# Using AlphaGenome to predict the cooperativity of multiple SNPs?

**URL:** <https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530>\
**Category:** Community\
**Created:** [July 28, 2025, 5:04am UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530 "2025-07-28T05:04:28Z")\
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**Author:** ![Jingyu\_Zeng](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/jingyu_zeng/32/418_2.png) [@Jingyu\_Zeng](https://www.alphagenomecommunity.com/u/Jingyu_Zeng)\
**Post date:** [July 28, 2025, 12:10pm UTC](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530/2 "2025-07-28T12:10:36Z")

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I have an idea, maybe try it?

Since there’s no restriction on variant length, you can try input a variant like this:  
Chromosome: chr1 (or others)  
Position: 12345…  
ref: ACT **G** CGAT **T** ACG (can be longer)  
alt: ACT **A** CGAT **T** ACG

This case showed a two-SNP situation, and you can add more as you wish.

There are two problems: 1. You have to find the sequence on the reference genome in this region. Use `samtools faidx hg38.fa chr1:123-456` can do this.  
2. The cover region of this variant can be so long, I’m not sure if the result will be weird. And the visualization can be hard too.

In my test cases, I tried a 50kb deletion, and still got a result. So it will work, but the result is not known. You can share the result with us!

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