# Conditional analysis results

This page has last been updated for R14.

### Conditional analysis algorithm

All regions with genome-wide significant results were subjected to Regenie conditional analysis (i.e. exactly the same regions that are also [finemapped](/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/finemapping-results-format.md)). The most significant variant is added as a covariate and all the other variants in the region are tested for association, conditionally on the top variant. This process is continued, adding new variants to the list of covariates, until there are no variants with conditional p-value < 1e-6. The same covariates were used as in the main FinnGen core GWAS analysis.

### Independent snps file

All independent top SNPs in the region tested. CHR\_POS\_REF\_ALT is the variant id for the most significant SNP in the region in unconditional analysis.

#### independent.snps file structure

| Column        | Description                                              |
| ------------- | -------------------------------------------------------- |
| VARIANT       | Top SNP of the iteration                                 |
| BETA          | unconditional beta of top SNP                            |
| SE            | unconditional standard error of top SNP                  |
| MLOG10P       | unconditional -log10 p-value of top SNP                  |
| BETA\_cond    | conditional beta of top SNP                              |
| SE\_cond      | conditional standard error of top SNP                    |
| MLOG10P\_cond | conditional -log10 p-value of top SNP                    |
| VARIANT\_cond | list of variants that were used as conditioning variants |

### Conditional file

Conditional results for all variants in each iteration in the above summary file. #ITER corresponds to each iteration in the independent snps file. CHR\_POS\_REF\_ALT is the variant id for the most significant SNP in the region in unconditional analysis.

#### conditional file structure

| Column  | Description                                                        |
| ------- | ------------------------------------------------------------------ |
| CHROM   | chromosome of tested variant                                       |
| GENPOS  | position of tested variant                                         |
| ID      | CHROM\_POS\_REF\_ALT of tested variant                             |
| ALLELE0 | Reference allele                                                   |
| ALLELE1 | Effect allele                                                      |
| A1FREQ  | Effect allele frequency                                            |
| INFO    | Imputation INFO score (IMPUTE method formula as output by REGENIE) |
| N       | sample size                                                        |
| TEST    | test performed                                                     |
| BETA    | condititional beta                                                 |
| SE      | conditional standard error                                         |
| CHISQ   | chisq statistic of association                                     |
| LOG10P  | -log10 p-value                                                     |
| EXTRA   | Additional notes by Regenie                                        |


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