How to interpret coloc.susie results with two different variants but has very high PP.H4.Prob?

[XiaoweiHu-Stat]

Hi, I used coloc.susie on gwas and eqtl with summary statistics. The results show that there are two different variants in one row with very high PP.H4.Probability (e.g., 0.99). I wonder how to interpret such result since H4: both traits are associated and share the same single causal variant.

Thank you. Xiaowei

[chr1swallace]

Are these variants in LD?

https://chr1swallace.github.io

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From: Hu999 @.> Sent: Friday, May 6, 2022 9:52:06 PM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] How to interpret coloc.susie results with two different variants but has very high PP.H4.Prob? (Issue #84)

Hi, I used coloc.susie on gwas and eqtl with summary statistics. The results show that there are two different variants in one row with very high PP.H4.Probability (e.g., 0.99). I wonder how to interpret such result since H4: both traits are associated and share the same single causal variant.

Thank you. Xiaowei

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchr1swallace%2Fcoloc%2Fissues%2F84&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C27ae84d8d3704727e94808da2fa24962%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637874671301014181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C5vnBX6HSMqHgN%2F2c4pRyTLsnXQ7DYNKodcCPylQDcw%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAQWR2BJCUJCXA25OLAHIRLVIWA7NANCNFSM5VJHDIFQ&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C27ae84d8d3704727e94808da2fa24962%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637874671301014181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FgvvgyYGkJx%2BCTfUat%2BlgzPmge4yaR2h3KORqtXSqLM%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[XiaoweiHu-Stat]

Hi Chris,

Thanks for your reply. Yes, in most cases, the two variants I found in such scenario are in high LD (e.g., genetic correlation R is 0.9).

Xiaowei

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From: Chris Wallace @.> Sent: Saturday, May 7, 2022 3:22 PM To: chr1swallace/coloc @.> Cc: Hu, Xiaowei (xh6dx) @.>; Author @.> Subject: Re: [chr1swallace/coloc] How to interpret coloc.susie results with two different variants but has very high PP.H4.Prob? (Issue #84)

Are these variants in LD?

https://chr1swallace.github.io

---

From: Hu999 @.> Sent: Friday, May 6, 2022 9:52:06 PM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] How to interpret coloc.susie results with two different variants but has very high PP.H4.Prob? (Issue #84)

Hi, I used coloc.susie on gwas and eqtl with summary statistics. The results show that there are two different variants in one row with very high PP.H4.Probability (e.g., 0.99). I wonder how to interpret such result since H4: both traits are associated and share the same single causal variant.

Thank you. Xiaowei

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchr1swallace%2Fcoloc%2Fissues%2F84&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C27ae84d8d3704727e94808da2fa24962%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637874671301014181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C5vnBX6HSMqHgN%2F2c4pRyTLsnXQ7DYNKodcCPylQDcw%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAQWR2BJCUJCXA25OLAHIRLVIWA7NANCNFSM5VJHDIFQ&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C27ae84d8d3704727e94808da2fa24962%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637874671301014181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FgvvgyYGkJx%2BCTfUat%2BlgzPmge4yaR2h3KORqtXSqLM%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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[chr1swallace]

then the result says that the two traits share a causal variant, but we are uncertain of what that variant is

On Mon, 2022-05-09 at 05:30 -0700, Hu999 wrote:

Hi Chris,

Thanks for your reply. Yes, in most cases, the two variants I found in such scenario are in high LD (e.g., genetic correlation R is 0.9).

Xiaowei

---

From: Chris Wallace @.> Sent: Saturday, May 7, 2022 3:22 PM To: chr1swallace/coloc @.> Cc: Hu, Xiaowei (xh6dx) @.>; Author @.> Subject: Re: [chr1swallace/coloc] How to interpret coloc.susie results with two different variants but has very high PP.H4.Prob? (Issue #84)

Are these variants in LD?

https://chr1swallace.github.io

---

From: Hu999 @.> Sent: Friday, May 6, 2022 9:52:06 PM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] How to interpret coloc.susie results with two different variants but has very high PP.H4.Prob? (Issue #84)

Hi, I used coloc.susie on gwas and eqtl with summary statistics. The results show that there are two different variants in one row with very high PP.H4.Probability (e.g., 0.99). I wonder how to interpret such result since H4: both traits are associated and share the same single causal variant.

Thank you. Xiaowei

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F% 2Fgithub.com%2Fchr1swallace%2Fcoloc%2Fissues%2F84&data=05%7C01%7Ccew5 4% 40universityofcambridgecloud.onmicrosoft.com%7C27ae84d8d3704727e94808 da 2fa24962%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637874671301014 18 1%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI 6I k1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C5vnBX6HSMqHgN%2F2c4pRyTL sn XQ7DYNKodcCPylQDcw%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3 A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe- auth%2FAAQWR2BJCUJCXA25OLAHIRLVIWA7NANCNFSM5VJHDIFQ&data=05%7C01%7Cce w5 4%40universityofcambridgecloud.onmicrosoft.com%7C27ae84d8d3704727e948 08 da2fa24962%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C6378746713010 14 181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBT iI 6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FgvvgyYGkJx%2BCTfUat% 2B lgzPmge4yaR2h3KORqtXSqLM%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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