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Prediction of functional regulatory SNPs in monogenic and complex disease.

Zhao Y, Clark WT, Mort M, Cooper DN, Radivojac P, Mooney SD.

Hum Mutat. 2011 Oct;32(10):1183-90. doi: 10.1002/humu.21559. Epub 2011 Sep 9.


is-rSNP: a novel technique for in silico regulatory SNP detection.

Macintyre G, Bailey J, Haviv I, Kowalczyk A.

Bioinformatics. 2010 Sep 15;26(18):i524-30. doi: 10.1093/bioinformatics/btq378.


atSNP: transcription factor binding affinity testing for regulatory SNP detection.

Zuo C, Shin S, Keleş S.

Bioinformatics. 2015 Oct 15;31(20):3353-5. doi: 10.1093/bioinformatics/btv328. Epub 2015 Jun 18.


rSNPBase: a database for curated regulatory SNPs.

Guo L, Du Y, Chang S, Zhang K, Wang J.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1033-9. doi: 10.1093/nar/gkt1167. Epub 2013 Nov 26.


Linking disease associations with regulatory information in the human genome.

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M.

Genome Res. 2012 Sep;22(9):1748-59. doi: 10.1101/gr.136127.111.


Powerful identification of cis-regulatory SNPs in human primary monocytes using allele-specific gene expression.

Almlöf JC, Lundmark P, Lundmark A, Ge B, Maouche S, Göring HH, Liljedahl U, Enström C, Brocheton J, Proust C, Godefroy T, Sambrook JG, Jolley J, Crisp-Hihn A, Foad N, Lloyd-Jones H, Stephens J, Gwilliam R, Rice CM, Hengstenberg C, Samani NJ, Erdmann J, Schunkert H, Pastinen T, Deloukas P, Goodall AH, Ouwehand WH, Cambien F, Syvänen AC.

PLoS One. 2012;7(12):e52260. doi: 10.1371/journal.pone.0052260. Epub 2012 Dec 26.


Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters.

Chadaeva IV, Ponomarenko MP, Rasskazov DA, Sharypova EB, Kashina EV, Matveeva MY, Arshinova TV, Ponomarenko PM, Arkova OV, Bondar NP, Savinkova LK, Kolchanov NA.

BMC Genomics. 2016 Dec 28;17(Suppl 14):995. doi: 10.1186/s12864-016-3353-3.


LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs.

Wang MC, Chen FC, Chen YZ, Huang YT, Chuang TJ.

BMC Res Notes. 2012 May 2;5:212. doi: 10.1186/1756-0500-5-212.


Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies.

Chorley BN, Wang X, Campbell MR, Pittman GS, Noureddine MA, Bell DA.

Mutat Res. 2008 Jul-Aug;659(1-2):147-57. doi: 10.1016/j.mrrev.2008.05.001. Epub 2008 May 4. Review.


FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.

Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H.

Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542. Epub 2012 Jun 8.


Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.

You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.

BMC Genomics. 2011 Jan 25;12:59. doi: 10.1186/1471-2164-12-59.


An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Yang JO, Hwang S, Oh J, Bhak J, Sohn TK.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S19. doi: 10.1186/1471-2105-9-S12-S19.


A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS.

Richardson K, Lai CQ, Parnell LD, Lee YC, Ordovas JM.

BMC Genomics. 2011 Oct 13;12:504. doi: 10.1186/1471-2164-12-504.


Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes.

Wang X, Tomso DJ, Liu X, Bell DA.

Toxicol Appl Pharmacol. 2005 Sep 1;207(2 Suppl):84-90. Review.


Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.

GuhaThakurta D, Xie T, Anand M, Edwards SW, Li G, Wang SS, Schadt EE.

BMC Genomics. 2006 Sep 15;7:235.


Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.

Ameur A, Rada-Iglesias A, Komorowski J, Wadelius C.

Nucleic Acids Res. 2009 Jul;37(12):e85. doi: 10.1093/nar/gkp381. Epub 2009 May 18.


Predicting functional regulatory SNPs in the human antimicrobial peptide genes DEFB1 and CAMP in tuberculosis and HIV/AIDS.

Flores Saiffe Farías A, Jaime Herrera López E, Moreno Vázquez CJ, Li W, Prado Montes de Oca E.

Comput Biol Chem. 2015 Dec;59 Pt A:117-25. doi: 10.1016/j.compbiolchem.2015.09.002. Epub 2015 Sep 9.


Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences.

Irizarry K, Kustanovich V, Li C, Brown N, Nelson S, Wong W, Lee CJ.

Nat Genet. 2000 Oct;26(2):233-6.


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