Functional annotation signatures of disease susceptibility loci improve SNP association analysis

BMC Genomics

Table 2 Summary of estimates for the model for association status given the functional annotation data

Coefficient	Mean	SD	Mean/SD	Coefficient	Mean	SD	Mean/SD
MAF1	0.029	0.0272	1.051	CalPC8	0.096	0.0608	1.584
MAF2	0.003	0.0185	0.151	CalPC9	0.009	0.0218	0.406
MAF3	0.018	0.0236	0.759	CalPC10	-0.019	0.0234	-0.809
MAF4	-0.008	0.0199	-0.425	CalPC11	-0.044	0.0468	-0.943
BrPC1	-0.348	0.0388	-8.983	PhyPC1	0.225	0.0452	4.982
BrPC2	0.174	0.0360	4.845	PhyPC2	-0.023	0.0308	-0.742
BrPC3	0.002	0.0172	0.099	PhyPC3	0.053	0.0395	1.336
BrPC4	-0.077	0.0301	-2.561	PhyPC4	0.024	0.0289	0.839
BrPC5	0.149	0.0301	4.932	funcIntron	-0.003	0.0199	-0.160
BrPC6	0.097	0.0329	2.961	funcNg3	0.002	0.0238	0.098
BrPC7	-0.019	0.0229	-0.825	funcNg5	0.003	0.0200	0.158
BrPC8	-0.078	0.0312	-2.498	funcNonsynon	0.089	0.0387	2.308
BrPC9	-0.012	0.0202	-0.573	funcSynon	-0.007	0.0236	-0.283
BrPC10	0.007	0.0182	0.407	funcUTR	0.002	0.0210	0.078
BrPC11	0.021	0.0239	0.887	logDNase	0.011	0.0253	0.419
BrPC12	-0.039	0.0290	-1.343	TFBSfreq	0.024	0.0267	0.885
BrPC13	-0.094	0.0318	-2.972	logTFBS	0.019	0.0299	0.641
BrPC14	-0.000	0.0175	-0.015	ORegInd	0.027	0.0236	1.163
BrPC15	-0.039	0.0286	-1.354	IndelInd	-0.023	0.0337	-0.693
BrPC16	0.009	0.0185	0.467	CNVInd	0.059	0.0321	1.842
BrPC17	-0.015	0.0213	-0.696	InvInd	0.090	0.0305	2.938
BrPC18	-0.014	0.0210	-0.688	rDBcat1	0.014	0.0257	0.550
CalPC1	-0.103	0.0492	-2.084	rDBcat2	0.066	0.0378	1.741
CalPC2	0.090	0.0441	2.030	rDBcat3	0.012	0.0264	0.467
CalPC3	-0.019	0.0270	-0.709	rDBcat4	0.116	0.0461	2.508
CalPC4	0.086	0.0457	1.889	rDBcat5	0.106	0.0527	2.003
CalPC5	0.053	0.0395	1.350	rDBcat6	-0.056	0.0552	-1.018
CalPC6	-0.012	0.0233	-0.496	pph2prob	0.078	0.0269	2.905
CalPC7	0.002	0.0207	0.078

Estimates of the posterior mean and standard deviation are provided for each coefficient in the model along with the ratio of these quantities, a ‘signal–to–noise’ measure analogous to the Z statistic.

ISSN: 1471-2164