Research Article

How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

Table 3

Known disease-related SNP markers insignificantly changing TBP affinity for human gene promoters, their SNP neighbors.

Gene 
()
RNA 
(TSS)
dbSNP [4]SNP 
hg19→min
5′-flankhg19
min
3′-flankmin versus hg19 
, nM
Known [reference] or hypothetical [this work] diseases[Reference], [this work]

FSHR
(3)
#2 
(+16)
rs1394205−29g→agcaaatgcagg
a
aagaaatcag7.3 versus 7.3=0>0.05No differences between proven fathers and infertile men [121, 122]

F9
(4)
#1 
(+1)
ND, see [123]−48g→cagctcagcttg
c
tactttggta6.4 versus 6.4=0>0.05Leiden hemophilia B,  
EMSA: HNF4-binding site disrupted rather than proximal TBP-binding site
[123]
ND, see [123]−42t→agcttgtacttt
a
ggtacaacta6.4 versus 6.4=0>0.05
rs371045754−32a→ctggtacaacta
c
atcgacctta9.6 versus 6.4510(Hypothetically)
Leiden hemophilia B
[This work]

StAR
(3)
#3 
(+31)
rs16887226−33c→tcagccttcagc
t
gggggacatt10.3 versus 10.3=0>0.05Hypertensive diabetic patients,  
EMSA: unknown TF-binding site disrupted rather than TBP-binding site
[124]
rs544850971−22a→gtcagcggggga
g
catttaagac12.1 versus 10.3510(Hypothetically)
Congenital adrenal hyperplasia
[This work],  [125]

GH1
(11)
#1 
(+1)
rs28399433del-50gaggggccaggg
tataaaaagg1.4 versus 1.5=1>0.05Short stature, 
EMSA: unknown TF-binding site disrupted rather than TBP-binding site
[126]

GSTM3
(8)
#4 
(+1)
rs1332018−49c→accccttatgtc
a
gggtataaag3.1 versus 3.6=1.9>0.05Risk of brain, lung, testicular, and renal cell carcinomas, 
LUC: “−49c” is 10% of “−49a
[127, 128]
rs200209906−36c→t,agtataaagccc
t,a
ctcccgctca4.3 versus 3.62.4<0.05(Hypothetically) Risk of brain, lung, testicular, and renal cell carcinomas[This work]

UGT1A7
(4)
#1 
(+1)
rs7586110−57t→gcttcttccact
g
tactatatta1.48 versus 1.54=1>0.05Oral cancer risk, 
LUC: “−57g” is 50% of “−57t
[129]
rs574890114−55a→gtcttccactta
g
ctatattata2.02 versus 1.54410(Hypothetically)
Higher risk of oral cancer
[This work]
rs542729995−52a→gtccacttacta
g
tattatagga2.28 versus 1.54510

GJA5
(8)
#1 
(+1)
rs10465885−55g→acaactaagatg
a
tattaaacac3.1 versus 3.4=1>0.05Arrhythmia, cardiovascular events 
LUC: “−55g” is 50% of “−55a
[130]
#2 
(+1)
rs35594137−39g→agaggagggaag
a
gcgacagata5.7 versus 5.7=0>0.05Arrhythmia, cardiovascular events 
LUC: “−39a/76g” is 50% of “−39g/76a
[131]
rs587745372−29a→tggcgacagata
t
cgattaaaaa6.8 versus 5.7310(Hypothetically)
Arrhythmia, cardiovascular events
[This work]

THBD
(3)
#1 
(+68)
rs13306848−33g→aagggagggccg
a
ggcacttata2.3 versus 2.1=110−7Thrombophlebitis risk 
LUC: “−33a” is 84% of “−33g
[132]

UGT1A1
(10)
#201 
(+1)
rs34983651ins-55atggtttttgcc
at
atatatatat0.65 versus 0.67=1>0.05Necessary but not sufficient in hyperbilirubinemia and jaundice[133]
rs398048306del-51(at)1;2ggtttttgccat(at)
atatatatat0.71 versus 0.67=1>0.05Ethnic differences such as 
rare alleles in humans
[12]