# version 2025-12-12

Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries
Nat Genet. 2023 May;55(5):796-806. doi: 10.1038/s41588-023-01384-0.

This document details the changes in Supplementary Table 8 (ST8_v2) following an updated IBD EAS+EUR meta-analysis. 

The previous EAS+EUR meta-analysis used a strict filter that removed the IBD causal variant (chr16:50729867:G:GC)  from the NFE summary statistics. We removed this filter and re-ran the analysis.
Based on the new results, we updated the index variants table (ST8_v2).
Among the 250 FE-meta method loci, 
  7 loci had their index variants updated (these loci_ID are marked in blue in ST8_v2);
  1 locus (chr14:105686797:A:G) is no longer genome-wide significant, and its loci_ID is marked in gray. 
Among the 11 Mantra method loci, 
  1 locus (chr8:89784739:T:G) is now non-significant, and its loci_ID is also marked in gray.
The remaining 51 loci are unaffected.



# EAS fixed-effect meta-analysis summary statistics:
7,372 CD and 15,456 Control
ibd_EAS_SiKJ_meta_CD.TBL.txt.gz
6,862 UC and 15,456 Control
ibd_EAS_SiKJ_meta_UC.TBL.txt.gz
14,393 IBD and 15,456 Control
ibd_EAS_SiKJ_meta_IBD.TBL.txt.gz


# v2: The EAS+EUR meta-analysis was re-executed without the NFE variant filter.  
EAS&EUR fixed-effect meta-analysis summary statistics:
20,873 CD and 346,719 Control
ibd_EAS_EUR_SiKJEF_meta_CD.v2.TBL.txt.gz
23,252 UC and 352,256 Control
ibd_EAS_EUR_SiKJEF_meta_UC.v2.TBL.txt.gz
45,106 IBD and 353,562 Control
ibd_EAS_EUR_SiKJEF_meta_IBD.v2.TBL.txt.gz


Format:
MarkerName: variant (chr:pos:ref:alt) (GRCh38/hg38)
Allele1: reference allele
Allele2: effect allele
Effect: effect size
StdErr: standard error
P-value: P value
Direction: Direction of effect in each cohorts (order for EAS: SHA1, ICH1, KOR1, JPN1;
                                                order for EAS&EUR: SHA1, ICH1, KOR1, JPN1, NFE, FIN)
HetISq: heterogeneity statistic I-squared
HetChiSq: heterogeneity statistic Chi-squared
HetDf: degrees of freedom of heterogeneity test
HetPVal: P-value of heterogeneity test
CHR: chromosome (GRCh38/hg38)
BP: position of variant (GRCh38/hg38)

#### below only for EAS&EUR ####
BETA_EAS: effect size in East Asian
SE_EAS: standard error in East Asian
P_EAS: P-value in East Asian
BETA_NFE: effect size in non-Finnish Europeans
SE_NFE: standard error in non-Finnish Europeans
P_NFE: P-value in non-Finnish Europeans
BETA_FIN: effect size in Finnish
SE_FIN: standard error in Finnish
P_FIN: P-value in Finnish