BioMed Research International

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 1

Known disease-related SNP markers increasing affinity of the TATA-binding protein (TBP) for human gene promoters, their SNP neighbors.
Gene
()		RNA
(TSS)		dbSNP [4]
rel. 141, 142		SNP
hg19→min		5′-flankhg19 
min		3′-flankmin versus hg19
, nM		Known [reference] diseases or hypothetical [this work] ones[Reference], [this work]
IL1B 
(3)		#2
(+1)		rs1143627−31c→tttttgaaagcc 
t		ataaaaacag2 versus 5↑1510−7Gastric cancer in Helicobacter pylori infection, hepatocellular carcinoma in hepatitis C virus infection, non-small cell lung cancer, chronic gastritis and gastric ulcer in H. pylori infection, Graves’ disease, and major recurrent depression[10, 70–75]
rs549858786−28a→ttgaaagccata 
t		aaaacagcga7 versus 5↓810(Hypothetically) 
Rheumatoid arthritis		[This work], [76]
F3 
(2)		#1
(+1)		rs563763767−21c→tccctttatagc 
t		gcgcggggca2 versus 3↑610−7Myocardial infarction and venous thromboembolism[78]
NOS2 
(7)		#1
(+1)		ND, see [79]−51t→cgtataaatact 
c		tcttggctgc1 versus 2↑310−2Resistance to malaria, epilepsy risk[79, 80]
DHFR 
(5)		#3
(+1)		rs10168−26g→actgcacaaatg 
a		gggacgaggg9 versus 15↑910−7Resistance to methotrexate therapy for leukemia[81]
PGR 
(3)		#2
(+270)		rs10895068−26g→agggagataaag 
a		gagccgcgtg6 versus 10↑810−7Endometrial cancer caused by a de novo occurrence of a spurious TBP-biding site [82]
rs544843047−33t→cagtcgggagat 
c		aaaggagccg22 versus 10↓1410(Hypothetically) 
Health		[This work]
CYP21A2 
(1)		#2
(+1)		ND, see [83]−20a→tgtcattccaga 
t		aaagggccac13 versus 24↑910−7A healthy Hungarian blood donor participating in a health check-up program[83]
TNFRSF18 
(5)		#3
(−120)		rs111426889−25c→tgtgctataaac 
t		gccgccccct2 versus 4↑810−7A healthy individual in the “Control” cohort selected for comparison with the “Autoimmune Diseases” cohort[84]
Note: , total number of SNPs processed; RNA, item number of mRNA in GENCODE v.19 [6]; TSS, transcription start site; hg19, ancestral allele; min, minor allele; , an estimate [55] of the dissociation constant () of the TBP-DNA complex in vitro [50]; ND, not documented; , the expression change in comparison with the norm: overexpression (↑), deficient expression (↓), and norm (=); , -score; , significance (, probability; Figure 1); TF, transcription factor; EMSA, electrophoretic mobility shift assay; CAT, chloramphenicol acetyl transferase activity; LUC, bioluminescence.