jcperezdraftwhyhumangenomesnps are more important by their location than by their tcag change

8/14/2019 JcPerezDRAFTwhyHumanGenomeSNPs Are More Important by Their LOCATION Than by Their TCAG Change

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Trans-Genomics and

“Functional SNPs” __________________ The “UNIVERSAL GENOMIC CODE”

The “MASTER CODE” ®

Evidence of the FUNCTIONAL roe

of the !OSITION of SN!"

Dr J.C. Perez – an old draft – Bordeaux 21 June 2001

revisited in 2013

jeanclaudeperez2@!ail.co!

"ttp#$$fr.scri%d.co!$jean&claude&perez$docu!ents "ttp#$$olden'ratio'in'dna.%lospot.fr$

"ttp#$$(((.a!azon.co.u)$Codex'Bioenesis'"ar!onies'*C3*+,no!e'

lato!e$dp$2-/3/0//-

“.../... 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” (!"s# are mar$ers that can allow epidemiologists

to uncover the genetic basis of many diseases..../...

%oreover, the analysis of !"s will provide us with the power to uncover the genetic basis of

our individual capabilities such as mathematicability, memory, physical coordination, andeven, perhaps, creativity.”

B Pr David B+4567 895B7 prize: in t"e "istorical ;u!an <eno!e issue of

9+=67 81> ?e%ruar 2001 pae -1/# A5ur eno!e unveiled:.

I - Highlights:

The “MASTER CODE” i" #$rti$% de"cri&ed in the &oo' “CODE(

)IOGENESIS” *ch$#ter +, $nd $nne-e./

mailto:[email protected]


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%A9nome-latome/dp/2874340448


http://fr.scribd.com/jean_claude_perez/documents

http://golden-ratio-in-dna.blogspot.fr/






htt#/001112$3$4on2co25'0Code-6)io7ene"i"6h$r3onie"67

8C98A:no3e6$to3e0d#0+;<=9=,==;

Thi" di"cover% 5nifie" the 9 $n75$7e" of 7enetic"/ DNA> RNA $nd

A3ino $cid" i'e "e?5ence"2

In http://file.scirp.org/Html/4-7401586_37457.htm

1e de3on"tr$ted th$t the @53$n Reference Geno3e *@RG. i"

t5ned on "#ecific n53eric$ #ro#ortion" $t codon #o#5$tion eve2

A the diference &et1een #er"on$ 7eno3e" i" oc$ted in SN!"2

Then 1e de3on"tr$te here th$t the SN!" of the h53$n 7eno3e

"ee3" to &e 3ore i3#ort$nt &% their oc$tion" 1ithin the 7eno3e

5n"te$d &% their TCAG 35t$tion v$5e"2There i" $ 'ind of AM!LIFICATION #erh$#" $ RESONANCE 6

of the SN! then #ro&$&% $ ne1 5n'no1n FUNCTION of SN!" $t

individ5$ #er"on$ 7eno3e"2 @ere $ DRAFT of 5n#5&i"he re"5t"

o&t$ined B+ %e$r" $7o222

II-About IFF!"!N#IATI$N

-$%!"%I!&S o' the SNP data

meaning: “F(N#TI$NA) SNPs”***

Summar+:

Collection and t"e availa%ilit of t"ousands of 9Ps of t"e "u!an eno!e

8"ttp#$$9P.cs"l.or et "ttp#$$(((.nc%i.nl!.ni".ov : 5P79 ver reat =759 li)e#

' Do 9Ps "ave an influence at lon distance in t"e eno!e 8sta%ilit etc.:E' Do 9Ps pla a crucial part pro!oters !odulation tunin in t"e function and

expression of enesE

' Do t"e 9Ps pla on t"e contrar a local role and at ver s"ort distanceE

' 7tcF

Ge studied t"is pro%le! accordin to various points of vie( and startin fro! our t(o

funda!ental discoveries to pu%lis" 8see joint Draft +:#

Git" t"e 4+76 C5D7 #

'local s"ort distance analsis 8,00 to 1000 %ases availa%le around eac" 9P in data

%ases:



http://file.scirp.org/Html/4-7401586_37457.htm

http://snp.cshl.orge/

http://www.ncbi.nlm.nih.gov/




http://file.scirp.org/Html/4-7401586_37457.htm

http://snp.cshl.orge/




'+nalsis of ver lare contis !ulti'9P# exa!ple of t"e stud of 120000%ases containin

1H 9Ps ("ic" one c"anes overall s(appin t"e! on t"eir extre!e nucleotides values:.

Git" t"e =niversal <7954C Codes#

' researc" of t"e scope of effects of t"e 9P on t"e c"aracteristic <7954C C5D7 of t"e

studied areas.

Curiousl it appeared t"e follo(in facts#

' at t"e lo%al level 8=niversal <7954C C5D7 and 4+76 C5D7: t"e 9P are

G;5= 7??7C.

' at t"e local level t"e 9P affects t"e 4+76 C5D7 onl at I76 ;56

D+9C7 8stud of a%out fift %ases:.

But especiall it appears G5 re!ar)a%le results# =niversal <7954C Code see!s

K conservative K and 9I+6+9 under t"e effect of t"e 9PFLLL

+nd especiall finall t"e follo(in re!ar)a%le result#

9Ps +67 5C+7D in t"e ver lare !ajorit of t"e cases in areas of t"e eno!e ("ic"

are AP57 or re!ar)a%le A7 accordin to t"e 4+76 C5D7 t"eor. n ot"er

(ords t"ere is a ver stron C5667+59 %et(een t"e site of t"e 9P and t"e c"aracter

K ?=9C59+ 7K 8"ollo( !ini!a or tops !axi!a: via t"e <eno!ics$Proteo!ics

analsis of t"e 4+76 C5D7.

;o(ever alt"ou" t"ese areas are ?=9C599+ 6+7<C at ver lon distance

t"e effect of t"e 9P is onl contradictoril 5C+ onl.

5ne t"us sou"t K 47+99< K to t"e infor!ation of 9Ps follo(in our dou%le point of

vie( of t"e K 4+76 C5D7 K 8total =nification <eno!ics$Proteo!ics: and of

K =niversal <eno!ic Code K 8<5B+ =9?C+59 and specific C5D7 c"aracterizin

eac" c"ro!oso!e or eno!e:.

C"ro!oso!e1 reion %ands 1M31 1M32.1. "e conti "as 20,21H %ps (it"out

undeter!ined...7tc...

o various K points of si"ts K (ere studied %ased on t"is sa!ple conti !ean("ile t"e are

not reported at t"is ti!e in t"is draft report... focusin our attention on t"e follo(in !ajor

result#

Ge (ill retain "ere t"e point !ost re!ar)a%le#

the SN!" $re LOCATED in "tr$te7ic $nd f5nction$ "ite"

$re$" 1ithin the 7eno3e2

)e%ond the n5ceotide v$5e of $ SN!

*35t$tion0#o%3or#hi"3.> It IS T@US MUC@ MORE ITS

ADDRESS @IC@ IS VER IM!ORTANT 2Ge (ill illustrate "ere onl t"is last re!ar)a%le discover on t"e 9Ps possi%le ?unctions.



%arious e,amles o' #$""!))ATI$NS bet.een

the !/T"!0(0S sites o' the 0AST!" #$!

1“Functional SIT!S”2 and the P$SITI$NS o'

SNPs3

Ge (ill de!onstrate no( t"e evidence of t"e K fractal'li)e K and A e!%edded A c"aracter of

t"e functional i!pact of t"e 5C+59 of t"e 9P.

“Fractal-li4e” character and “ embedded structure “ o'

the F(N#TI$NA) )$#ATI$N o' the SNPs*

766+=4 # in all t"e follo(in fiures title plase read @53Chro3B instead

@53Chro3+B.

Ge (or) (it" t"e pu%lic 9Ps G7B data%ase fro! AC; "ttp#$$(((.snp.cs"l.or$

TS#

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Table

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Chromosome:

SNP dbSNP # Chrom Band GenBank Ver Golden Path SNP Pos Relative to:

Contig GB Contig Chrom (kb)

C123/313 Chr1 +3,13>,.> ct12/-3 156469 44525 75159.9

C100/,2 2-22/1 Chr1 +3,13>,.H ct12/-3 72652 46392 75161.8

C100/,1 2-22/0 Chr1 +3,13>,.H ct12/-3 72614 46430 75161.8

C100/,0 2-223, Chr1 +3,13>,.H ct12/-3 71259 47785 75163.2

C100/,H, 2-223- Chr1 +3,13>,.H ct12/-3 71095 47949 75163.3

C100/,H- 2-223 Chr1 +3,13>,.H ct12/-3 70464 48580 75164.0

http://www.snp.cshl.org/

http://snp.cshl.org/


http://snp.cshl.org/db/snp/dynamap


http://snp.cshl.org/db/snp/search_contig


http://snp.cshl.org/db/snp/snpgb


http://snp.cshl.org/db/snp/index


http://snp.cshl.org/db/searches/text/snp


http://snp.cshl.org/db/searches/query/snp


http://snp.cshl.org/db/snp/snpftp

http://snp.cshl.org/db/snp/snp?name=TSC1234313

http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=n&form=1&field=Sequence+ID&term=AL391359

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg4&position=ctg12483


http://www.ncbi.nlm.nih.gov/SNP/snp_retrieve.cgi?subsnp_id=2827241



















http://www.snp.cshl.org/















http://snp.cshl.org/db/snp/snpftp


























C100/,H 2-223H Chr1 +3,13>,.H ct12/-3 69058 49986 75165.4

C100/,HH 2-223> Chr1 +3,13>,.H ct12/-3 68768 50276 75165.7

C100/,H> 2-223/ Chr1 +3,13>,.H ct12/-3 68592 50452 75165.9

C100/,H/ 2-2233 Chr1 +3,13>,.H ct12/-3 66204 52840 75168.2

C100/,-/ 2-22>3 Chr1 +3,13>,.H ct12/-3 77267 54217 75169.6

C100/,-- 2-22> Chr1 +3,13>,.H ct12/-3 77382 54332 75169.7

C13201/ Chr1 +3,13>,.> ct12/-3 5240 55549 75170.9

C0,1,0- 23>/, Chr1 +3,13>,.H ct12/-3 106773 62823 75178.2

C123/31/ Chr1 +3,13>,.> ct12/-3 73540 64240 75179.6

C100/,,1 2-22H0 Chr1 +3,13>,.H ct12/-3 109830 65880 75181.3

C100/,,2 2-22H1 Chr1 +3,13>,.H ct12/-3 109953 66003 75181.4

C100/,,3 2-22H2 Chr1 +3,13>,.H ct12/-3 112795 68845 75184.2

C100/,,/ 2-22H3 Chr1 +3,13>,.H ct12/-3 112889 68939 75184.3

C00-3H>, 20H132 Chr1 +3,13>,.H ct12/-3 113010 69060 75184.5

C00-0--1 20H0,1 Chr1 +3,13>,.H ct12/-3 114011 70061 75185.5

C100/,,H 2-22H/ Chr1 +3,13>,.H ct12/-3 117905 73955 75189.4

C123/31> Chr1 +3,13>,.> ct12/-3 94954 74560 75190.0

C123/31H Chr1 +3,13>,.> ct12/-3 94974 74580 75190.0

C01>213H 20-H23 Chr1 +3,13>,.H ct12/-3 119523 75573 75191.0

C01>213 20-H23- Chr1 +3,13>,.H ct12/-3 119736 75786 75191.2

C01/H331 2011/ Chr1 +3,13>,.H ct12/-3 133175 77224 75192.6

C100/,H3 2-2232 Chr1 +3,13>,.H ct12/-3 132681 77718 75193.1C123/311 Chr1 +3,13>,.> ct12/-3 120577 78581 75194.0

C123/310 Chr1 +3,13>,.> ct12/-3 120548 78610 75194.0

C100/,H2 2-2231 Chr1 +3,13>,.H ct12/-3 130072 80327 75195.7

C123/30, Chr1 +3,13>,.> ct12/-3 117314 81844 75197.2

C123/30- Chr1 +3,13>,.> ct12/-3 117244 81914 75197.3

C123/30 Chr1 +3,13>,.> ct12/-3 116922 82236 75197.6

C100/,> 2-22// Chr1 +3,13>,.H ct12/-3 151041 93765 75209.2

C103>21 2-/,/H3 Chr1 +3,13>,.H ct12/-3 146216 98590 75214.0

C100/,/ 2-22/3 Chr1 +3,13>,.H ct12/-3 145323 99483 75214.9

C123/312 Chr1 +3,13>,.> ct12/-3 141892 100046 75215.4

C100/,3 2-22/2 Chr1 +3,13>,.H ct12/-3 141889 102917 75218.3

C100/,H 2-22/> Chr1 +3,13>,.H ct12/-3 159486 109880 75225.3

C120>/ Chr1 +3,13>,.> ct12/-3 58769 119837 75235.2

C120>3 Chr1 +3,13>,.> ct12/-3 58750 119856 75235.3

C100/,-2 2-22>1 Chr1 +3,13>,.H ct12/-3 100106 135969 75251.4

C100/,-1 2-22>0 Chr1 +3,13>,.H ct12/-3 99910 136165 75251.6

C100/,-0 2-22/, Chr1 +3,13>,.H ct12/-3 99848 136227 75251.6

C100/,, 2-22/- Chr1 +3,13>,.H ct12/-3 98814 137261 75252.7











































































































































































































































































































C0>H>>2H 21-2>H Chr1 +3,13>,.H ct12/-3 97561 138514 75253.9

C0/>11, 23311, Chr1 +3,13>,.H ct12/-3 96950 139125 75254.5

C0/>11- 23311,H Chr1 +3,13>,.H ct12/-3 96594 139481 75254.9

C100/, 2-22/H Chr1 +3,13>,.H ct12/-3 94425 141650 75257.1

/

C0/--- 213/>/ Chr1 +3,13>,.H ct12/-3 123663 160198 75275.6

C0/--, 213/>/- Chr1 +3,13>,.H ct12/-3 123623 160238 75275.6

C0/---0 213/>/, Chr1 +3,13>,.H ct12/-3 123421 160440 75275.8

C100/,H1 2-2230 Chr1 +3,13>,.H ct12/-3 122023 161838 75277.2

/

to t"e next pae 820>: of C"ro!oso!e 1.

Anal+sing a 'irst SNP b+ the “0AST!" #$!”***

Ge run t"e 4+76 C5D7 zoo!in reions around t"e 9P position.

6+C7 N554# 12000%ps H000%ps 3000%ps 1>00%ps >0%ps around SNP osition 55567

12000%ps vie(...

































http://snp.cshl.org/chromtables/chr1-205.html





































H000%ps vie(F

3000%ps vie(F



1>00%ps vie(F

>0 %ps vie(F



Co!!ents # (e note t"at t"is 9P is located in a 4+76 C5D7 ?=9C59+ 67<59

8c"aracterized top classified positions or do(n classified positions:. Ge !ust recall "ere t"at

extre!u! reions 8lo%al and local opti!u!s !axi!u!s and !ini!u!s: are lin)ed (it"

?=9C59+ sinification Oactive sites in proteins pro!oters in eno!ic contis etc...:.

Anal+sing a second SNP b+ the “0AST!" #$!”***12000%ps vie(F



H000%ps vie(F

3000%ps vie(F

1>00%ps vie(F



>0%ps vie(F

Co!!ents # "ere (e "ave a op ite Q location 9PF



Anal+sing a third SNP b+ the “0AST!" #$!”***12000%ps vie(F

H000%ps vie(F



3000%ps vie(F

1>00%ps vie(F



>0%ps vie(F

Co!!ents # ;ere (e discover in t"e last zoo! fiure t"e tpical “teeth of "$1” ("ic"

c"aracterize t"e “(ni8ersal G!N$0I# #ode” discover 8see R:.



Anal+sing a 'ourth SNP b+ the “0AST!" #$!”***12000%ps vie(F

H000%ps vie(F

3000%ps vie(F



1>00%ps vie(F

>0%ps vie(...



Co!!ents # (e note "ere a transition fro! %otto! Q status 812000 and H000%ps: to !ediu!

status 83000%ps: t"en finall to Aop status 81>00 and >0%ps:...



Anal+sing a 'i'th SNP b+ the “0AST!" #$!”***12000%ps vie(F 8local !ini!u!F:.

H000%psF

3000%ps vie(F



1>00%ps vie(F

>0%ps vie(F"en finall t"is local !ini!u! appears to %e a stron deep !ini!u!...



Anal+sing a last si,th SNP b+ the “0AST!" #$!”***12000%ps vie(...

H000%ps vie(F

3000%ps vie(F



1>00%ps vie(F

>0%ps vie(F



?inall t"is !ini!u! appear to %e a real "i"l deep !ini!u! in all e!%edded fractal

scales # lon'rane 12000%ps and H000%ps !ediu! rane 3000 and 1>00%ps local s"ort'

rane >0%ps...



1>00%ps vie(F

>0%ps vie(F

jcperezdraftwhyhumangenomesnps are more important by their location than by their tcag change

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