# Archive **URL:** https://community.opentargets.org/c/archive/40.md [Latest](https://community.opentargets.org/latest.md) · [Categories](https://community.opentargets.org/categories.md) · [Tags](https://community.opentargets.org/tags.md) --- ## [About the Archive category](https://community.opentargets.org/t/about-the-archive-category/1844)
**Author:** [@hcornu](https://community.opentargets.org/u/hcornu)\ **Replies:** 0\ **Last updated:** [30 June 2025 14:15 UTC](https://community.opentargets.org/t/about-the-archive-category/1844 "2025-06-30T14:15:51Z")
Archived posts and categories from the Open Targets Community. --- ## [BigQuery data genetics credset table identifiers](https://community.opentargets.org/t/bigquery-data-genetics-credset-table-identifiers/1876)
**Author:** [@Estefania\_Rojas](https://community.opentargets.org/u/Estefania_Rojas)\ **Replies:** 2\ **Last updated:** [30 July 2025 21:04 UTC](https://community.opentargets.org/t/bigquery-data-genetics-credset-table-identifiers/1876 "2025-07-30T21:04:46Z")
Hi there, I have a query regarding the Google BigQuery-public-data.open\_targets\_genetics. In the tab of variant\_disease\_credset table, I am not sure how to identify each credible set as there is not a unique identifier… --- ## [Do you plan to integrate TWAS into Open Targets Genetics?](https://community.opentargets.org/t/do-you-plan-to-integrate-twas-into-open-targets-genetics/642)
**Author:** [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\ **Replies:** 3\ **Last updated:** [7 November 2023 23:27 UTC](https://community.opentargets.org/t/do-you-plan-to-integrate-twas-into-open-targets-genetics/642 "2023-11-07T23:27:01Z")
Dear Opentargets team, I am wondering is there any roadmap to integrate TWAS workflow to opentargets platform? Thanks. Shicheng --- ## [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… --- ## [Open Targets Genetics should support chrX variants](https://community.opentargets.org/t/open-targets-genetics-should-support-chrx-variants/1058)
**Author:** [@jschwart37](https://community.opentargets.org/u/jschwart37)\ **Replies:** 0\ **Last updated:** [26 April 2023 14:05 UTC](https://community.opentargets.org/t/open-targets-genetics-should-support-chrx-variants/1058 "2023-04-26T14:05:36Z")
As a user of the Open Targets Genetics, I would like to see associations for variants on the X chromosome. Use case: We were investigating a variant (Open Targets Genetics) which is associated with SLE in a GWAS (GWAS … --- ## [Implement zooming in PheWAS plot](https://community.opentargets.org/t/implement-zooming-in-phewas-plot/1059)
**Author:** [@jschwart37](https://community.opentargets.org/u/jschwart37)\ **Replies:** 0\ **Last updated:** [26 April 2023 14:28 UTC](https://community.opentargets.org/t/implement-zooming-in-phewas-plot/1059 "2023-04-26T14:28:10Z")
In many cases, Open Targets Genetics reports one association for a variant that is vastly stronger than the others. As a result, this one dominates the scale of the plot, and it is difficult to see whether other associat… --- ## [Metadata for columns in bigQuery database?](https://community.opentargets.org/t/metadata-for-columns-in-bigquery-database/1052)
**Author:** [@bycgen](https://community.opentargets.org/u/bycgen)\ **Replies:** 2\ **Last updated:** [17 April 2023 18:07 UTC](https://community.opentargets.org/t/metadata-for-columns-in-bigquery-database/1052 "2023-04-17T18:07:02Z")
Hi there, I am wondering if there is documentation somewhere explaining the columns in the tables in the bigQuery database? Currently curious about the meaning of the column ‘is\_cc’ in the sa\_gwas table, but would be … --- ## [Is Open Targets Genetics considering integrating Mendelian gene enrichment as a feature for GWAS locus prioritisation?](https://community.opentargets.org/t/is-open-targets-genetics-considering-integrating-mendelian-gene-enrichment-as-a-feature-for-gwas-locus-prioritisation/619)
**Author:** [@hcornu](https://community.opentargets.org/u/hcornu)\ **Replies:** 0\ **Last updated:** [23 May 2022 17:05 UTC](https://community.opentargets.org/t/is-open-targets-genetics-considering-integrating-mendelian-gene-enrichment-as-a-feature-for-gwas-locus-prioritisation/619 "2022-05-23T17:05:00Z")
A recent discussion in our GitHub issue tracker was centred around adding Mendelian gene enrichment as a feature of GWAS locus prioritisation in Open Targets Genetics (see issue #2103). We thought the ideas shared might… --- ## [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… --- ## [Can we have data as flat files instead of JSON?](https://community.opentargets.org/t/can-we-have-data-as-flat-files-instead-of-json/540)
**Author:** [@zx8754](https://community.opentargets.org/u/zx8754)\ **Replies:** 4\ **Last updated:** [8 May 2022 18:41 UTC](https://community.opentargets.org/t/can-we-have-data-as-flat-files-instead-of-json/540 "2022-05-08T18:41:02Z")
According to data access docs, data is available at EBI FTP and GoogleCloud as multiple JSON files. Is there anyway we can have them as flat text files - CSV, TSV? --- ## [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… --- ## [API request for associations with gene](https://community.opentargets.org/t/api-request-for-associations-with-gene/815)
**Author:** [@simbaum](https://community.opentargets.org/u/simbaum)\ **Replies:** 4\ **Last updated:** [26 October 2022 12:57 UTC](https://community.opentargets.org/t/api-request-for-associations-with-gene/815 "2022-10-26T12:57:12Z")
Dear team and community, I would like to receive the genetic associations and scores from opentargets over the API. Some time ago I had this script: import requests import json import pandas as pd def associated\_stu… --- ## [Susztaklab Human Kidney eQTL Atlas](https://community.opentargets.org/t/susztaklab-human-kidney-eqtl-atlas/609)
**Author:** [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\ **Replies:** 3\ **Last updated:** [4 October 2022 02:15 UTC](https://community.opentargets.org/t/susztaklab-human-kidney-eqtl-atlas/609 "2022-10-04T02:15:58Z")
I’d like to share a kidney eQTL data. This table provides 1,179,179 significant SNP~gene pairs identified by a false discovery rate (FDR) threshold of \<0.01 (Storey’s q method) after meta-analysis of four eQTL studies (S… --- ## [Defined schema for v2g and variant-index data](https://community.opentargets.org/t/defined-schema-for-v2g-and-variant-index-data/723)
**Author:** [@K\_J\_Finnegan](https://community.opentargets.org/u/K_J_Finnegan)\ **Replies:** 2\ **Last updated:** [5 August 2022 14:20 UTC](https://community.opentargets.org/t/defined-schema-for-v2g-and-variant-index-data/723 "2022-08-05T14:20:08Z")
Afternoon, I’m working on the v2g and variant-index data. I’m just wondering if the schemas for these datasets are available for me to query programmatically. I’ve found a link here that links to a GitHub file for the v… --- ## [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 … --- ## [Integrating Genome-wide Causal Study (GWCS) vs Genome-wide Association Study (GWAS)?](https://community.opentargets.org/t/integrating-genome-wide-causal-study-gwcs-vs-genome-wide-association-study-gwas/645)
**Author:** [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\ **Replies:** 1\ **Last updated:** [20 June 2022 12:46 UTC](https://community.opentargets.org/t/integrating-genome-wide-causal-study-gwcs-vs-genome-wide-association-study-gwas/645 "2022-06-20T12:46:22Z")
Dear Team, I am wondering whether OT team could have an internal discussion on GWCA jiaorong007/Bivariate-Causal-Discovery: Genome-wide Causal Study (GWCS) (github.com) Thanks. Shicheng --- ## [Roadmap to compatible to T2T-CHM13](https://community.opentargets.org/t/roadmap-to-compatible-to-t2t-chm13/638)
**Author:** [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\ **Replies:** 1\ **Last updated:** [1 June 2022 15:07 UTC](https://community.opentargets.org/t/roadmap-to-compatible-to-t2t-chm13/638 "2022-06-01T15:07:16Z")
Dear OT team, I am curious about the roadmap of OpenTargets to compatible to T2T-CHM13? Thanks. Shicheng --- ## [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… --- ## [Are you considering implementing two-sample MR?](https://community.opentargets.org/t/are-you-considering-implementing-two-sample-mr/564)
**Author:** [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\ **Replies:** 1\ **Last updated:** [20 May 2022 11:52 UTC](https://community.opentargets.org/t/are-you-considering-implementing-two-sample-mr/564 "2022-05-20T11:52:22Z")
Dear Team, I am wondering why Mendelian Randomization (two-sample MR) is not implemented in Open Targets platform which will be very helpful for target identification and validation. Thanks. Shicheng --- ## [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… [Next page](https://community.opentargets.org/c/archive/40.md?page=1)