Table 5. Mutation analyses on promoters of TF targets.
| TF | Target | Normal cluster | Normal binding site § | SNP ID § | Variant binding site § | Variant
cluster ‡ |
Classifier
output |
||
|---|---|---|---|---|---|---|---|---|---|
| Variant † | Wild-
type |
||||||||
| EGR1
( R sequence = 12.2899 bits) |
EID2B | Cluster 1
of 2 |
GA
GGGGGC
ATC
(chr19:39540296, -, 7.22 bits) |
rs538610162
(chr19:39540296C>G) |
CAGGGGGCATC
(chr19:39540286, -, 4.84 bits) |
Abolished | √ | × | √ |
| rs759233998
(chr19:39540294C>T) |
GA
AGGGGCATC
(chr19:39540286, -, 0.06 bit) |
Abolished | √ | ||||||
| rs974735901
(chr19:39540288T>A) |
GAGGGGGC
TTC
(chr19:39540286, -, 6.90 bits) |
Cluster 1
of 2 |
√ | ||||||
| rs978230260
(chr19:39540287A>T) |
GAGGGGGCA
AC
(chr19:39540286, -, 5.31 bits) |
Abolished | √ | ||||||
| Cluster 2
of 2 |
GCGTGCGT
GGG
(chr19:39540162, +, 1.59 bits) |
rs764734511
(chr19:39540162G>A) (chr19:39540162G>C) |
ACGTGCGTGGG
(chr19:39540162, +, -0.72 bit) |
Cluster 2
of 2 |
√ | ||||
|
CCGTGCGTGGG
(chr19:39540162, +, -0.79 bit) |
Cluster 2
of 2 |
√ | |||||||
| rs996639427
(chr19:39540170G>C) |
GCGTGCGT
CGG
(chr19:39540162, +, -5.21 bits) |
Abolished | √ | ||||||
| GCGT
GGGC
GC
T
(chr19:39540166, +, 9.72 bits) |
GCGT
CGGCGCT
(chr19:39540165, +, -0.85 bit) |
||||||||
| rs1027751538
(chr19:39540174G>A) |
GCGTGGGC
ACT
(chr19:39540166, +, 5.16 bits) |
Abolished | √ | ||||||
|
rs887888062
(chr19:39540176T>A) |
GCGTGGGCGC
A
(chr19:39540166, +, 10.94 bits) |
Cluster 2
of 2 |
√ | ||||||
| ELF1
( R sequence = 11.2057 bits) |
HIST1H4H | Cluster 1
of 2 |
GC
GGAAG
CGTG
(chr6:26286540, +, 9.92 bits) |
rs760968937
(chr6:26286547C>T) (chr6:26286547C>A) |
GCGGAAG
TGTG
(chr6:26286540, +, 10.71 bits) |
Cluster 1
of 2 |
√ | √ | √ |
| GCGGAAG
AGTG
(chr6:26286540, +, 8.84 bits) |
Cluster 1
of 2 |
√ | × | ||||||
| rs1000196206
(chr6:26286542G>C) |
GC
CGAAGCGTG
(chr6:26286540, +, -6.26 bits) |
Abolished | √ | ||||||
| rs144759258
(chr6:26286543G>A) |
GCG
AAAGCGTG
(chr6:26286540, +, -3.60 bits) |
Abolished | √ | ||||||
| rs966435996
(chr6:26286544A>G) |
GCGG
GAGCGTG
(chr6:26286540, +, 5.28 bits) |
Abolished | √ | ||||||
| rs950986427
(chr6:26286548G>A) |
GCGGAAGC
ATG
(chr6:26286540, +, 8.28 bits) |
Cluster 1
of 2 |
√ | ||||||
| Cluster 2
of 2 |
CAG
GAGATGC
G
(chr6:26286483, -, 6.98 bits) |
rs373649904
(chr6:26286483G>A) |
TAGGAGATGCG
(chr6:26286473, -, 0.61 bit) |
Abolished | √ | ||||
| rs926919149
(chr6:26286480C>T) |
CAG
AAGATGCG
(chr6:26286473, -, -6.53 bits) |
Abolished | √ | ||||||
| rs751263172
(chr6:26286479T>G) |
CAGG
CGATGCG
(chr6:26286473, -, 1.24 bits) |
Abolished | √ | ||||||
| rs369076253
(chr6:26286473C>G) |
CAGGAGATGC
C
(chr6:26286473, -, 6.92 bits) |
Cluster 2
of 2 |
√ | ||||||
|
rs751263172
(chr6:1044474314C>T) |
CAGGA
A
ATGCG
(chr6:26286473, -, 11.43 bits) |
Cluster 2
of 2 |
√ | √ | |||||
| ELK1
( R sequence = 11.9041 bits) |
G0S2 | Cluster 1
of 2 |
C
AGGGAAG
ACC
(chr1:209667969, -, 1.92 bits) |
rs146048477
(chr1:209667961T>A) |
CAGGGAAG
TCC
(chr1:209667959, -, 2.24 bits) |
Cluster 1
of 2 |
√ | √ | √ |
| rs887606802
(chr1:209667968T>C) |
C
GGGGAAGACC
(chr1:209667959, -, -3.35 bits) |
Cluster 1
of 2 |
√ | × | |||||
| rs1021034916
(chr1:209667967C>T) |
CA
AGGAAGACC
(chr1:209667959, -, -3.57 bits) |
Cluster 1
of 2 |
√ | ||||||
| GAGGA
AATGAG
(chr1:209667969, +, 8.14 bits) |
rs941962117
(chr1:209667974A>G) |
GAGGA
GATGAG
(chr1:209667969, +, 4.11 bits) |
Abolished | √ | |||||
| Cluster 2
of 2 |
CTGGAAGA
GCA
(chr1:209673554, -, 5.91 bits) |
rs896117033
(chr1:209673545G>A) |
CTGGAAGAG
TA
(chr1:209673544, -, 3.95 bits) |
Cluster 2
of 2 |
√ | ||||
| rs971962577
(chr1:209673546C>T) |
CTGGAAGA
ACA
(chr1:209673544, -, 3.49 bits) |
Cluster 2
of 2 |
√ | ||||||
| rs1011969709
(chr1:209673554G>C) |
GTGGAAGAGCA
(chr1:209673544, -, 3.92 bits) |
Abolished | √ | ||||||
| CCA
GAAGTCA
A
(chr1:209673551, +, 7.44 bits) |
CCA
CAAGTCAA
(chr1:209673551, +, -5.50 bits) |
||||||||
|
rs1023312090
(chr1:209673561A>G) |
CCAGAAGTCA
G
(chr1:209673551, +, 8.40 bits) |
Cluster 2
of 2 |
√ | √ | |||||
| ETS1
( R sequence = 10.0788 bits) |
TTC19 | Cluster 1
of 1 |
GCA
GGGAA
AGG
(chr17:16022293, +, 7.92 bits) |
rs1022234223
(chr17:16022296G>C) |
GCA
CGGAAAGG
(chr17:16022293, +, -4.98 bits) |
Abolished | × | × | √ |
|
rs968299415
(chr17:16022301A>T) |
GCAGGGAA
TGG
(chr17:16022293, +, 10.01 bits) |
Cluster 1
of 1 |
√ | √ | |||||
| GABPA
( R sequence = 10.8567 bits) |
PLEKHB2 | Cluster 1
of 1 |
A
CA
GGAAAGGG
(chr2:131112770, +, 10.36 bits) |
rs997328042
(chr2:131112771C>T) |
A
TAGGAAAGGG
(chr2:131112770, +, -3.68 bits) |
Abolished | × | × | √ |
| rs1020720126
(chr2:131112773G>C) |
ACA
CGAAAGGG
(chr2:131112770, +, -4.16 bits) |
Abolished | × | ||||||
| T
CTGGAAAC
TA
(chr2:131112760, +, 1.53 bits) |
rs185306857
(chr2:131112761C>A) |
T
ATGGAAACTA
(chr2:131112760, +, -2.86 bits) |
Cluster 1
of 1 |
√ | |||||
|
rs772728699
(chr2:131112762T>A) |
TC
AGGAAACTA
(chr2:131112760, +, 5.23 bits) |
Cluster 1
of 1 |
√ | ||||||
|
rs965753671
(chr2:131112769T>C) |
TCTGGAAAC
CA
(chr2:131112760, +, 2.13 bits) |
Cluster 1
of 1 |
√ | ||||||
| IRF1
( R sequence = 13.5544 bits) |
SMIM13 | Cluster 1
of 1 |
GAG
AA
TGAA
AGC
A
(chr6:11093663, +, 12.56 bits) |
rs950528541
(chr6:11093663G>C) |
CAGAATGAAAGCA
(chr6:11093663, +, 8.97 bits) |
Cluster 1
of 1 |
√ | × | √ |
| rs886259573
(chr6:11093664A>G) |
G
GGAATGAAAGCA
(chr6:11093663, +, 9.65 bits) |
Cluster 1
of 1 |
√ | ||||||
| rs982931728
(chr6:11093666A>G) |
GAG
GATGAAAGCA
(chr6:11093663, +, 8.09 bits) |
Cluster 1
of 1 |
√ | ||||||
| rs1020218811
(chr6:11093668T>G) |
GAGAA
GGAAAGCA
(chr6:11093663, +, 9.36 bits) |
Cluster 1
of 1 |
√ | ||||||
| rs570723026
(chr6:11093672A>G) |
GAGAATGAA
GGCA
(chr6:11093663, +, 8.01 bits) |
Cluster 1
of 1 |
√ | ||||||
| rs1004825794
(chr6:11093675A>C) (chr6:11093675A>T) |
GAGAATGAAAGC
C
(chr6:11093663, +, 10.47 bits) |
Cluster 1
of 1 |
√ | ||||||
| GAGAATGAAAGC
A
(chr6:11093663, +, 10.42 bits) |
Cluster 1
of 1 |
√ | |||||||
| AA
GACCAA
AGGCA
(chr6:11093641, +, 2.43 bits) |
rs1030185383
(chr6:11093649A>C) |
AAGACCAA
CGGCA
(chr6:11093641, +, -3.39 bits) |
Cluster 1
of 1 |
√ | |||||
| rs5874306
(chr6:11093650delG) |
AAGACCAAAGCAG
(chr6:11093641, +, 0.90 bit) |
Cluster 1
of 1 |
√ | ||||||
|
rs558896490
(chr6:11093643G>A) |
AA
AACCAAAGGCA
(chr6:11093641, +, 7.06 bits) |
Cluster 1
of 1 |
√ | √ | |||||
| YY1
( R sequence = 12.8554 bits) |
CKLF | Cluster 1 of 1 |
GC
GGC
CATCGGC
(chr16:66549797, -, 10.06 bits) |
rs865922947
(chr16:66549791G>A) |
CCGGCCATCGGC
(chr16:66549785, -, 6.80 bits) |
Cluster 1 | √ | × | √ |
| rs946037930
(chr16:66549794C>A) |
GC
TGCCATCGGC
(chr16:66549785, -, 8.02 bits) |
Cluster 1 | √ | ||||||
| rs917218063
(chr16:66549793C>T) |
GCG
ACCATCGGC
(chr16:66549785, -, 5.41 bits) |
Abolished | × | ||||||
| rs928017336
(chr16:66549791G>A) |
GCGGC
TATCGGC
(chr16:66549785, -, -3.62 bits) |
Abolished | × | ||||||
| GCCGCCCCCGTC
(chr16:66549792, +, 1.34 bits) |
|||||||||
§All coordinates are based on the hg38 genome assembly. A bold italic letter in a binding site sequence indicates the base where a SNP occurs. For each normal and variant binding site sequence, the genome coordinate of its most 5’-end base and its R i value are indicated. The negative R i value of a variant binding site sequence implies this site is abolished. The SNPs strengthening binding sites and corresponding variant binding site sequences are underlined.
‡The impact on whether the occurrence of a single SNP resulted in the disappearance of the cluster containing it is shown; ‘Abolished’ indicates that the cluster is eliminated by the existence of the variant allele.
†After a single SNP occurred or multiple SNPs simultaneously occurred, the classifier produced a new prediction on whether the TF is still capable of significantly affecting gene expression via the variant promoter.