalisation-software-does-open-targets-genetics-use/259 "2021-07-14T11:08:16Z")
Until recently, we performed all fine-mapping, but only for studies with summary statistics and with primarily European ancestry, using an LD reference panel from 10,000 randomly sampled UK biobank individuals. We use G… --- ## [How are tag variants identified in Open Targets Genetics?](https://community.opentargets.org/t/how-are-tag-variants-identified-in-open-targets-genetics/258)
**Author:** [@JeremyS](https://community.opentargets.org/u/JeremyS)\ **Replies:** 0\ **Last updated:** [12 July 2021 09:24 UTC](https://community.opentargets.org/t/how-are-tag-variants-identified-in-open-targets-genetics/258 "2021-07-12T09:24:47Z")
In Open Targets Genetics, two methods are used to expand lead disease-associated variants into a more complete set of possibly causal tag variants, depending on whether or not a study has summary statistics: For studi… --- ## [How are UK Biobank study traits identified in Open Targets Genetics?](https://community.opentargets.org/t/how-are-uk-biobank-study-traits-identified-in-open-targets-genetics/252)
**Author:** [@hcornu](https://community.opentargets.org/u/hcornu)\ **Replies:** 0\ **Last updated:** [7 July 2021 13:02 UTC](https://community.opentargets.org/t/how-are-uk-biobank-study-traits-identified-in-open-targets-genetics/252 "2021-07-07T13:02:46Z")
An Open Targets Genetics user recently contacted the Open Targets helpdesk to ask: In the Open Targets Platform, NEALE2\_6152\_9 is given as “Hayfever, allergic rhinitis or eczema | blood clot, dvt, bronchitis, emphysema… --- ## [What do scores represent in downloaded tables of eQTL data for query variants](https://community.opentargets.org/t/what-do-scores-represent-in-downloaded-tables-of-eqtl-data-for-query-variants/911)
**Author:** [@paditabi](https://community.opentargets.org/u/paditabi)\ **Replies:** 1\ **Last updated:** [4 January 2023 17:40 UTC](https://community.opentargets.org/t/what-do-scores-represent-in-downloaded-tables-of-eqtl-data-for-query-variants/911 "2023-01-04T17:40:17Z")
I have downloaded tables of eQTL data for a number of query variants I am interested in from the Open Targets Genetics portal. However, I am not clear what the numbers/scores in the downloaded table represent. The scor… --- ## [Beta values in study colocalisation table of study locus page](https://community.opentargets.org/t/beta-values-in-study-colocalisation-table-of-study-locus-page/850)
**Author:** [@roman-hillje](https://community.opentargets.org/u/roman-hillje)\ **Replies:** 2\ **Last updated:** [17 November 2022 10:21 UTC](https://community.opentargets.org/t/beta-values-in-study-colocalisation-table-of-study-locus-page/850 "2022-11-17T10:21:50Z")
On the study locus page, study colocalisation results are shown as a table. For example, see the one below taken from study-locus/GCST002222/19\_44886339\_G\_A My question is about the beta values in the “Study beta” co… --- ## [Conserved regions variants](https://community.opentargets.org/t/conserved-regions-variants/707)
**Author:** [@Sophia\_2M](https://community.opentargets.org/u/Sophia_2M)\ **Replies:** 2\ **Last updated:** [27 July 2022 13:14 UTC](https://community.opentargets.org/t/conserved-regions-variants/707 "2022-07-27T13:14:19Z")
Hello! Apologies if this has an obvious answer; I am new here! Is there a way to find which of the variants in the database are in conserved regions? Basically, apart from the annotation of coding or intron variant, is … --- ## [Which version of GTEx does Open Targets Genetics use for colocalization analysis?](https://community.opentargets.org/t/which-version-of-gtex-does-open-targets-genetics-use-for-colocalization-analysis/491)
**Author:** [@SirTarget](https://community.opentargets.org/u/SirTarget)\ **Replies:** 1\ **Last updated:** [20 May 2022 20:36 UTC](https://community.opentargets.org/t/which-version-of-gtex-does-open-targets-genetics-use-for-colocalization-analysis/491 "2022-05-20T20:36:52Z")
Hello! I am a bit confused with the GTEx version used for the colocalization analyses. Your latest publication mentions v7, so do the data sources. But as for eQTL data on the Data Portal v8 is being shown, and there w… --- ## [How was LD clumping performed to select eQTLs for candidate gene?](https://community.opentargets.org/t/how-was-ld-clumping-performed-to-select-eqtls-for-candidate-gene/488)
**Author:** [@SirTarget](https://community.opentargets.org/u/SirTarget)\ **Replies:** 3\ **Last updated:** [11 May 2022 00:53 UTC](https://community.opentargets.org/t/how-was-ld-clumping-performed-to-select-eqtls-for-candidate-gene/488 "2022-05-11T00:53:37Z")
I am wondering How LD clumping was performed to select eQTLs for candidate gene in eQTL-based two-sample Mendelian Randomization? How to handle pleiotropy eQTL issue? for example, a SNP is eQTLs for candidate gene, but a… --- ## [Where to find eQTL information regarding a SNP in Open Targets Genetics?](https://community.opentargets.org/t/where-to-find-eqtl-information-regarding-a-snp-in-open-targets-genetics/514)
**Author:** [@Aaronchoi](https://community.opentargets.org/u/Aaronchoi)\ **Replies:** 1\ **Last updated:** [21 March 2022 09:49 UTC](https://community.opentargets.org/t/where-to-find-eqtl-information-regarding-a-snp-in-open-targets-genetics/514 "2022-03-21T09:49:56Z")
I am looking for the eQTL information of a SNP. To be specific, I searched for rs11983798, and the website showed that it was an eQTL of RINT1. I was looking for more detailed information, such as which tissue this eQTL … --- ## [Empty results pages](https://community.opentargets.org/t/empty-results-pages/477)
**Author:** [@matteofloris](https://community.opentargets.org/u/matteofloris)\ **Replies:** 6\ **Last updated:** [10 March 2022 11:37 UTC](https://community.opentargets.org/t/empty-results-pages/477 "2022-03-10T11:37:38Z")
Hi Community! Why are many studies having a completely empty results page? For example Open Targets Genetics --- ## [How are rsIDs mapped to unique variants in Open Targets Genetics?](https://community.opentargets.org/t/how-are-rsids-mapped-to-unique-variants-in-open-targets-genetics/460)
**Author:** [@SirTarget](https://community.opentargets.org/u/SirTarget)\ **Replies:** 1\ **Last updated:** [1 March 2022 10:48 UTC](https://community.opentargets.org/t/how-are-rsids-mapped-to-unique-variants-in-open-targets-genetics/460 "2022-03-01T10:48:44Z")
Hello! In the Genetics portal FAQs you mention, regarding mapping conflicts: Many multi-allelic sites can be assigned a single rsID, and some rsIDs can point to different positions in the genome. This means that rsID…