Trans-Genomics and

“Functional SNPs”
__________________
The “UNIVERSAL GENOMIC CODE”
The “MASTER CODE” ®
Evidence of the FUNCTIONAL role
of the POSITION of SNPs
Dr J.C. Perez – an old draft – Bordeaux 21 June 2001
revisited in 2013
jeanclaudeperez2@gmail.com
http://fr.scribd.com/jean_claude_perez/documents
http://golden-ratio-in-dna.blogspot.fr/
http://www.amazon.co.uk/Codex-Biogenesis-harmonies-g%C3%A9nomelatome/dp/2874340448
“.../... Fourth, we need to turn our new genomic information into an engine of pharmaceutical
discovery. Individuals human differ from one another by about one base pair per thousand.
These “single nucleotide polymorphisms” (SNPs) are markers that can allow epidemiologists
to uncover the genetic basis of many diseases..../...
Moreover, the analysis of SNPs will provide us with the power to uncover the genetic basis of
our individual capabilities such as mathematicability, memory, physical coordination, and
even, perhaps, creativity.”
By Pr David BALTIMORE (NOBEL prize) in the historical Human Genome issue of
NATURE (15 February 2001, page 814: “Our genome unveiled”).

I - Highlights:
The “MASTER CODE” is partially described in the book “CODEX
BIOGENESIS” (chapter 20 and annexe):

http://www.amazon.co.uk/Codex-Biogenesis-harmonies-g
%C3%A9nome-latome/dp/2874340448
This discovery unifies the 3 languages of genetics: DNA, RNA and
Amino acids like sequences.
In http://file.scirp.org/Html/4-7401586_37457.htm
we demonstrated that the Human Reference Genome (HRG) is
tuned on specific numerical proportions at codon population level.
All the diference between personal genomes is located in SNPs.
Then we demonstrate here that the SNPs of the human genome
seems to be more important by their locations within the genome
unstead by their TCAG mutation values.
There is a kind of AMPLIFICATION – perhaps a RESONANCE of the SNP then probably a new unknown FUNCTION of SNPs at
individual personal genomes. Here a DRAFT of unpublishe results
obtained 12 years ago...

II-About DIFFERENCIATION
-OVERVIEWS of the SNP data
meaning: “FUNCTIONAL SNPs”...
Summary:
Collection and the availability of thousands of SNPs of the human genome
(http://SNP.cshl.org et http://www.ncbi.nlm.nih.gov ) OPEN very great QUESTIONS like:
- Do SNPs have an influence at long distance in the genome (stability etc.)?
- Do SNPs play a crucial part promoters, modulation, tuning in the function and
expression of genes?
- Do the SNPs play on the contrary a local role and at very short distance?
- Etc…
We studied this problem according to various points of view and starting from our two
fundamental discoveries to publish (see joint Draft A):
With the MASTER CODE :
-local short distance analysis (900 to 1000 bases available around each SNP in data
bases)

-Analysis of very large contigs multi-SNP: example of the study of 120000bases containing
16 SNPs which one changes overall swapping them on their extreme nucleotides values).
With the Universal GENOMIC Codes:
- research of the scope of effects of the SNP on the characteristic GENOMIC CODE of the
studied areas.
Curiously, it appeared the following facts:
- at the global level (Universal GENOMIC CODE and MASTER CODE) the SNP are
WITHOUT EFFECTS.
- at the local level, the SNP affects the MASTER CODES only at VERY SHORT
DISTANCE (study of about fifty bases).
But especially it appears TWO remarkable results: Universal GENOMIC Code seems
" conservative " and INVARIANT under the effect of the SNP…!!!
And especially, finally, the following remarkable result:
SNPs ARE LOCATED in the very large majority of the cases in areas of the genome which
are “POLES” or remarkable “SITES” according to the MASTER CODE theory. In other
words, there is a very strong CORRELLATION between the site of the SNP and the character
" FUNCTIONAL SITE" (hollow minima or tops maxima) via the Genomics/Proteomics
analysis of the MASTER CODES.
However, although these areas are FUNCTIONNALLY STRATEGICS at very long distance,
the effect of the SNP is only, contradictorily, LOCAL only.
One thus sought " MEANING " to the information of SNPs following our double point of
view of the " MASTER CODES " (total Unification Genomics/Proteomics) and of
" Universal Genomic Code " (GLOBAL UNIFICATION and specific CODE characterizing
each chromosome or genome).
Chromosome1 region bands 1q31 1q32.1. The contig has 209216 bps without
undetermined...Etc...
So, various " points of sights " were studied based on this sample contig, meanwhile they are
not reported at this time in this draft report... focusing our attention on the following major
result:
We will retain here the point most remarkable:

" the SNPs are LOCATED in strategic and functional sites
areas within the genome.
Beyond the nucleotide value of a SNP
(mutation/polymorphism), It IS THUS MUCH MORE ITS
ADDRESS WHICH IS VERY IMPORTANT ".
We will illustrate here only this last remarkable discovery on the SNPs possible Functions.

Various examples of CORRELLATIONS between
the EXTREMUMS sites of the MASTER CODE
(“Functional SITES”) and the POSITIONS of
SNPs…
We will demonstrate now the evidence of the " fractal-like " and “ embedded “ character of
the functional impact of the LOCATION of the SNP.

“Fractal-like” character and “ embedded structure “ of
the FUNCTIONAL LOCATION of the SNPs.
    ERRATUM : in all the following figures title, plase read HumChrom1 instead
HumChrom21.
We work with the public SNPs WEB database from “CSHL” http://www.snp.cshl.org/
TSC
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Chromosome:

SNP

dbSNP # Chrom Band GenBank Ver

Golden Path
Contig

TSC1234313

SNP Pos Relative to:
GB

Contig

Chrom (kb)

Chr1

AL391359.5

ctg12483

156469 44525

75159.9

TSC1004972

2827241

Chr1

AL391359.6

ctg12483

72652

46392

75161.8

TSC1004971

2827240

Chr1

AL391359.6

ctg12483

72614

46430

75161.8

TSC1004970

2827239

Chr1

AL391359.6

ctg12483

71259

47785

75163.2

TSC1004969

2827238

Chr1

AL391359.6

ctg12483

71095

47949

75163.3

TSC1004968

2827237

Chr1

AL391359.6

ctg12483

70464

48580

75164.0

TSC1004967

2827236

Chr1

AL391359.6

ctg12483

69058

49986

75165.4

TSC1004966

2827235

Chr1

AL391359.6

ctg12483

68768

50276

75165.7

TSC1004965

2827234

Chr1

AL391359.6

ctg12483

68592

50452

75165.9

TSC1004964

2827233

Chr1

AL391359.6

ctg12483

66204

52840

75168.2

TSC1004984

2827253

Chr1

AL391359.6

ctg12483

77267

54217

75169.6

TSC1004988

2827257

Chr1

AL391359.6

ctg12483

77382

54332

75169.7

Chr1

AL391359.5

ctg12483

5240

55549

75170.9

Chr1

AL391359.6

ctg12483

106773 62823

75178.2

Chr1

AL391359.5

ctg12483

73540

64240

75179.6

TSC1320714
TSC0917908

2773549

TSC1234314
TSC1004991

2827260

Chr1

AL391359.6

ctg12483

109830 65880

75181.3

TSC1004992

2827261

Chr1

AL391359.6

ctg12483

109953 66003

75181.4

TSC1004993

2827262

Chr1

AL391359.6

ctg12483

112795 68845

75184.2

TSC1004994

2827263

Chr1

AL391359.6

ctg12483

112889 68939

75184.3

TSC0083659

2076132

Chr1

AL391359.6

ctg12483

113010 69060

75184.5

TSC0080881

2076091

Chr1

AL391359.6

ctg12483

114011 70061

75185.5

TSC1004996

2827264

Chr1

AL391359.6

ctg12483

117905 73955

75189.4

TSC1234315

Chr1

AL391359.5

ctg12483

94954

74560

75190.0

TSC1234316

Chr1

AL391359.5

ctg12483

94974

74580

75190.0

TSC0152136

2086237

Chr1

AL391359.6

ctg12483

119523 75573

75191.0

TSC0152137

2086238

Chr1

AL391359.6

ctg12483

119736 75786

75191.2

TSC0146331

2077114

Chr1

AL391359.6

ctg12483

133175 77224

75192.6

TSC1004963

2827232

Chr1

AL391359.6

ctg12483

132681 77718

75193.1

TSC1234311

Chr1

AL391359.5

ctg12483

120577 78581

75194.0

TSC1234310

Chr1

AL391359.5

ctg12483

120548 78610

75194.0

Chr1

AL391359.6

ctg12483

130072 80327

75195.7

TSC1234309

Chr1

AL391359.5

ctg12483

117314 81844

75197.2

TSC1234308

Chr1

AL391359.5

ctg12483

117244 81914

75197.3

TSC1234307

Chr1

AL391359.5

ctg12483

116922 82236

75197.6

TSC1004962

2827231

TSC1004975

2827244

Chr1

AL391359.6

ctg12483

151041 93765

75209.2

TSC1035721

2849463

Chr1

AL391359.6

ctg12483

146216 98590

75214.0

TSC1004974

2827243

Chr1

AL391359.6

ctg12483

145323 99483

75214.9

Chr1

AL391359.5

ctg12483

141892 100046 75215.4

TSC1234312
TSC1004973

2827242

Chr1

AL391359.6

ctg12483

141889 102917 75218.3

TSC1004976

2827245

Chr1

AL391359.6

ctg12483

159486 109880 75225.3

TSC1270754

Chr1

AL391359.5

ctg12483

58769

119837 75235.2

TSC1270753

Chr1

AL391359.5

ctg12483

58750

119856 75235.3

TSC1004982

2827251

Chr1

AL391359.6

ctg12483

100106 135969 75251.4

TSC1004981

2827250

Chr1

AL391359.6

ctg12483

99910

136165 75251.6

TSC1004980

2827249

Chr1

AL391359.6

ctg12483

99848

136227 75251.6

TSC1004979

2827248

Chr1

AL391359.6

ctg12483

98814

137261 75252.7

TSC0565526

2187256

Chr1

AL391359.6

ctg12483

97561

138514 75253.9

TSC0745119

2331197

Chr1

AL391359.6

ctg12483

96950

139125 75254.5

TSC0745118

2331196

Chr1

AL391359.6

ctg12483

96594

139481 75254.9

TSC1004977

2827246

Chr1

AL391359.6

ctg12483

94425

141650 75257.1

TSC0488778

2134547

Chr1

AL391359.6

ctg12483

123663 160198 75275.6

TSC0488779

2134548

Chr1

AL391359.6

ctg12483

123623 160238 75275.6

TSC0488780

2134549

Chr1

AL391359.6

ctg12483

123421 160440 75275.8

TSC1004961

2827230

Chr1

AL391359.6

ctg12483

122023 161838 75277.2

…/…

…/…

to the next page (205) of Chromosome 1.

Analysing a first SNP by the “MASTER CODE”...
We run the MASTER CODE zooming regions around the SNP position.
TRACE ZOOMS: 12000bps 6000bps 3000bps 1500bps 750bps around SNP position 55549
12000bps view...

6000bps view…

3000bps view…

1500bps view…

750 bps view…

Comments : we note that this SNP is located in a MASTER CODE FUNCTIONAL REGION
(characterized top classified positions or down classified positions). We must recall here that
extremum regions (global and local optimums, maximums and minimums) are linked with
FUNCTIONAL signification ‘active sites in proteins, promoters in genomic contigs etc...).

Analysing a second SNP by the “MASTER CODE”...
12000bps view…

6000bps view…

3000bps view…

1500bps view…

750bps view…

Comments : here, we have a « Top Site » location SNP…

Analysing a third SNP by the “MASTER CODE”...
12000bps view…

6000bps view…

3000bps view…

1500bps view…

750bps view…

Comments : Here, we discover in the last zoom figure the typical “teeth
characterize the “Universal

of saw” which

GENOMIC Code” discovery (see §II).

Analysing a fourth SNP by the “MASTER CODE”...
12000bps view…

6000bps view…

3000bps view…

1500bps view…

750bps view...

Comments : we note here a transition from « bottom » status (12000 and 6000bps) to medium
status (3000bps) then, finally, to “Top” status (1500 and 750bps)...

Analysing a fifth SNP by the “MASTER CODE”...
12000bps view… (local minimum…).

6000bps…

3000bps view…

1500bps view…

750bps view…Then, finally, this local minimum appears to be a strong deep minimum...

Analysing a last sixth SNP by the “MASTER CODE”...
12000bps view...

6000bps view…

3000bps view…

1500bps view…

750bps view…

Finally, this minimum appear to be a real highly deep minimum in all embedded fractal
scales : long-range 12000bps and 6000bps, medium range 3000 and 1500bps, local shortrange 750bps...

Sorry, analysing the last seventh SNP by the “MASTER CODE”...
12000bps view…

6000bps view…

3000bps view…

1500bps view…

750bps view…

No comments…

So, generalizing this type of analyses reveals the evidence
of this astonishing law: " in the human genome, it would
seem that SNPs are more important by their POSITION
than by their VALUE. It is, probably, this position
Located in strategic functional sites which " amplifies "
the scope of effect and the global differentiation of these
simple local specific changes which are SNPs single
mutations" …

III-Conclusions and Perspectives...
Analysing the SNP locations within genomic contigs establishes the evidence of a strong link
between the “FUNCTIONAL SITES” proposed by MASTER CODE law and the exact
LOCATIONS of SNPs within the genome.

In other hand: SNPs LOCATIONS are FUNCTIONAL...

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