Table 1 Counts of SNP variants by functional class, initial identified, before and after indel and MAF filtering
Functional class | Variant type | Initially identified | Before indel and MAF | After indels and MAF |
|---|---|---|---|---|
GWAS | GWAS | 1847 | 1248 | 1124 |
RNA-seq | eeQTL | 7229 | 5900 | 5328 |
aseQTL | 5625 | 4200 | 4154 | |
ieQTL | 1856 | 1600 | 903 | |
seQTL | 821 | 690 | 608 | |
Histone-related | asbQTL | 6937 | 5704 | 5682 |
ChIP-seq QTL | 6121 | 4940 | 4496 | |
ATAC-QTL | 12,303 | 10,368 | 9068 | |
| Â | Coding | 2515 | 1499 | 1389 |
RNA-seq | eeQTL + aseQTL + ieQTL + seQTL | 12,344 | 11,310 | 10,576 |
Histone-related | ATAC-QTL + absQTL + ChIP-seq QTL | 25,361 | 18,523 | 17,407 |
|  | eeQTL + GWAS | 9076 | 7111 | 6416 |
eeQTL + GWAS + asbQTL | 16,014 | 12,712 | 11,996 | |
eeQTL + GWAS + asbQTL + aseQTL | 21,638 | 16,658 | 15,932 | |
All | 43,319 | 34,927 | 32,595 |