Regression based predictor for p53 transactivation

Gowrisankar, Sivakumar; Jegga, Anil G

doi:10.1186/1471-2105-10-215

BMC Bioinformatics

Table 2 Thirty-six non-coding SNPs overlapping with a validated p53-RE.

From: Regression based predictor for p53 transactivation

Genes	p53 RE Location	Spacer Length	SNP ID	Allele	Wt-Binding Prediction	Minor Allele-Binding Prediction	Reference
SERTAD1	chr19: 45623874–45623893	0	rs268682	C/G	0	1	[7]
TAP1	chr6: 32929058–32929083	6	rs2228108	C/G	3	1	[10]
TP73	chr1: 3597020–3597050	11	rs12121865	A/G	2	3	[8, 10]
PLK2	chr5: 57793125–57793147	3	rs702720	A/G	1	2	[7, 9, 10]
HSP90AB1	chr6: 44322842–44322871	10	rs35074133	A/T	2	3	[10]
BDKRB2	chr14: 95740864–95740883	0	rs1800508	C/T	0	3	[9, 10]
DSCC1	chr18: 48118859–48118878	0	rs934345	C/G	2	3	[7]
TP73	chr1: 3556376–3556406	11	rs12040834	G/T	1	2	[10]
EEF1A1	chr6: 74286408–74286431	4	rs11550799	G/T	1	2	[9, 10]
EEF1A1	chr6: 74286408–74286431	4	rs11550790	G/T	1	2	[9, 10]
EEF1A1	chr6: 74286408–74286431	4	rs11556652	C/T	1	3	[9, 10]
EEF1A1	chr6: 74285585–74285606	2	rs11556679	C/G	1	1	[10]
EEF1A1	chr6: 74286408–74286431	4	rs11550844	C/T	1	1	[9, 10]
KRT8	chr12: 51585038–51585059	2	rs11554493	C/T	0	0	[10]
EEF1A1	chr6: 74285784–74285805	2	rs11556702	A/G	2	2	[10]
ADARB1	chr21: 45316682–45316701	0	rs2838769	A/G	2	2	[10]
SCGB1D2	chr11: 61765841–61765860	0	rs2232945	A/G	3	3	[7]
TP63	chr3: 190989527–190989549	3	rs9844460	C/T	4	4	[10]
EOMES	chr3: 27739623–27739643	1	rs3806624	C/T	2	2	[7]
PMS2	chr7: 6012202–6012223	2	rs2881029	A/C	1	1	[7, 10]
SIVA	chr14: 103984243–103984262	0	rs11628179	G/T	3	3	[7]
KRT8	chr12: 51585038–51585059	2	rs13098	A/T	0	0	[10]
PLK3	chr1: 45038183–45038202	0	rs17880745	A/T	2	2	[8]
PLK3	chr1: 45038183–45038208	6	rs17880745	A/T	2	2	[7, 10]
HSPA8	chr11: 122437379–122437406	8	rs11823704	A/C	0	0	[9, 10]
ARHGEF7	chr13: 110602821–110602840	0	rs1658728	G/T	3	3	[7]
RRM2B	chr8: 103318244–103318263	0	rs28999675	C/G	4	4	[7–10]
TP73	chr1: 3556358–3556385	8	rs12040834	G/T	2	2	[10]
TP73	chr1: 3597020–3597039	0	rs12121865	A/G	3	3	[7]
EEF1A1	chr6: 74285784–74285805	2	rs11550818	C/T	2	2	[10]
TRIM22	chr11: 5668357–5668376	0	rs35926783	A/G	4	4	[10]
EDN2	chr1: 41720668–41720687	0	rs11572355	A/G	3	3	[7, 8, 10]
CASP1	chr11: 104411147–104411166	0	rs3809024	A/G	3	3	[7, 10]
HSPA8	chr11: 122437379–122437406	8	rs41302367	A/G	On Spacer	On Spacer	[9, 10]
SLC38A2	chr12: 45037706–45037735	10	rs7960147	C/T	On Spacer	On Spacer	[9, 10]
MSH2	chr2: 47483388–47483420	13	rs1863332	A/C	On Spacer	On Spacer	[10]

Of these, 33 SNPs overlap with dimers, out of which 10 SNPs were predicted to impact the transactivation capacity by our predictor (See Additional File 9 for more details).

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ISSN: 1471-2105

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