Supplementary Table 9. Top 20 single SNPs from the ASD GWASs 1-5 1-5 (Supplementary Table 1). The 15 genes encoding
proteins that could be directly placed in one or more of the three networks involved in ASDs (Figures 1-3) are indicated in
bold.
SNP
rs5918959
rs6529461
rs12392447
rs12392447
rs9932538
rs5972577
rs9822786
rs6646569
rs6646569
rs9919560
rs793094
rs7766973
rs1550976
rs6886828
rs3755827
rs3755827
rs10510837
rs892055
rs4394668
rs10774538
P value
1,22E-10
6,40E-09
5,64E-08
5,64E-08
1,94E-07
2,67E-07
2,98E-07
9,75E-07
9,75E-07
1,13E-06
1,29E-06
2,14E-06
2,30E-06
3,20E-06
3,54E-06
3,54E-06
3,56E-06
4,70E-06
4,89E-06
6,22E-06
Locus
Xq12
Xq26.1
Xq28
Xq28
16p12.3
Xp21.1
3q13.2
Xq24
Xq24
11p15.3
10p11.22
6p22.3
11q25
5q33.3
3p14.2
3p14.2
3p14.2
19q13.2
1p36.22
12q24.23
Gene
MSN
ARHGAP36
FAM3A
SLC10A3
SYT17
DMD
SLC9A10
RHOXF1
RHOXF2
GALNTL4
ZNF438
JARID2
NTM
SGCD
CADPS
FEZF2
FHIT
RASGRP4
DHRS3
CCDC64
Position within gene
66 kb downstream
42 kb downstream
10 kb downstream
5 kb upstream
intronic
intronic
intronic
1.2 kb downstream
51 kb upstream
intronic
66 kb upstream
intronic
intronic
intronic
24 kb downstream
5’ near gene
intronic
nonsyn, coding
intronic
24 kb upstream
Supplementary Table 9. Top 20 single SNPs from four published GWASs for type 1 diabetes
yielding the lowest P value in any of the four GWASs is shown.
SNP
rs2476601
rs2292239
rs12708716
rs17696736
rs3825932
rs11755527
rs1990760
rs100446
rs6356
rs763361
rs1445898
rs10255021
rs229541
rs3764021
rs17388568
rs380421
rs6017667
rs6897932
rs6546909
rs213950
P value
2.07E-80
1.52E-20
2.57E-18
2.31E-16
3.17E-15
4.66E-12
1.77E-11
6.75E-11
2.70E-09
1.38E-08
1.45E-08
1.71E-08
1.98E-08
5.80E-08
6.35E-07
8.84E-07
1.78E-06
7.70E-06
8.53E-06
1.95E-05
Locus
1p13.2
12q13.2
16p13.13
12q24.13
15q25.1
6q15
2q24.2
11p15.5
11p15.5
18q22.2
5p13.2
7q21.3
22q12.3
12p13.31
4q27
20q13.12
20q13.12
5p13.2
2p13.1
7q31.2
Gene
PTPN22
ERBB3
CLEC16A
C12orf30
CTSH
BACH2
IFIH1
INS
TH
CD226
CAPSL
COL1A2
C1QTNF6
CLEC2D
ADA1
SPINT2
SPINT4
IL7R
DQX1
CFTR
Position within gene
nonsyn, coding
intronic
intronic
intronic
intronic
intronic
nonsyn, coding
intronic
nonsyn, coding
nonsyn, coding
nonsyn, coding
intronic
intronic
nonsyn, coding
intronic
nonsyn, coding
nonsyn, coding
nonsyn, coding
syn, coding
nonsyn, coding
GWAS reference
(1)
(1)
(1)
(1)
(1)
(1)
(2)
(1)
(1)
(2)
(1)
(3)
(4)
(3)
(1)
(1)
(4)
(4)
(2)
(1)
6-9
. For each gene, the SNP
GWAS reference
(7)
(7)
(7)
(7)
(9)
(9)
(7)
(8)
(8)
(7)
(7)
(8)
(9)
(6)
(6)
(7)
(7)
(7)
(6)
(7)
Supplementary Table 9 - continued. Top 20 single SNPs from four published GWASs for Crohn’s disease
gene, the SNP yielding the lowest p value in any of the four GWASs is shown.
SNP
rs11465804
rs3828309
rs2076756
rs2301436
rs3197999
rs744166
rs4263839
rs11175593
rs6908425
rs2274910
rs4807569
rs3763313
rs2476601
rs780094
rs12529198
rs9858542
rs1131095
rs17309827
rs1925411
rs13003464
P value
6.66E-63
2.36E-32
7.01E-14
1.04E-12
1.15E-12
6.82E-12
2.60E-10
3.08E-10
8.96E-10
1.46E-09
2.12E-09
5.20E-09
1.46E-08
3.14E-07
6.96E-07
7.70E-07
1.21E-06
2.08E-06
3.58E-06
4.60E-06
Locus
1p31.3
2q37.1
16q12.1
6q27
3p21.31
17q21.2
9q32
12q12
6p22.3
1q23.3
19p13.3
6p21.32
1p13.2
2p23.3
6p25.1
3p21.31
3p21.31
6p25.2
1p31.3
2p16.1
Gene
IL23R
ATG16L1
NOD2
FGFR1OP
MST1
STAT3
TNFSF15
LRRK2
CDKAL1
ITLN1
SBNO2
BTNL2
PTPN22
GCKR
LYRM4
BSN
APEH
SLC22A23
WDR78
PUS10
Position within gene
intronic
intronic
intronic
intronic
nonsyn, coding
intronic
intronic
intronic
intronic
intronic
intronic
intronic
nonsyn, coding
intronic
intronic
syn, coding
syn, coding
intronic
intronic
intronic
6,10-12
For each
GWAS reference
(12)
(12)
(10)
(12)
(12)
(12)
(12)
(12)
(12)
(12)
(12)
(12)
(12)
(12)
(12)
(6)
(11)
(12)
(11)
(12)
Abbreviations: ASD(s), autism spectrum disorder(s); GWAS, genome-wide association study; GWASs, genome-wide
association studies; nonsyn, nonsynonymous; SNP(s), single nucleotide polymorphism(s)
*
The size of each gene in kilobase (kb) was derived from its exact start and end positions according to the
Ensembl Human Genome Browse (http://www.ensembl.org/Homo_sapiens/).
References
1. Wang K, Zhang H, Ma D, Bucan M, Glessner JT, Abrahams BS et al. Common genetic variants on 5p14.1
associate with autism spectrum disorders. Nature 2009; 459: 528-533.
2. Ma D, Salyakina D, Jaworski JM, Konidari I, Whitehead PL, Andersen AN et al. A genome-wide
association study of autism reveals a common novel risk locus at 5p14.1. Ann Hum Genet 2009; 73: 263273.
3. Weiss LA, Arking DE, Brune CW, West K, O'Connor A, Hilton G. et al. A genome-wide linkage and
association scan reveals novel loci for autism. Nature 2009; 461: 802-808.
4. Salyakina D, Ma DQ, Jaworski JM, Konidari I, Whitehead PL, Henson R et al. Variants in several genomic
regions associated with asperger disorder. Autism Res 2010; 3: 303-310.
5. Hussman JP, Chung RH, Griswold AJ, Jaworski JM, Salyakina D, Ma D et al. A noise-reduction GWAS
analysis implicates altered regulation of neurite outgrowth and guidance in autism. Mol Autism 2011; 2: 1.
6. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven
common diseases and 3,000 shared controls. Nature 2007; 447: 661-678.
7. Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V et al. Robust associations of four new
chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 2007; 39: 857-864.
8. Hakonarson H, Grant SF, Bradfield JP, Marchand L, Kim CE, Glessner JT et al. A genome-wide
association study identifies KIAA0350 as a type 1 diabetes gene. Nature 2007; 448: 591-594.
9. Cooper JD, Smyth DJ, Smiles AM, Plagnol V, Walker NM, Allen JE et al. Meta-analysis of genome-wide
association study data identifies additional type 1 diabetes risk loci. Nat Genet 2008; 40: 1399-1401.
10. Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A et al. Genome-wide association study
identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat
Genet 2007; 39: 596-604.
11. Raelson JV, Little RD, Ruether A, Fournier H, Paquin B, Van Eerdewegh P et al. Genome-wide
association study for Crohn's disease in the Quebec Founder Population identifies multiple validated
disease loci. Proc Natl Acad Sci. USA 2007; 104: 14747-14752.
12. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD et al. Genome-wide association defines
more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008; 40: 955-962.