# Fine-Mapping Window Size

**URL:** https://isgw-forum.colorado.edu/t/fine-mapping-window-size/917
**Category:** Day 8
**Created:** [June 11, 2026, 10:50pm UTC](https://isgw-forum.colorado.edu/t/fine-mapping-window-size/917 "2026-06-11T22:50:46Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![anonymous](https://isgw-forum.colorado.edu/letter_avatar_proxy/v4/letter/a/8491ac/32.png) [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)
#### Post date: [June 11, 2026, 10:50pm UTC](https://isgw-forum.colorado.edu/t/fine-mapping-window-size/917/1 "2026-06-11T22:50:46Z")

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In the prerecorded videos Ran suggested using a 3MB window around the lead variant, but I’ve also seen pipelines use 1Mb or even 500kb. How should we think about what window size is best to use?

> Replying to “In the prerecorded videos Ran suggested using a 3M…”:

The bigger the region the more computationally expensive the fine-mapping becomes but the more likely you are to capture the true causal variant

> Replying to “In the prerecorded videos Ran suggested using a 3M…”:

Great question, there are some limited investigations into how to set the regions. Looking at the LD is a good way to do it. You don’t want to leave out variants in non-trivial LD with the lead variant. In some regions, if the LD is low, you can use a smaller window, but some regions have extensive LD, you may have to use a big region. Usually computational constraint is the determining factor, secondarily, I usually wouldn’t use 3Mb if I run ABF because ABF has the single-causal-variant assumption, which only picks up 1 causal variant in the region. If the region is big, it may contain multiple causal variants that ABF will miss.

> Replying to “In the prerecorded videos Ran suggested using a 3M…”:

Thank you that’s very helpful!