General Statistics

Number of coding non synonymous SNPs 133505

Number of regulatory SNPs 4965073

Number of disease mutations 14935

Number of proteins 43797

Number of coding non synonymous SNPs	133505
Number of regulatory SNPs	4965073
Number of disease mutations	14935
Number of proteins	43797

Table 1.Statistics on putative deleterious SNPs and the affected phenotypic property.

Property	# SNPs analysed	# SNPs affected	% SNPs affected

PupaSuite
Exonic splicing - Silencers	275189	24329	8.8
Exonic splicing - Enhancers	275189	111814	40.6
TFBS-TRANSFAC	604772	115171	19.0
TFBS-JASPAR	604772	61070	10.1
Splice sites	4043130	1716	0.0
Splice sites (GeneID)	4965073	13697	0.3
Triplex	4757372	457631	9.6
miRNAs	112330	21029	18.7
Selective pressure at codon level (w)	72220	22138	30.7

Total PupaSuite	4965073	752692	15.2

SNPeffect
Tango	132748	830	0.6
Waltz	133505	6291	4.7
DnaK binding	133505	11658	8.7
FoldX	8321	541 (*)	6.5
Phobius	133505	37325	28.0
Protein Turnover	133505	582	0.4
Farnesylation	133505	13	0.0
Myristoylation	133505	14	0.0
GPI-anchoring	133505	24	0.0
PTS1 peroxisomal targeting	133505	63	0.0
TypeI geranylgeranylation	133505	4	0.0
TypeII geranylgeranylation	133505	0	0.0
Psort	133554	2182	1.6
CSA literature	72225	0	0.0
CSA extended	72225	13	0.0
SASDNA (**)	-	-	-
SASPROT (**)	-	-	-
SASLIG (**)	-	-	-
NetAcet 1.0	72225	18	0.0
NetNES 1.1	72225	270	0.4
NetNGlyc 1.0	72225	22	0.0
NetOGlyc 3.1	72225	114	0.2
NetPhos 2.0	72225	1822	2.5
ProP 1.0	72225	5489	7.6
SecretomeP 1.0 (**)	-	-	-
SignalP 3.0	72225	790	1.1
TMHMM 2.0	72225	54	0.1
TargetP 1.01 (**)	-	-	-

Total SNPeffect	133505	31415	23.5

All phenotypic properties combined	5098578	784107	15.4

(*) not all modeling runs were completed at the time of submission, this number may increase.
(**) only available at the time as full protein- annotation, no positional information available

Table 2. SNPeffect annotations results for known human disease mutations from the Uniprot Knowledge Base release 52.0.

Property	# disease mutations analysed	# disease mutations affected	% disease mutations affected
Tango	14935	687	4.6
Waltz	14935	881	5.9
DnaK binding	14935	1322	8.9
Phobius	14935	668	4.5
Protein Turnover	14935	6	0.0
Farnesylation	14935	182	1.2
Myristoylation	14935	75	0.5
GPI-anchoring	14935	219	1.5
PTS peroxisomal targeting	14935	732	4.9
Type I geranylgeranylation	14935	119	0.8
Type II geranylgeranylation	14935	13	0.1
Psort	14935	232	1.6
CSA	14935	0	0.3
CSA extended	14935	44	0.0
NetAcet 1.0	14935	1	0.0
NetNES 1.1	14935	38	0.3
NetNGlyc 1.0	14935	25	0.2
NetOGlyc 3.1	14935	6	0.0
NetPhos 2.0	14935	293	2.0
ProP 1.0	14935	256	1.7
SignalP 3.0	14935	190	1.3
TMHMM 2.0	14935	95	0.6

Total Disease Mutations	14935	3660	24.5