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A Catalog of Published Genome-Wide Association Studies

New Potential etiologic and functional implications of genome-wide association loci for human diseases and traitsPDF file
Click here to read our recent Proceedings of the Academy of Sciences (PNAS) article on catalog methods and analysis.


Go to the Catalog

Published Genome-Wide Associations (view)PowerPoint file
Credit: Darryl Leja and Teri Manolio
The genome-wide association study (GWAS) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator).

SNP-trait associations listed here are limited to those with p-values < 1.0 x 10-5. Note that we are now including all identified SNP-trait associations meeting this p-value threshhold. Multipliers of powers of 10 in p-values are rounded to the nearest single digit; odds ratios and allele frequencies are rounded to two decimals. Standard errors are converted to 95 percent confidence intervals where applicable. Allele frequencies, p-values, and odds ratios derived from the largest sample size, typically a combined analysis (initial plus replication studies), are recorded below if reported; otherwise statistics from the initial study sample are recorded. Odds ratios < 1 in the original paper are converted to OR > 1 for the alternate allele. Where results from multiple genetic models are available, we prioritized effect sizes (OR's or beta-coefficients) as follows: 1) genotypic model, per-allele estimate; 2) genotypic model, heterozygote estimate, 3) allelic model, allelic estimate.

Gene regions corresponding to SNPs were identified from the UCSC Genome Browser. Gene names are those reported by the authors in the original paper. Only one SNP within a gene or region of high linkage disequilibrium is recorded unless there was evidence of independent association.

Occasionally the term "pending" is used to denote one or more studies that we identified as an eligible GWAS, but for which SNP information has not yet been extracted; studies of CNVs are also noted as pending.

How to cite the GWAS Catalog:
Hindorff LA, Junkins HA, Mehta JP, and Manolio TA. A Catalog of Published Genome-Wide Association Studies. Available at: www.genome.gov/gwastudies. Accessed [date of access].

How to cite the GWAS Catalog paper:
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, and Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. [May 27, 2009.]

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As of 07/01/09, this table includes 356 publications and 1640 SNPs.
Date Added to Catalog (since 11/25/08) First Author/Date/ Journal/Study Disease/Trait Initial
Sample Size		 Replication Sample Size Region Reported Gene(s) Strongest SNP-Risk Allele Risk Allele Frequency in Controls P-value OR or beta-coefficient and [95% CI] Platform
[SNPs passing QC]		 CNV
07/01/09 Thorleifsson
June 28, 2009
Nat Genet
Sequence variants in the CLDN14 gene associate with kidney stones and bone mineral density 		Kidney stones 1,507 Icelandic cases, 34,033 Icelandic controls 1,520 Icelandic cases, 4,726 Icelandic controls, 746 Dutch cases, 3,751 Dutch controls 21q22.13 CLDN14 rs219780-C 0.79 4 x 10-12 1.25 [1.17-1.33] Illumina
[303,120]		 N
07/01/09 Heard-Costa
June 26, 2009
PLoS Genet
NRXN3 Is a Novel Locus for Waist Circumference: A Genome-Wide Association Study from the CHARGE Consortium 		Waist circumference 31,373 Caucasian individuals 38,641 Caucasian individuals 16q12.2
14q31.1
18q21.32
12q13.13
5p14.3
6p12.2
11p15.4		 FTO
NRXN3
MC4R
FAIM2, BCDIN3D
CDH12
PKHD1
OVCH2		 rs1558902-?
rs10146997-G
rs489693-?
rs7138803-?
rs4701252-?
rs1555967-?
rs7932813-?		 NR
NR
NR
NR
NR
NR
NR		 5 x 10-19
5 x 10-8
4 x 10-7
8 x 10-7
2 x 10-6
3 x 10-6
5 x 10-6 		NR
.65 [NR] cm increase
NR
NR
NR
NR
NR		 Affymetrix & Illumina
[up to 512,349]		 N
07/01/09 Lindgren
June 26, 2009
PLoS Genet
Genome-Wide Association Scan Meta-Analysis Identifies Three Loci Influencing Adiposity and Fat Distribution 		Adiposity 38,580 European-ancestry individuals Up to 102,064 European-ancestry individuals 6p12.3
8p23.1
1q41
1q42.3		 TFAP2B
MSRA
LYPLAL1
TBCE		 rs987237-G
rs7826222-G
rs2605100-G
rs6429082-C		 0.164
0.183
0.692
0.46		 2 x 10-11 (WC)
9 x 10-9 (WC)
3 x 10-8 (WHR in women)
3 x 10-7 (WC)		 .04 [0.03-0.05] z-score unit increase
.04 [0.03-0.05] z-score unit increase
.04 [0.03-0.05] z-score unit increase
NR		 Affymetrix & Illumina
[2,573,738] (imputed)		 N
07/01/09 Cotsapas
June 24, 2009
Hum Mol Genet
Common BMI-associated variants confer risk of extreme obesity 		Obesity (extreme) 775 Caucasian cases, 3,197 Caucasian controls NR 16q12.2
10p11.21
2p16.1
6p21.31
4q26
11p14.2
3p24.2
5q23.3
10q22.1
20p12.1
3p24.3
6p21.31
2q33.3		 FTO
ZNF248
RTN4
ITPR3
TRAM1L1
MUC15
RARB
FBN2
PRF1
C20orf133
RAFTLIN
MLN
FLJ20309		 rs9941349-T
rs7474896-T
rs6726292-G
rs999943-T
rs10433903-T
rs12295638-C
rs1435703-T
rs374748-G
rs10999409-T
rs6110577-C
rs12635698-C
rs2274459-A
rs7603514-A		 0.43
0.14
0.73
0.72
0.66
0.10
0.06
0.11
0.45
0.16
0.15
0.17
0.20		 6 x 10-12
9 x 10-7
1 x 10-6
1 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
8 x 10-6 		1.48 [1.33-1.66]
1.46 [1.25-1.69]
1.39 [1.22-1.59]
1.37 [1.20-1.56]
1.33 [1.19-1.52]
1.49 [1.26-1.77]
1.66 [1.34-2.06]
1.47 [1.25-1.73]
1.3 [1.16-1.45]
1.4 [1.21-1.61]
1.41 [1.21-1.63]
1.38 [1.20-1.58]
1.36 [1.19-1.56]		 Illumina
[457,251]		 N
06/30/09 Bahlo
June 14, 2009
Nat Genet
Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20 		Multiple sclerosis 1,618 European ancestry cases, 3,413 European ancestry controls 2,256 European ancestry cases, 2,310 European ancestry controls 6p21.32
12q14.1
1p13.1
20q13.12
16p12.1
8q24.21
1p22.1
10p15.1		 HLA-DRB1
METTL1, CYP27B1
CD58
CD40
NR
ASAP1, DDEF1
EVI5, RPL5
IL2RA		 rs9271366-G
rs703842-A
rs1335532-A
rs6074022-G
rs8049603-T
rs6984045-C
rs6604026-G
rs2104286-G		 0.15
0.67
0.87
0.25
0.20
0.02
0.28
0.73		 7 x 10-184
5 x 10-11
1 x 10-7
1 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6
7 x 10-6 		2.78 [NR]
1.23 [NR]
1.28 [NR]
1.2 [NR]
1.19 [NR]
1.59 [NR]
1.17 [NR]
1.16 [NR]		 Illumina
[302,098]		 N
06/29/09 De Jager
June 14, 2009
Nat Genet
Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci 		Multiple sclerosis 2,624 cases, 7,220 controls 2,215 cases, 2,116 controls 6p21.32
6p22.1
12p13.31
1p13.1
11q12.2
16q24.1
10p15.1
2q22.1
16p13.13
5p13.1
12q24.31
10q22.3
5p13.2
12p13.31
3q25.33		 HLA-DRB1
HLA-B
TNFRSF1A
CD58
CD6
IRF8
IL2RA
CXCR4
CLEC16A
PTGER4
MPHOSPH9
ZMIZ1
IL7R
TNFRSF1A
IL12A		 rs3135388-A
rs2523393-A
rs1800693-C
rs2300747-A
rs17824933-G
rs17445836-G
rs2104286-T
rs882300-C
rs11865121-C
rs6896969-C
rs1790100-G
rs1250540-G
rs6897932-C
rs4149584-T
rs4680534-C		 0.22
0.59
0.45
0.88
0.25
0.81
0.76
0.61
0.69
0.62
0.24
0.35
0.75
0.022
0.37		 4 x 10-225
1 x 10-17
2 x 10-11
3 x 10-10
4 x 10-9
4 x 10-9
9 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
7 x 10-7
2 x 10-6
2 x 10-6
5 x 10-6
6 x 10-6 		2.75 [2.46-3.07]
1.28 [1.18-1.39]
1.2 [1.10-1.31]
1.3 [1.14-1.47]
1.18 [1.07-1.30]
1.25 [1.12-1.39]
1.15 [1.04-1.27]
1.19 [1.09-1.30]
1.15 [1.04-1.25]
1.1 [1.01-1.20]
1.11 [1.00-1.22]
1.12 [1.02-1.22]
1.12 [1.02-1.23]
1.58 [1.15-2.17]
1.12 [1.02-1.22]		 Affymetrix & Illumina
[~2.56 million] (imputed)		 N
06/26/09 Malarstig
June 12, 2009
Blood
Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study 		Plasma homocysteine 387 individuals from 21 Spanish families 1,238 European individuals NR NR NR NR NS NR Illumina
[283,437]		 N
06/19/09 Knauff
June 09, 2009
Hum Reprod
Genome-wide association study in premature ovarian failure patients suggests ADAMTS19 as a possible candidate gene 		Premature ovarian failure 99 Caucasian cases, 235 Caucasian controls 60 Caucasian cases, 90 Caucasian controls NR NR NR NR NS NR Illumina
[309,158]		 N
06/19/09 Zhai
June 08, 2009
J Med Genet
A genome-wide association study suggests that a locus within the ataxin 2 binding protein 1 gene is associated with hand osteoarthritis: the Treat-OA consortium 		Osteoarthritis 1,804 Caucasian individuals 3,266 Caucasian individuals NR NR NR NR NS NR Illumina
[up to 535,188]		 N
06/17/09 Gregersen
June 07, 2009
Nat Genet
REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis 		Rheumatoid arthritis 2,418 cases, 4,504 controls 2,604 cases, 2,882 controls 1p13.2
2p16.1
2q33.2
8p23.1
9q33.2		 PTPN22
REL
CTLA4
BLK
TRAF1-C5		 rs2476601-?
rs13017599-A
rs231735-T
rs2736340-A
rs881375-?		 NR
0.34
0.51
0.24
NR		 2 x 10-21
2 x 10-12
6 x 10-9
6 x 10-9
4 x 10-8 		NR
1.21 [1.15-1.28]
1.17 [1.11-1.23]
1.19 [1.13-1.27]
NR		 Illumina
[278,502]		 N
06/17/09 Elmore
June 06, 2009
J Vasc Surg
Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association 		Abdominal aortic aneurysm 123 cases, 112 controls 827 cases, 594 controls NR NR NR NR NS NR Affymetrix
[306,330] (pooled)		 N
06/22/09 Kolz
June 05, 2009
PLoS Genet
Meta-Analysis of 28,141 Individuals Identifies Common Variants within Five New Loci That Influence Uric Acid Concentrations 		Uric acid concentrations 12,328 European males, 15,813 European females NR 4p16.1
4p16.1
4q22.1
6p22.2
11q13.1
4q22.1
2p23.3
11q13.1
1q21.1
6p22.2
10q21.1		 SLC2A9
SLC2A9
ABCG2
SLC17A1
SLC22A11
ABCG2
GCKR
SLC22A12
PDZK1
LRRC16A, SCGN
SLC16A9		 rs734553-T
rs734553-T
rs2231142-T
rs1183201-A
rs17300741-A
rs2231142-T
rs780094-T
rs505802-T
rs12129861-A
rs742132-A
rs12356193-A		 0.77
0.77
0.11
0.48
0.51
0.11
0.42
0.70
0.46
0.70
0.83		 1 x 10-192 (women)
1 x 10-41 (men)
2 x 10-18 (men)
3 x 10-14
7 x 10-14
1 x 10-10 (women)
1 x 10-9
2 x 10-9
3 x 10-9
9 x 10-9
1 x 10-8 		.4 [0.371-0.423] mg/dl increase
.22 [0.188-0.252] mg/dl increase
.22 [0.171-0.270] mg/dl increase
.06 [0.459-0.078] mg/dl decrease
.06 [0.046-0.078] mg/dl increase
.14 [0.096-0.181] mg/dl increase
.05 [0.035-0.068] mg/dl increase
.06 [0.038-0.074] mg/dl decrease
.06 [0.042-0.083] mg/dl decrease
.05 [0.036-0.072] mg/dl increase
.08 [0.051-0.105] mg/dl increase		 Affymetrix and Illumina
[2,493,963] (imputed)		 N
06/16/09 Smith
June 02, 2009
Mol Psychiatry
Genome-wide association study of bipolar disorder in European American and African American individuals 		Bipolar disorder 1,001 Caucasian cases, 345 African American cases, 1,033 Caucasian controls, 670 African American controls 1,749 Caucasian family members, 1,263 Caucasian cases, 431 Caucasian controls 19q13.11 DPY19L3 rs2111504-T 0.23 2 x 10-6 (AA) 1.74 [NR] Affymetrix
[702,044]		 N
06/15/09 Daly
May 31, 2009
Nat Genet
HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin 		Drug-induced liver injury (flucloxacillin) 58 cases, 282 controls NR 6p21.33
3q27.3
3q11.2
12q12
9p21.2
15q26.2		 HCP5, HLA-B
ST6GAL1
OR5H2
ALG10B
C9org82
MCTP2		 rs2395029-?
rs10937275-?
rs1497546-?
rs6582630-?
rs10812428-?
rs4984390-?		 0.05
0.09
0.02
0.38
0.31
0.41		 9 x 10-33
1 x 10-8 (B*5701 positive)
2 x 10-7
1 x 10-6
1 x 10-6
4 x 10-6 		45 [19.4-105]
4.1 [NR]
6.57 [NR]
2.82 [NR]
2.85 [NR]
3.27 [NR]		 Illumina
[866,399]		 N
06/14/09 Kanetsky
May 31, 2009
Nat Genet
Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer 		Testicular cancer 277 white, non-Hispanic cases, 919 non-Hispanic controls 371 non-Hispanic cases + 204 sets of parents, 860 non-Hispanic controls 12q21.32 KITLG rs4474514-A NR 6 x 10-15 3.07 [2.29-4.13] Affymetrix
[611,254]		 N
06/14/09 Rapley
May 31, 2009
Nat Genet
A genome-wide association study of testicular germ cell tumor 		Testicular germ cell tumor 730 cases, 1,435 controls 571 cases, 1,806 controls 12q21.32
12q21.32
6p21.31
5q31.3
4q24
1q24.1		 KITLG
KITLG
BAK1
SPRY4
Intergenic
Intergenic		 rs995030-G
rs1508595-G
rs210138-G
rs4624820-A
rs4699052-C
rs4657482-A		 0.80
0.83
0.20
0.54
0.61
0.33		 1 x 10-31
3 x 10-30
1 x 10-13
3 x 10-13
2 x 10-7
2 x 10-6 		2.55 [2.05-3.19]
2.69 [2.10-3.44]
1.5 [1.28-1.75]
1.37 [1.19-1.58]
1.21 [1.05-1.39]
1.14 [0.99-1.31]		 Illumina
[307,666]		 N
06/14/09 Ng
May 29, 2009
J Hum Genet
A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma. 		Nasopharyngeal carcinoma 111 Chinese cases, 260 Chinese controls 168 Chinese cases, 252 Chinese controls 3p22.2 ITGA9 rs189897-A 0.09 7 x 10-8 3.18 [1.94-5.21] Illumina
[533,048]		 N
06/16/09 Aston
May 28, 2009
J Androl
Genome-wide Study of Single Nucleotide Polymorphisms Associated with Azoospermia and Severe Oligozoospermia 		Male infertility 52 oligozoospermic Caucasian males, 40 non-obstructive azoospermic Caucasian males, 80 Caucasian male controls NR 12p12.2
20q13.2
3q11.2
2q22.1
12p13.32		 PDE3A
SALL4
ARL6
NXPH2
EFCAB4B		 rs10841496-?
rs6068020-?
rs9814870-?
rs1399645-?
rs10848911-?		 0.58
0.49
0.15
0.02
0.11		 5 x 10-7 (azoospermia)
5 x 10-7 (azoospermia)
7 x 10-7 (oligozoospermia)
9 x 10-7 (azoospermia)
4 x 10-6 (azoospermia)		 NR
NR
NR
NR
NR		 Illumina
[314,776]		 N
06/10/09 Ma
May 28, 2009
Ann Hum Genet
A genome-wide association study of autism reveals a common novel risk locus at 5p14.1 		Autism 1,390 family members 2,390 family members 5p14.1 Intergenic rs10038113-T 0.59 3 x 10-6 1.33 [1.11-1.43] Illumina
[775,311]		 N
06/14/09 Jallow
May 24, 2009
Nat Genet
Genome-wide and fine-resolution association anaylsis of malaria in West Africa 		Malaria 958 Gambian cases, 1,382 Gambian controls, all children 1,087 Gambian cases, 2,376 Gambian controls, all children 11p15.4
17p13.1
7p12.2		 HBB
SCO1
DDC		 rs11036238-?
rs6503319-T
rs1451375-?		 0.14
0.45
0.78		 4 x 10-11
7 x 10-7
6 x 10-6 		1.59 [1.39-1.82]
1.21 [1.12-1.31]
1.33 [1.18-1.52]		 Affymetrix
[402,814]		 N
06/04/09 Norris
May 21, 2009
Obesity
Genome-wide Association Study and Follow-up Analysis of Adiposity Traits in Hispanic Americans: The IRAS Family Study 		Obesity-related traits 229 Hispanic family members 961 Hispanic family members NR NR NR NR NS NR Illumina
[309,200]		 N
06/21/09 Hirschfield
May 20, 2009
N Engl J Med
Primary Biliary Cirrhosis Associated with HLA, IL12A, and IL12RB2 Variants 		Primary biliary cirrhosis 505 cases, 1,507 controls up to 526 cases, 1,206 controls 3q26.1
1p31.3
6p21.32
6p21.3
7q32.1
3q26.1
17q12		 IL12A
IL12RB2
c6orf10, BTNL2, HLA-DQB1
c6orf10, BTNL2, HLA-DQB1
IRFS-TNPO3
ARF7
IKZF3		 rs6441286-G
rs3790567-A
4-SNP haplotype-1
4-SNP haplotype-2
rs10488631-G
rs4679904-G
rs907092-A		 0.39
0.24
0.01
0.20
NR
0.72
0.45		 2 x 10-14
3 x 10-11
1 x 10-10 (AACA)
7 x 10-10 (CACA)
2 x 10-7
1 x 10-6
8 x 10-6 		1.54 [1.38-1.72]
1.51 [1.33-1.70]
NR
NR
1.52 [1.30-1.78]
1.38 [1.21-1.57]
1.29 [1.15-1.44]		 Illumina
[305,724]		 N
06/14/09 Arnett
May 19, 2009
BMC Med Genet
Genome-wide association study identifies single-nucleotide polymorphism in KCNB1 associated with left ventricular mass in humans: The HyperGEN Study 		Left ventricular mass 101 Caucasian cases, 101 Caucasian controls 704 Caucasian siblings, 1,467 African American siblings 5p13.2
7q21.11		 RAI14
CD36		 rs409045-?
rs10499859-?		 0.38
0.45		 8 x 10-7 (Caucasian)
3 x 10-6 (Caucasian)		 0 [NR] (LVMI)
.09 [NR] (LVMI)		 Affymetrix
[96,258]		 N
06/04/09 Landers
May 18, 2009
Proc Natl Acad Sci USA
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis 		Amyotrophic lateral sclerosis 1,821 cases, 2,258 controls 538 cases, 556 controls 1q24.2
7q36.1
18q12.1
2p16.1
5q23.2
1q24.2
6p22.3
2q24.3
3p26.3
17q24.3
1p34.2
1q42.2
2p22.1
5q23.1
21q21.1
2q24.2		 KIFAP3
ZNF746
B4GALT6
EFEMP1
CSNK1G3
SELL
ATXN1
SCN7A
CNTN4
SLC39A11
NT5C1A
DISC1
NR
SEMA6A
NR
RBMS1		 rs1541160-C
rs855913-A
rs10438933-G
rs7577894-T
rs11241713-T
rs3177980-G
rs697739-A
rs13015447-T
rs2619566-G
rs8066857-C
rs873917-T
rs16856202-A
rs3099950-?
rs7702057-C
rs2823962-?
rs10192369-T		 NR
NR
0.12
0.39
NR
NR
NR
0.34
NR
NR
0.29
0.04
NR
0.03
NR
0.47		 2 x 10-8 (survival)
4 x 10-8 (survival)
1 x 10-6 (susceptibilty)
1 x 10-6 (site of onset)
3 x 10-6 (survival)
4 x 10-6 (survival)
4 x 10-6 (age of onset)
7 x 10-6 (site of onset)
7 x 10-6 (age of onset)
8 x 10-6 (site of onset)
8 x 10-6 (susceptibilty)
8 x 10-6 (susceptibilty)
8 x 10-6 (survival)
8 x 10-6 (site of onset)
9 x 10-6 (survival)
9 x 10-6 (susceptibilty)		 .58 [0.38-0.78] years older
1.08 [0.70-1.46] years older
1.3 [NR]
1.41 [NR]
.79 [0.46-1.12] years older
.51 [0.46-0.56] years older
2.04 [1.18-2.90] years younger
1.41 [NR]
3.03 [1.71-4.35] years younger
1.48 [NR]
1.16 [NR]
2 [NR]
NR
2.05 [NR]
NR
1.17 [NR]		 Illumina
[288,357]		 N
06/04/09 He
May 17, 2009
Nat Genet
Genome-wide association studies identify loci associated with age at menarche and age at natural menopause 		Menarche and menopause (age at onset) 17,438 Caucasian women NR 20p12.3
19q13.42
5q35.2
6q21
9q31.2
6p24.2		 TRMT6, MCM8
BRSK1
UIMC1
LIN28B
Intergenic
GCM2, SYCP2L		 rs16991615-A
rs1172822-T
rs365132-T
rs314277-A
rs7861820-C
rs2153157-T		 0.06
0.37
0.49
0.14
0.48
0.49		 1 x 10-21 (age at natural menopause)
2 x 10-19 (age at natural menopause)
8 x 10-14 (age at natural menopause)
3 x 10-13 (age at menarche)
3 x 10-9 (age at menarche)
5 x 10-8 (age at natural menopause)		 1.07 [0.85-1.29] years older
.49 [0.38-0.60] years younger
.39 [0.29-0.49] years older
.16 [0.12-0.20] years older
.09 [0.06-0.12] years younger
.29 [0.19-0.39] years older		 Illumina
[317,759]		 N
06/01/09 Ong
May 17, 2009
Nat Genet
Genetic variation in LIN28B is associated with the timing of puberty 		Menarche (age at onset) 4,714 women 16,373 women 6q21 LIN28B rs314276-C 0.33 4 x 10-16 .14 [0.11-0.17] years younger Affymetrix
[up to 390,631]		 N
05/28/09 Perry
May 17, 2009
Nat Genet
Meta-analysis of genome-wide association data identifies two loci influencing age at menarche 		Menarche (age at onset) 17,510 women NR 9q31.2
6q21		 TMEM38B, SLC44A1, FKTN, FSD1L, TAL2, ZNF462
LIN28B		 rs2090409-A
rs7759938-C		 0.31
0.33		 2 x 10-9
7 x 10-9 		.1 [0.06-0.14] years younger
.09 [0.05-0.13] years older		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
06/01/09 Perlis
May 15, 2009
Am J Psychiatry
A Genomewide Association Study of Response to Lithium for Prevention of Recurrence in Bipolar Disorder 		Reponse to lithium treatment in bipolar disorder 458 lithium-treated subjects, 719 non-lithium treated subjects 359 subjects NR NR NR NR NS NR Affymetrix
[~1.4 million] (imputed)		 N
05/28/09 Stolk
May 15, 2009
Nat Genet
Loci at chromosomes 13, 19 and 20 influence age at natural menopause. 		Menopause (age at onset) 2,979 women 2,560 women 19q13.42
20p12.3
13q34
9q21.31
16q24.2
11q25
8p12
7q22.3
6p21.32
3q26.2
20p12.3
2q23.3
14q32.31		 BRSK1, TMEM224, SUV420H2
MCM8
LOC121793, ARHGEF7
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 rs1172822-T
rs236114-A
rs7333181-A
rs2151145-?
rs4843747-?
rs4397868-?
rs6468442-?
rs17153527-?
rs494620-?
rs4955755-?
rs2326679-?
rs11889862-?
rs4906172-?		 0.39
0.21
0.12
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 6 x 10-11
1 x 10-10
3 x 10-8
1 x 10-7
2 x 10-7
3 x 10-7
3 x 10-7
4 x 10-7
5 x 10-7
7 x 10-7
2 x 10-6
2 x 10-6
3 x 10-6 		.39 [0.27-0.51] years younger
.5 [0.34-0.65] years older
.52 [0.34-0.70] years older
.41 [0.26-0.56] years older
.39 [0.24-0.54] years older
.4 [0.25-0.55] years younger
.39 [0.24-0.54] years younger
.51 [0.31-0.71] years older
.3 [0.18-0.42] years older
.34 [0.21-0.47] years older
.32 [0.19-0.45] years older
.36 [0.21-0.51] years younger
.36 [0.21-0.51] years younger		 Illumina
[315,418]		 N
06/01/09 Sulem
May 15, 2009
Nat Genet
Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche 		Menarche (age at onset) 15,297 Icelandic women 10,040 Icelandic women 6q21 LIN28B, HACE1, E3 ubiquitin protein ligase 1, BVES, POPDC3 rs314280-T 0.48 2 x 10-14 1.2 [0.9-1.5] months older Illumina
[304,226]		 N
05/26/09 Fei
May 14, 2009
Arthritis Res Ther
Identification of novel genetic susceptibility loci for Behcet's disease using a genome-wide association study 		Behcet's disease 152 cases, 170 controls NR NR NR NR NR NS NR Affymetrix
[~500,000] (pooled)		 N
06/01/09 Barrett
May 10, 2009
Nat Genet
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes 		Type 1 diabetes 7,514 cases, 9,045 controls 4,267 cases, 4,670 controls, 4,342 trios 6p21.32
1p13.2
11p15.5
10q23.31
12q24.12
12q13.2
16p13.13
22q12.2
2q33.2
16q23.1
18p11.21
10p15.1
16p11.2
6q22.32
4q27
17q12
14q24.1
9p24.2
20p13
12p13.31
19q13.32
4p15.2
17q21.2
1q32.1
21q22.3
14q32.2
7p15.2
2q24.2
Xq28
7p12.1
6q15
15q25.1
10p15.1
16p12.3
22q13.1
1p31.3
17p13.1
2p25.1		 MHC
PTPN22
INS
C10orf59
SH2B3
ERBB3
CLEC16A
Intergenic
CTLA4
Intergenic
PTPN2
IL2RA
IL27
C6orf173
IL2
ORMDL3
Intergenic
GLIS3
Intergenic
CD69
Intergenic
Intergenic
Intergenic
IL10
UBASH3A
Intergenic
Intergenic
IFIH1
Intergenic
COBL
BACH2
CTSH
PRKCQ
Intergenic
C1QTNF6
PGM1
Intergenic
Intergenic		 rs9268645-?
rs2476601-?
rs7111341-?
rs10509540-?
rs3184504-?
rs2292239-?
rs12708716-?
rs5753037-T
rs3087243-?
rs7202877-G
rs1893217-?
rs12251307-?
rs4788084-G
rs9388489-G
rs4505848-?
rs2290400-?
rs1465788-?
rs7020673-?
rs2281808-?
rs4763879-A
rs425105-?
rs10517086-A
rs7221109-?
rs3024505-?
rs11203203-?
rs4900384-G
rs7804356-?
rs1990760-?
rs2664170-G
rs4948088-?
rs11755527-?
rs3825932-?
rs11258747-?
rs12444268-A
rs229541-?
rs2269241-G
rs16956936-?
rs1534422-G		 NR
NR
NR
0.71
NR
NR
NR
0.39
NR
1.0
NR
NR
0.42
0.45
NR
0.50
0.71
0.50
0.64
0.37
0.84
0.30
0.65
0.83
NR
0.29
0.76
NR
0.32
0.95
NR
NR
NR
0.30
NR
0.19
0.86
0.46		 1 x 10-100
9 x 10-85
4 x 10-48
1 x 10-28
3 x 10-27
2 x 10-25
2 x 10-16
3 x 10-16
1 x 10-15
3 x 10-15
4 x 10-15
1 x 10-13
3 x 10-13
4 x 10-13
5 x 10-13
6 x 10-13
2 x 10-12
5 x 10-12
1 x 10-11
2 x 10-11
3 x 10-11
5 x 10-10
1 x 10-9
2 x 10-9
2 x 10-9
4 x 10-9
5 x 10-9
7 x 10-9
8 x 10-9
4 x 10-8
5 x 10-8
8 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
4 x 10-7
5 x 10-7
2 x 10-6 		NR
NR
NR
1.33 [1.25-1.43]
NR
NR
NR
1.1 [1.04-1.17]
NR
1.28 [1.17-1.41]
NR
NR
1.09 [1.02-1.16]
1.17 [1.10-1.24]
NR
1.15 [1.08-1.22]
1.16 [1.10-1.25]
1.14 [1.08-1.20]
1.11 [1.05-1.19]
1.09 [1.02-1.16]
1.16 [1.08-1.27]
1.09 [1.02-1.17]
1.05 [0.99-1.12]
1.19 [1.10-1.30]
NR
1.09 [1.02-1.16]
1.14 [1.06-1.22]
NR
1.16 [1.07-1.24]
1.3 [1.11-1.49]
NR
NR
NR
1.1 [1.03-1.17]
NR
1.1 [1.02-1.18]
1.09 [1.00-1.19]
1.08 [1.02-1.15]		 Affymetrix & Illumina
[841,622] (imputed)		 N
05/27/09 Kottgen
May 10, 2009
Nat Genet
Multiple loci associated with indices of renal function and chronic kidney disease 		Renal function and chronic kidney disease 19,877 individuals, up to 2,388 cases 21,466 individuals, up to 1,932 cases 16p12.3
15q21.1
4q21.1
16p12.3		 UMOD
SPATA5L1, GATM
SHROOM3
UMOD		 rs12917707-T
rs2467853-G
rs17319721-A
rs12917707-G		 0.18
0.38
0.44
0.18		 5 x 10-16 (eGFRcrea)
6 x 10-14 (eGFRcrea)
1 x 10-12 (eGFRcrea)
2 x 10-12 (CKD)		 .02 [0.014-0.022] ml/min/1.73m2 increase
.01 [0.009-0.017] ml/min/1.73m2 decrease
.01 [0.008-0.016] ml/min/1.73m2 decrease
1.25 [1.18-1.33]		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
05/19/09 Levy
May 10, 2009
Nat Genet
Genome-wide association study of blood pressure and hypertension 		Diastolic Blood Pressure 29,136 individuals 34,433 individuals 12q24.12
15q24.1
12q21.33
3p22.1
10p12.33
12q24.21
11p15.1		 SH2B3
CSK, ULK3
ATP2B1
ULK4
CACNB2
TBX3, TBX5
PLEKHA7		 rs3184504-T
rs6495122-A
rs2681472-A
rs9815354-A
rs11014166-A
rs2384550-A
rs11024074-T		 0.48
0.42
0.83
0.17
0.66
0.35
0.72		 3 x 10-14
2 x 10-10
1 x 10-9
3 x 10-9
1 x 10-8
4 x 10-8
1 x 10-6 		.48 [0.36-0.60] mm Hg increase
.4 [0.28-0.52] mm Hg increase
.5 [0.34-0.66] mm Hg increase
.49 [0.33-0.65] mm Hg increase
.37 [0.25-0.49] mm Hg increase
.35 [0.23-0.47] mm Hg decrease
.33 [0.19-0.47] mm Hg decrease		 Affymetrix & Illumina
[2,533,153](imputed)		 N
05/19/09 " Hypertension 29,136 individuals 34,433 individuals 12q21.33
10p12.33
20q13.32
8p23.1		 ATP2B1
CACNB2
ZNF831, EDN3
MSRA		 rs2681472-A
rs11014166-A
rs16982520-A
rs11775334-A		 0.83
0.66
0.88
0.32		 2 x 10-11
6 x 10-8
2 x 10-7
4 x 10-6 		.15 [0.11-0.19] increase in log odds
.09 [0.05-0.13] increase in log odds
.13 [0.09-0.17] decrease in log odds
.08 [0.04-0.12] increase in log odds		 Affymetrix & Illumina
[2,533,153](imputed)		 N
05/19/09 " Systolic blood pressure 29,136 individuals 34,433 individuals 12q21.33
10q24.32
11p15.1
12q24.12
3q26.2
10p12.33
1p36.22		 ATP2B1
CYP17A1
PLEKHA7
SH2B3
MDS1
CACNB2
CASZ1		 rs2681492-T
rs1004467-A
rs381815-T
rs3184504-T
rs448378-A
rs11014166-A
rs12046278-T		 0.80
0.90
0.26
0.48
0.52
0.66
0.64		 4 x 10-11
1 x 10-10
2 x 10-9
5 x 10-9
1 x 10-7
7 x 10-7
5 x 10-6 		.85 [0.60-1.10] mm Hg increase
1.05 [0.74-1.36] mm Hg increase
.65 [0.43-0.87] mm Hg increase
.58 [0.38-0.78] mm Hg increase
.51 [0.31-0.71] mm Hg decrease
.5 [0.30-0.70] mm Hg increase
.53 [0.29-0.77] mm Hg decrease		 Affymetrix & Illumina
[2,533,153](imputed)		 N
05/19/09 Newton-Cheh
May 10, 2009
Nat Genet
Genome-wide association study identifies eight loci associated with blood pressure 		Diastolic Blood Pressure 34,433 individuals Up to 100,347 white individuals, up to 12,889 Indian Asian individuals 15q24.1
4q21.21
12q24.12
10q21.2
17q21.32
3q26.2		 CYP1A1, CYP1A2, CSK, LMAN1L, CPLX3, ARID3B
FGF5, PRDM8, c4orf22
ATXN2, SH2B3
c10orf107, TMEM26, RTKN2, RHOBTB1, ARID5B
ZNF652, PHB
MDS1		 rs1378942-C
rs16998073-T
rs653178-T
rs1530440-T
rs16948048-G
rs1918974-T		 0.36
0.21
0.53
0.19
0.39
0.54		 1 x 10-23
1 x 10-21
3 x 10-18
1 x 10-9
5 x 10-9
8 x 10-8 		.43 [0.35-0.51] mm Hg increase
.5 [0.40-0.60] mm Hg increase
.46 [0.36-0.56] mm Hg decrease
.39 [0.27-0.51] mm Hg decrease
.31 [0.21-0.41] mm Hg increase
.27 [0.17-0.37] mm Hg decrease		 Affymetrix & Illumina
[2,497,993] (imputed)		 N
05/19/09 " Systolic blood pressure 34,433 individuals Up to 100,347 white individuals, up to 12,889 Indian Asian individuals 10q24.32
1p36.22
17q21.31		 CYP17A1, AS3MT, CNNM2, NT5C2
MTHFR, NPPA, CLCN6, NPPB, AGTRAP
PLCD3, ACBD4, HEXIM1, HEXIM2		 rs11191548-T
rs17367504-G
rs12946454-T		 0.91
0.14
0.28		 7 x 10-24
2 x 10-13
1 x 10-8 		1.16 [0.92-1.40] mm Hg increase
.85 [0.63-1.07] mm Hg decrease
.57 [0.37-0.77] mm Hg increase		 Affymetrix & Illumina
[2,497,993] (imputed)		 N
05/21/09 Rich
May 09, 2009
Diabetologia
A genome-wide association scan for acute insulin response to glucose in Hispanic-Americans: the Insulin Resistance Atherosclerosis Family Study (IRAS FS). 		Insulin response 229 family members 961 family members NR NR NR NR NS NR Illumina
[309,200]		 N
05/20/09 Himes
May 07, 2009
Am J Hum Genet
Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene 		Asthma 422 cases, 1,533 controls 3,750 white cases, 13,365 white controls, 592 white trios, 1,903 black cases, 2,432 black controls, 929 black family members 5q12.1 PDE4D rs1588265-G 0.29 3 x 10-8 .85 [0.77-0.93] Illumina
[518,230]		 N
05/21/09 Yang
May 07, 2009
PLoS ONE
Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan 		Hypertension (young onset) 175 Han Chinese cases, 175 Han Chinese controls 833 Han Chinese cases, 833 Han Chinese controls 2p22.3 LOC344371, MYADML, FAM98A, RASGRP3 4-SNP-haplotype NR 3 x 10-10 NR Affymetrix
[91,713]		 N
05/19/09 Sanna
May 06, 2009
Hum Mol Genet
Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia 		Bilirubin levels 4,300 individuals 2,692 individuals 12p12.2 SLC01B3 rs2117032-C 0.47 3 x 10-14 .13 [0.08-0.18] SD increase Affymetrix
[362,129]		 N
05/14/09 Scott
May 05, 2009
Proc Natl Acad Sci USA
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry 		Bipolar disorder 3,683 cases, 14,507 controls NR 5q15
1p32.1
3p21.1
11q13.1
19p13.3
2p12
2q11.2
4q12
3q26.1
8p12
9q34.13
15q23
17q21.33		 MCTP1
NF1A
ITIH1, NEK4
NR
NR
CTNNA2
Intergenic
KIT
NR
NR
NR
NR
NR		 rs17418283-C
rs472913-C
rs1042779-A
rs2242663-T
rs7250872-T
rs13409348-G
rs6733011-G
rs2537859-T
rs7427021-G
rs6990255-T
rs2905072-A
rs6494849-A
rs1035050-T		 0.28
0.50
0.63
0.25
0.69
0.24
0.46
0.60
0.56
0.95
0.77
0.12
0.40		 1 x 10-7
2 x 10-7
2 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
9 x 10-6 		1.21 [1.13-1.30]
1.18 [1.11-1.25]
1.19 [1.11-1.27]
1.2 [1.11-1.29]
1.21 [1.12-1.31]
1.2 [1.11-1.29]
1.17 [1.10-1.25]
1.16 [1.09-1.24]
1.16 [1.09-1.24]
1.33 [1.18-1.51]
1.21 [1.11-1.32]
1.23 [1.13-1.35]
1.17 [1.09-1.25]		 Affymetrix and Illumina
[2,366,197] (imputed)		 N
05/12/09 Johnson
May 04, 2009
Hum Mol Genet
Genome-wide association meta-analysis for total serum bilirubin levels 		Serum bilirubin levels 9,264 individuals NR 2q37.1
12p12.1
11p15.4
2p11.2
6p22.1
4q28.1
7q21.11
13q34		 UGT1A1
SLCO1B1,LST-3TM12,SLCO1A2
SLC22A18
KRCC1
HIST1H2BC
Intergenic
SEMA3C
ARHGEF7		 rs6742078-T
rs4149056-C
rs16928809-A
rs12714207-T
rs12206204-T
rs1986655-A
rs4236644-A
rs4773330-A		 0.32
0.15
0.09
0.03
0.02
0.17
0.26
0.12		 5 x 10-324
7 x 10-13
1 x 10-7
5 x 10-7
8 x 10-7
2 x 10-6
2 x 10-6
8 x 10-6 		.23 [0.21-0.25] umol/l increase in log(tbil)
.05 [0.03-0.07] umol/l increase in log(tbil)
.06 [0.04-0.08] umol/l increase in log(tbil)
.03 [0.01-0.05] umol/l decrease in log(tbil)
.18 [0.10-0.26] umol/l increase in log(tbil)
.02 [0.00-0.04] umol/l decrease in log(tbil)
.02 [0.00-0.04] umol/l decrease in log(tbil)
.04 [0.02-0.06] umol/l decrease in log(tbil)		 Affymetrix & Illumina
[2,555,103] (imputed)		 N
05/07/09 Capasso
May 03, 2009
Nat Genet
Common variants in BARD1 influence susceptibility to high-risk neuroblastoma 		Neuroblastoma (high-risk) 397 cases, 2,043 controls 189 cases, 1,178 controls 2q35 BARD1 rs6435862-G 0.29 9 x 10-18 1.68 [1.49-1.90] Illumina
[462,866]		 N
05/07/09 Hallmayer
May 03, 2009
Nat Genet
Narcolepsy is strongly associated with the T-cell receptor alpha locus 		Narcolepsy 807 Caucasian cases, 1,074 Caucasian controls 363 Caucasian cases, 355 Caucasian controls, 561 Asian cases, 605 Asian controls, 133 African American cases, 144 African American controls 14q11.2 TRA-alpha, TRAJ10 rs1154155-C 0.14 3 x 10-22 1.69 [1.52-1.88] Affymetrix
[549,596]		 N
05/07/09 Takeuchi
April 29, 2009
Diabetes
Confirmation of multiple risk loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population 		Type 2 diabetes 519 Japanese cases, 503 Japanese controls 5,629 Japanese cases, 7,370 Japanese controls 9p21.3
11p15.5
6p22.3
8q24.11
10q22.33
10q25.2
3q27.2		 CDKN2A, CDKN2B
KCNQ1
CDKAL1
SLC30A8
HHEX
TCF7L2
IGF2BP2		 rs2383208-A
rs2237892-C
rs4712523-G
rs13266634-C
rs1111875-C
rs7903146-T
rs4402960-T		 0.55
0.59
0.41
0.57
0.28
0.04
0.31		 2 x 10-29
1 x 10-26
7 x 10-20
2 x 10-14
7 x 10-12
8 x 10-12
1 x 10-6 		1.34 [1.27-1.41]
1.33 [1.27-1.41]
1.27 [1.21-1.33]
1.22 [1.16-1.28]
1.21 [1.15-1.28]
1.54 [1.36-1.74]
1.14 [1.08-1.21]		 Illumina
[482,625]		 N
05/11/09 Wang
April 28, 2009
Nature
Common genetic variants on 5p14.1 associate with autism spectrum disorders 		Autism 3,101 family members, 1,204 cases, 6,491 controls 1,390 family members, 108 cases, 540 controls 5p14.1 CDH10,CDH9 rs4307059-T 0.61 2 x 10-10 1.19 [NR] Illumina
[474,019]		 N
05/05/09 Cho
April 26, 2009
Nat Genet
A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits 		Biomedical quantitative traits 8,842 Korean individuals 7,861 Korean individuals 12q24.13
7q31.31
6q22.31
1q32.2
12q21.33
16q12.2
7q31.31
12q21.33		 C12orf51
FAM3C
LOC644502
CD46, LOC148696
ATP2B1
FTO
FAM3C
ATP2B1		 rs2074356-T
rs7776725-C
rs12110693-A
rs12731740-T
rs17249754-A
rs9939609-A
rs7776725-C
rs17249754-A		 0.15
0.13
0.49
0.10
0.37
0.13
0.13
0.37		 8 x 10-12 (waist-hip ratio)
1 x 10-11 (BD-RT)
2 x 10-9 (pulse rate)
3 x10-9 (pulse rate)
1 x 10-7 (SBP)
2 x 10-7 (BMI)
2 x 10-6 (BD-TT)
3 x10-6 (DBP)		 .01 [0.004-0.008] decrease
NR
.66 [0.45-0.87] beats per minute increase
1.09 [0.72-1.44] beats per minute increase
1.06 [0.67-1.45] mm Hg decrease
.24 [0.14-0.32] kg/m2 increase
NR
.63 [0.37-0.89] mm Hg decrease		 Affymetrix
[2,156,535] (imputed)		 N
05/05/09 " Height 8,842 Korean individuals 7,861 Korean individuals 3q23
8q12.1
2p16.1
6p21.31
1p12		 ZBTB38
PLAG1
EFEMP1
HMGA1
Intergenic		 rs10513137-A
rs13273123-G
rs3791675-G
rs6918981-G
rs17038182-C		 0.26
0.07
0.22
0.21
0.42		 6 x10-12
1 x10-9
2 x10-9
3 x10-8
5 x10-7 		.46 [0.33-0.59] cm increase
.71 [0.48-0.94] cm decrease
.42 [0.28-0.56] cm increase
.4 [0.26-0.54] cm increase
.3 [0.18-0.42] cm decrease		 Affymetrix
[2,156,535] (imputed)		 N
04/23/09 Ikram
April 15, 2009
N Engl J Med
Genomewide Association Studies of Stroke 		Stroke 19,602 Caucasian individuals 3,004 African American individuals, 652 Caucasian cases, 3,613 Caucasian controls 12p13.33 NINJ2 rs12425791-A 0.19 1 x 10-9 (ischemic stroke) 1.29 [1.19-1.41] Affymetrix & Illumina
[2,194,468]		 N
04/22/09 Poduslo
April 14, 2009
Am J Med Genet B Neuropsychiatr Genet
A genome screen of successful aging without cognitive decline identifies LRP1B by haplotype analysis 		Successful cognitive aging 89 cases, 227 controls NR 2q22.1 LRP1B rs12474609-? NR 6 x 10-9 NR Affymetrix
[469,218]		 N
05/05/09 Hiura
April 10, 2009
Circ J
Identification of Genetic Markers Associated With High-Density Lipoprotein-Cholesterol by Genome-Wide Screening in a Japanese Population 		LDL cholesterol 900 Japanese individuals 1,810 Japanese individuals 16q13 CETP rs3764261-A 0.20 3 x 10-12 6.2 mg/dl increase Illumina
[368,274]		 N
04/22/09 Mangino
April 08, 2009
J Med Genet
A genome-wide association study identifies a novel locus on chromosome 18q12.2 influencing white cell telomere length 		Telomere length 1,625 women 1,165 individuals 18q12.2 BRUNOL4, VPS34 rs2162440-G NR 3 x 10-6 106 [62.88-149.12] base pairs shorter Illumina
[~314,075]		 N
04/14/09 Esparza-Gordillo
April 06, 2009
Nat Genet
A common variant on chromosome 11q13 is associated with atopic dermatitis 		Atopic dermatitis 939 cases, 975 controls, 1,097 family members 2,637 cases, 3,957 controls 11q13.5 C11orf30 rs7927894-A 0.36 8 x 10-10 1.22 [1.15-1.30] Affymetrix
[342,303]		 N
04/16/09 Kamatani
April 06, 2009
Nat Genet
A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians 		Hepatitis B 179 Japanese cases, 934 Japanese controls 1,599 Japanese cases, 2,821 Japanese controls, 308 Thai cases, 546 Thai controls 6p21.32 HLA-DPB1 rs9277535-G 0.56 6 x 10-39 1.75 [1.61-1.92] Illumina
[499,544]		 N
05/11/09 Yamada
April 05, 2009
Atherosclerosis
Identification of CELSR1 as a susceptibility gene for ischemic stroke in Japanese individuals by a genome-wide association study 		Ischemic stroke 131 cases, 135 controls 776 cases, 5,205 controls NR NR NR NR NS NR Affymetrix
[~520,000]		 N
04/22/09 Soranzo
April 03, 2009
PLoS Genet
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size 		Height 12,611 individuals 7,187 individuals 12q14.3
20q11.22
3q23
6p22.1
7p15.1
6q24.1
6p21.31
13q14.3
7p22.2
4p15.32
7q21.2
4q21.21
15q25.2
6p21.33
1p36.11
14q24.3
5p13.3
9p13.3
4q31.22
8q12.1		 HMGA2
UQCC
ZBTB38
HIST1H1D
JAZF1
GPR126
HMGA1,C6orf106
DLEU7
GNA12
LCORL
CDK6
PRKG2
ADAMTSL3
HLA-B
CATSPER4
TMED10
NPR3
WDR40A
HHIP
PLAG1		 rs8756-?
rs6088813-?
rs6763931-?
rs10946808-?
rs849141-?
rs6570507-?
rs1776897-?
rs3118914-?
rs1182188-?
rs6830062-?
rs2282978-?
rs710841-?
rs4842838-?
rs13437082-?
rs11809207-?
rs910316-?
rs10472828-?
rs7871764-?
rs1812175-?
rs7815788-?		 0.17
0.11
0.35
0.43
0.23
0.42
0.49
0.39
0.27
0.23
0.08
0.12
0.32
0.13
0.23
0.15
0.26
0.44
0.49
0.39		 5 x 10-14
1 x 10-13
3 x 10-12
6 x 10-12
3 x 10-11
4 x 10-11
8 x 10-11
4 x 10-10
3 x 10-9
5 x 10-9
1 x 10-8
2 x 10-8
3 x 10-8
5 x 10-8
6 x 10-8
1 x 10-7
3 x 10-7
2 x 10-6
4 x 10-6
5 x 10-6 		.08 [0.06-0.10] SD decrease
.09 [0.07-0.11] SD decrease
.07 [0.05-0.09] SD increase
.07 [0.04-0.10] SD increase
.08 [0.06-0.10] SD increase
.08 [0.06-0.10] SD decrease
.12 [0.08-0.16] SD increase
.08 [0.05-0.11] SD decrease
.07 [0.04-0.10] SD increase
.1 [0.07-0.13] SD increase
.06 [0.04-0.08] SD decrease
.07 [0.04-0.10] SD increase
.06 [0.04-0.07] SD decrease
.07 [0.04-0.10] SD decrease
.07 [0.04-0.10] SD increase
.05 [0.03-0.07] SD increase
.06 [0.04-0.08] SD decrease
.06 [0.03-0.09] SD increase
.06 [0.03-0.09] SD decrease
.07 [0.04-0.10] SD decrease		 Illumina
[229,216]		 N
04/13/09 Nan
April 02, 2009
J Invest Dermatol
Genome-Wide Association Study of Tanning Phenotype in a Population of European Ancestry 		Tanning 2,287 women 870 controls 6p25.3
11q14.3
5p13.3
16q24.3
11q14.3
16q24.3
14q32.2
12q13.13
21q22.3
5q33.1		 EXOC2
TYR
MATP
MC1R
GRM5
MC1R
Intergenic
LOC440100
PRDM15
PPARGC1B		 rs12210050-T
rs1393350-A
rs35391-T
rs11648785-T
rs10831496-G
rs154659-C
rs17094273-A
rs7969151-A
rs7279297-G
rs32579-A		 NR
NR
NR
NR
NR
NR
NR
0.21
NR
NR		 5 x 10-14
2 x 10-13
3 x 10-10
3 x 10-9
5 x 10-9
7 x 10-8
9 x 10-8
2 x 10-6
3 x 10-6
4 x 10-6 		.22 [0.16-0.28] increase in tanning ability score
.19 [0.13-0.25] increase in tanning ability score
.44 [0.30-0.58] decrease in tanning ability score
.14 [0.10-0.18] decrease in tanning ability score
.14 [0.10-0.18] decrease in tanning ability score
.14 [0.08-0.20] increase in tanning ability score
.2 [0.12-0.28] increase in tanning ability score
.13 [0.07-0.19] increase in tanning ability score
.12 [0.06-0.18] decrease in tanning ability score
.11 [0.07-0.15] decrease in tanning ability score		 Illumina
[528,173]		 N
04/03/09 Thomas
March 29, 2009
Nat Genet
A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1) 		Breast cancer 1,145 cases, 1,142 controls 8,625 cases, 9,657 controls 10q26.13
1p11.2
16q12.1
2q35
14q24.1
5q11.2		 FGFR2
Intergenic
TOX3
Intergenic
RAD51L1
MAP3K1		 rs2981579-T
rs11249433-C
rs3803662-T
rs13387042-A
rs999737-C
rs16886165-G		 0.41
0.39
0.27
0.51
0.76
0.15		 2 x 10-10
7 x 10-10
1 x 10-9
2 x 10-8
2 x 10-7
5 x 10-7 		1.17 [1.07-1.27]
1.16 [1.09-1.24]
1.16 [1.07-1.27]
1.25 [1.15-1.37]
1.06 [1.01-1.14]
1.23 [1.12-1.35]		 Illumina
[528,173]		 N
03/31/09 Newton-Cheh
March 22, 2009
Nat Genet
Common variants at ten loci influence QT interval duation in the QTGEN Study 		QT interval 13,685 individuals 15,854 individuals 1q23.3
1q23.3
1q23.3
16q21
6q22.31
11p15.5
1p36.31
7q36.1
7q36.1
11p15.5
16p13.13
3p22.2
17q12		 NOS1AP
NOS1AP
NOS1AP
CNOT1,GINS3, NDRG4, SLC38A7, GOT2
c6orf204,SLC35F1, PLN, ASF1A
KCNQ1
RNF207,NPHP4, CHDS, ACOT7, PLEKHG5, KLH21
KCNH2
KCNH2
KCNQ1
LITAF,CLEC16A, SNN, ZC3H7A, TNFRSF17
SCN5A
LIG3,RFFL		 rs12143842-T
rs12029454-A
rs16857031-G
rs37062-G
rs11756438-A
rs2074238-T
rs846111-C
rs4725982-T
rs2968864-C
rs12576239-T
rs8049607-T
rs12053903-C
rs2074518-T		 0.26
0.15
0.14
0.24
0.47
0.06
0.28
0.22
0.25
0.13
0.49
0.34
0.46		 2 x 10-78
3 x 10-45
1 x 10-34
3 x 10-25
5 x 10-22
3 x 10-17
1 x 10-16
5 x 10-16
8 x 10-16
1 x 10-15
5 x 10-15
1 x 10-14
6 x 10-12 		3.15 [2.81-3.49] msec increase
2.98 [2.63-3.32] msec increase
2.63 [2.28-2.97] msec increase
1.75 [1.41-2.09] msec decrease
1.4 [1.06-1.74] msec increase
7.88 [6.16-9.59] msec decrease
1.75 [1.41-2.09] msec increase
1.58 [1.23-1.92] msec increase
1.4 [1.06-1.74] msec decrease
1.75 [1.41-2.09] msec increase
1.23 [0.88-1.57] msec increase
1.23 [0.88-1.57] msec decrease
1.05 [0.71-1.39] msec decrease		 Affymetrix and Illumina
[up to 2,543,686] (imputed)		 N
04/02/09 Pfeufer
March 22, 2009
Nat Genet
Common variants at ten loci modulate the QT interval duration in the QTSCD Study 		QT interval 15,842 individuals up to 13,602 individuals 1q23.3
1q23.3
16q21
6q22.31
6q22.31
11p15.5
1p36.31
1q24.2
7q36.1
16p13.13
3p22.2
17q24.3		 NOS1AP
NOS1AP
NDRG4
PLN
PLN
KCNQ1
RNF207
ATP1B1
KCNH2
LITAF
SCN5A
KCNJ2		 rs12143842-T
rs4657178-T
rs7188697-A
rs11970286-T
rs12210810-C
rs12296050-T
rs846111-C
rs10919071-A
rs2968863-T
rs8049607-T
rs11129795-A
rs17779747-T		 0.24
0.33
0.74
0.44
0.06
0.20
0.29
0.87
0.29
0.46
0.23
0.35		 2 x 10-78
7 x 10-33
7 x 10-25
2 x 10-24
2 x 10-17
3 x 10-17
4 x 10-16
1 x 10-15
2 x 10-15
6 x 10-15
5 x 10-14
6 x 10-12 		2.88 [2.43-3.33] ms increase
2.19 [1.76-2.62] ms increase
1.66 [1.20-2.12] ms increase
1.64 [1.25-2.03] ms increase
3.13 [2.29-3.97] ms decrease
1.44 [0.95-1.93] ms increase
1.49 [1.00-1.98] ms increase
2.05 [1.48-2.62] ms increase
1.35 [0.90-1.80] ms decrease
1.25 [0.81-1.69] ms increase
1.27 [0.82-1.72] ms decrease
1.02 [0.53-1.51] ms decrease		 Affymetrix and Illumina
[unsure] (imputed)		 N
04/02/09 Org
March 20, 2009
Hum Mol Genet
Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations 		Hypertension 364 cases, 590 controls 1,043 cases, 1,769 controls 16q23.3 CDH13 rs11646213-T 0.60 8 x 10-6 1.28 [1.15-1.43] Affymetrix
[395,912]		 N
03/31/09 Pillai
March 20, 2009
PLoS Genet
A Genome-Wide Association Study in Chronic Obstructive Pulmonary Disease (COPD): Identification of Two Major Susceptibility Loci 		Chronic Obstructive Pulmonary Disease 823 cases, 810 controls 2,840 family members, 389 cases, 472 controls 15q25.1
4q31.22		 CHRNA3,CHRNA4,CHRNA5, IREB2, PSMA4, NP_001013641.2,Q9UD29
HHIP		 rs8034191-C
rs1828591-?		 0.33
NR		 1 x 10-10
1 x 10-7 		1.4 [1.18-1.67]
1.38 [1.17-1.63]		 Ilumina
[493,609]		 N
03/30/09 Takeuchi
March 20, 2009
PLoS Genet
A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose 		Warfarin maintenance dose 1,053 individuals 588 individuals 16p11.2
10q23.33
10q23.33
19p13.12		 VKORC1
CYP2C9
CYP2C9
CYP4F2		 rs9923231-T
rs1057910-?
rs1799853-?
rs2108622-?		 0.40
0.07
0.11
0.24		 3 x 10-181
3 x 10-79
1 x 10-31
3 x 10-10 		.97 [0.91-1.02] mg/week decrease
1.11 [1.00-1.22] mg/week decrease
.54 [0.45-0.63] mg/week decrease
.21 [0.14-0.27] mg/week increase		 Illumina
[325,997]		 N
03/31/09 Wilk
March 20, 2009
PLoS Genet
A Genome-Wide Association Study of Pulmonary Function Measures in the Framingham Heart Study 		Pulmonary function measures 7,691 individuals 835 individuals 4q31.22 HHIP rs13147758-G 0.39 8 x 10-11 .1 [NR] % increase in FEV1/FVC ratio Affymetrix
[2,540,223] (imputed)		 N
04/01/09 Tanaka
March 18, 2009
Am J Hum Genet
Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations 		Folate pathway vitamins 2,934 individuals 686 individuals 19q13.33
1p36.12
10p13
11q12.1
3p14.1		 FUT2
ALPL
CUBN
TCN1
PRICKLE2		 rs602662-A
rs4654748-C
rs11254363-A
rs526934-A
rs153734-T		 0.53
0.50
0.70
0.67
0.84		 3 x 10-20 (vitamin B12)
8 x 10-18 (vitamin B6)
1 x 10-6 (vitamin B12)
2 x 10-6 (vitamin B12)
7 x 10-6 (folate)		 49.77 [37.09-62.45] pg/ml increase
1.45 [0.90-2.00] ng/ml decrease
21.49 [7.71-35.27] pg/mL decrease
27.62 [11.65-43.59] pg/mL increase
.29 [0.13-0.45] ng/ml increase		 Affymetrix and Illumina
[~2.5 million] (imputed)		 N
03/31/09 Kilpivaara
March 15, 2009
Nat Genet
A germline JAK2 SNP is associated with predisposition to the development of JAK2(V617F)-positive myeloproliferative neoplasms 		Myeloproliferative neoplasms 324 cases, 2,999 controls NR 9p24.1 JAK2 rs10974944-? NR 4 x 10-20 3.1 [2.40-4.00] Affymetrix
[62,775]		 N
03/31/09 Cui
March 14, 2009
Mol Med
Genome Wide Association Study of Determinants of Anti-cyclic Citrullinated Peptide Antibody Titer in Adults with Rheumatoid Arthritis 		Anti-cyclic Citrullianted Peptide Antibody 531 individuals with rheumatoid arthritis 849 individuals with rheumatoid arthritis 6p21.32 HLA-DRA, HLA-DR3,BTNL2 rs1980493-? 0.13 5 x 10-7 NR Affymetrix
[97,248]		 N
03/29/09 Liu
March 13, 2009
PLoS Genet
Genome-wide association analyses identify SPOCK as a key novel gene underlying age at menarche 		Menarche (age at onset) 477 women 854 siblings, 762 women, 1,387 Chinese women NR NR NR NR NS NR Affymetrix
[379,319]		 N
03/30/09 Tregouet
March 10, 2009
Blood
Common susceptibility allele are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach 		Venous thromboembolism 419 cases, 1,228 controls 1,757 cases, 1,480 controls 9q34.2 ABO rs505922-C 0.35 4 x 10-15 1.81 [1.56-2.11] Illumina
[291,872]		 N
03/28/09 Birnbaum
March 08, 2009
Nat Genet
Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24 		Nonsyndromic cleft lip with or without cleft palate 224 cases, 383 controls 246 cases, 954 controls 8q24.21
1q32.2		 PVT1, GSDMC
IRF6		 rs987525-A
rs642961-A		 0.20
NR		 3 x 10-24
2 x 10-6 		2.57 [2.02-3.26]
NR		 Illumina
[521,176]		 N
03/24/09 Liu
March 04, 2009
Am J Hum Genet
Genome-wide Association and Replication Studies Identified TRHR as an Important Gene for Lean Body Mass 		Body mass (lean) 1,000 individuals 1,488 individuals, 1,972 family members, 2,955 Chinese individuals 8q23.1 TRHR rs7832552-T 0.32 4 x 10-10 .1 [0.04-0.16] kg increase Affymetrix
[379,319]		 N
03/24/09 Vink
March 04, 2009
Am J Hum Genet
Genome-wide Association Study of Smoking Initiation and Current Smoking 		Smoking behavior 3,540 individuals 6,405 individuals, 824 twin pairs NR NR NR NR NS NR Perlegen
[427,037]		 N
03/28/09 Hattori
March 02, 2009
Am J Med Genet B Neuropsychiatr Genet
Preliminary genome-wide association study of bipolar disorder in the Japanese population 		Bipolar disorder 107 cases, 107 controls 395 cases, 409 controls NR NR NR NR NS NR Affymetrix
[88,671]		 N
04/01/09 Caporaso
February 27, 2009
PLoS ONE
Genome-wide and candidate gene association study of cigarette smoking behaviors 		Smoking behavior 4,611 individuals (2,617 smokers) NR 3q13.12
1p22.3
1p35.2
3q24
12q21.2
16p13.2
18q11.2
19p12
5q14.3
9p21.2
9q31.1
Xq23
14q24.1
17p13.2
Xp11.3
12q21.33
13q33.1
4q31.1
7p15.2
3q27.2
4q28.1		 BBX
AK002179
Intergenic
Intergenic
Intergenic
Intergenic
CABLES1
ZNF505
LOC133789
Intergenic
Intergenic
TRPC5
ACTN1
CAMKK1
MAOA
Intergenic
Intergenic
SET7
Intergenic
Intergenic
Intergenic		 rs6437740-?
rs7553864-?
rs910696-?
rs800082-?
rs1402279-?
rs3112740-?
rs11082304-?
rs10411195-?
rs933688-?
rs1889899-?
rs10989661-?
rs7050529-?
rs2268983-?
rs758642-?
rs3027409-?
rs1847461-?
rs912969-?
rs17050782-?
rs886716-?
rs6444087-?
rs950063-?		 0.24
0.39
0.31
0.42
0.95
0.86
0.49
0.03
0.17
0.37
0.74
0.07
0.51
0.34
0.95
0.94
0.07
0.21
0.69
0.26
0.39		 2 x 10-7 (CPD)
3 x 10-6 (SMKDU)
3 x 10-6 (CPD)
3 x 10-6 (PKYRS)
5 x 10-6 (EVNV)
6 x 10-6 (CPDBI)
6 x 10-6 (SMKAGE)
6 x 10-6 (CPD)
6 x 10-6 (EVNV)
6 x 10-6 (EVNV)
6 x 10-6 (CIGSTAT)
6 x 10-6 (CPD)
7 x 10-6 (CPDBI)
7 x 10-6 (CPD)
7 x 10-6 (CPDBI)
8 x 10-6 (CIGSTAT)
8 x 10-6 (SMKDU)
8 x 10-6 (SMKAGE)
8 x 10-6 (CPDBI)
9 x 10-6 (EVNV)
9 x 10-6 (SMKDU)		 .1 [NR] fewer cigarettes per day
.08 [NR] more years
.08 [NR] more cigarettes per day
.12 [NR] more pack years
1.51 [NR]
2.16 [NR]
.03 [NR] years older
.21 [NR] fewer cigarettes per day
1.48 [NR]
1.26 [NR]
1.68 [NR]
.06 [NR] fewer cigarettes per day
1.52 [NR]
.08 [NR] more cigarettes per day
1.73 [NR]
1.8 [NR]
.14 [NR] fewer years
.03 [NR] years older
1.52 [NR]
1.28 [NR]
.08 [NR] fewer years		 Illumina
[~518,000] (pooled)		 N
03/18/09 Pezzolesi
February 27, 2009
Diabetes
Genome-wide Association Scan for Diabetic Nephropathy Susceptibility Genes in Type 1 Diabetes Mellitus 		Diabetic nephropathy 820 cases, 885 controls 1,304 individuals NR NR NR NR NS NR Affymetrix
[359,193]		 N
03/18/09 Gu
February 25, 2009
Nature
Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease 		Cystic fibrosis severity 160 severe lung disease patients, 160 mild lung disease patients (all homozygous for CFTR deltaF508 variant) 101 severe lung disease patients, 381 mild lung disease patients, 1,118 family members NR NR NR NR NS NR Affymetrix
[100,198] (pooled)		 N
03/18/09 Xiong
February 25, 2009
Am J Hum Genet
Genome-wide Association and Follow-Up Replication Studies Identified ADAMTS18 and TGFBR3 as Bone Mass Candidate Genes in Different Ethnic Groups 		Bone mineral density 1,000 white individuals 4,925 white individuals, 350 Chinese hip fracture cases, 350 Chinese controls, 2,955 Chinese individuals, 908 West African men 16q23.1
1p22.2		 ADAMTS18
TGFBR3		 rs11864477-C
rs17131547-A		 0.12
0.01		 2 x 10-8 (hip BMD)
1 x 10-6 (spine BMD)		 1 % [NR] of variance explained
1.2 % [NR] of variance explained		 Affymetrix
[379,319]		 N
03/01/09 Schrauwen
February 18, 2009
Am J Hum Genet
A Genome-wide Analysis Identifies Genetic Variants in the RELN Gene Associated with Otosclerosis 		Otosclerosis 302 cases, 302 controls 847 cases, 872 controls 7q22.1 RELN rs3914132-? 0.23 2 x 10-8 1.54 [1.32-1.79] Illumina
[~555,000] (pooled)		 N
05/07/09 Smith
February 15, 2009
Heart Rhythm
Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae 		Electrocardiographic conduction measures 1,262 Kosraen individuals NR 3p22.2
4p16.1
3p22.2
1q32.1
4q31.3
2q31.1
6p12.2		 SCN5A
MSX1
SCN5A
NR
NR
Intergenic
NR		 rs7638909-G
rs2008242-?
rs2070488-A
rs7512898-?
rs17030434-?
rs2461751-G
rs283566-?		 0.40
0.15
0.33
0.41
0.43
0.44
0.16		 2 x 10-6 (PR interval)
3 x 10-6 (PR segment)
4 x 10-6 (PR interval)
5 x 10-6 (PR segment)
5 x 10-6 (P wave duration)
8 x 10-6 (PR interval)
9 x 10-6 (P wave duration)		 4.8 [2.84-6.76] ms increase
NR
5 [2.84-7.16] ms decrease
NR
NR
4.54 [2.58-6.50] ms increase
NR		 Affymetrix
[338,049]		 N
02/28/09 Zheng
February 15, 2009
Nat Genet
Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1 		Breast cancer 1,505 Chinese cases, 1,522 Chinese controls 1,554 Chinese cases, 1,576 Chinese controls 6q25.1 C6orf97 rs2046210-A 0.37 2 x 10-15 1.29 [1.21-1.37] Affymetrix
[up to 607,728]		 N
02/28/09 Soranzo
February 12, 2009
Blood
A novel variant on chromosome 7Q22.3 associated with mean platelet volume, counts and function 		Mean platelet volume 1,221 individuals 7,365 individuals 7q22.3 Intergenic rs342293-G 0.45 1 x 10-24 .02 [0.014-0.018] log fl increase Affymetrix
[361,352]		 N
03/01/09 Erdmann
February 08, 2009
Nat Genet
New susceptibility locus for coronary artery disease on chromosome 3q22.3 		Coronary artery disease 6,990 cases, 8,955 controls 12,417 cases, 12,411 controls 3q22.3
12q24.31		 MRAS
HNF1A,C12orf43		 rs9818870-T
rs2259816-T		 0.15
0.36		 7 x 10-13
5 x 10-7 		1.15 [1.11-1.19]
1.08 [1.05-1.11]		 Affymetrix
[567,119]		 N
03/01/09 Gudbjartsson
February 08, 2009
Nat Genet
Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction 		Plasma eosinophil count 9,392 individuals 12,118 individuals 12q24.12
3q21.3
2q12.1
5q31.1
2q34
5q22.1
6p21.32		 SH2B3
GATA2
IL1RL1
IL5
IKZF2
WDR36, TSLP
MHC		 rs3184504-T
rs4857855-T
rs1420101-A
rs4143832-C
rs12619285-G
rs2416257-G
rs2269426-T		 0.38
0.82
0.41
0.16
0.74
0.85
0.76		 7 x 10-19 (European)
9 x 10-17 (European)
5 x 10-14 (European)
1 x 10-10 (European)
5 x 10-10 (European)
1 x 10-6 (European)
3 x 10-6 (European)		 7.6 [5.9-9.3] % standard unit increase
9.4 [7.2-11.6] % standard unit increase
6.4 [4.7-8.1] % standard unit increase
7.1 [4.9-9.2] % standard unit increase
6.3 [4.3-8.3] % standard unit increase
6.1 [3.7-8.6] % standard unit increase
4.6 [2.7-6.6] % standard unit increase		 Illumina
[312,179]		 N
03/01/09 Kathiresan
February 08, 2009
Nat Genet
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants 		Myocardial infarction (early onset) 2,967 cases, 3,075 controls 9,746 cases, 9,746 controls 9p21.3
1p13.3
21q22.11
1q41
6p24.1
19p13.2
10q11.21
1p32.3
2q33.1		 CDKN2A, CDKN2B
CELSR2, PSRC1, SORT1
SLC5A3, MRPS6, KCNE2
MIA3
PHACTR1
LDLR
CXCL12
PCSK9
WDR12		 rs4977574-G
rs646776-T
rs9982601-T
rs17465637-C
rs12526453-C
rs1122608-G
rs1746048-C
rs11206510-T
rs6725887-C		 0.56
0.81
0.13
0.72
0.65
0.75
0.84
0.81
0.14		 3 x 10-44
8 x 10-12
6 x 10-11
1 x 10-9
1 x 10-9
2 x 10-9
7 x 10-9
1 x 10-8
1 x 10-8 		1.29 [1.25-1.34]
1.19 [1.13-1.26]
1.2 [1.14-1.27]
1.14 [1.10-1.19]
1.12 [1.08-1.17]
1.15 [1.10-1.20]
1.17 [1.11-1.24]
1.15 [1.10-1.21]
1.17 [1.11-1.23]		 Affymetrix
[~2.5 million] (imputed)		 N
04/01/09 Tregouet
February 08, 2009
Nat Genet
Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease 		Coronary artery disease 1,926 cases, 2,938 controls 7,073 cases, 7,325 controls 6q25.3
6q25.3		 SLC22A3,LPAL2,LPA
SLC22A3,LPAL2,LPA		 4-SNP haplotype-2
4-SNP haplotype-1		 0.02
0.16		 4 x 10-15 (CCTC)
1 x 10-9 (CTTG)		 1.82 [1.57-2.12]
1.2 [1.13-1.28]		 Affymetrix
[~500,000]		 N
02/28/09 Gudmundsson
February 06, 2009
Nat Genet
Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations 		Thyroid cancer 192 cases, 37,196 controls 432 cases, 1,727 controls 9q22.33
14q13.3		 FOXE1
NKX2-1		 rs965513-A
rs944289-T		 0.34
0.57		 2 x 10-27
2 x 10-9 		1.75 [1.59-1.94]
1.37 [1.24-1.52]		 Illumina
[304,083]		 N
02/27/09 Garcia-Barcelo
February 05, 2009
Proc Natl Acad Sci USA
Genome-wide association study identifies NRG1 as a susceptibility locus for Hirschsprung's disease 		Hirschsprung's disease 181 Chinese cases, 346 Chinese controls 190 Chinese cases, 510 Chinese controls 10q21.1
8p12		 RET, GALNACT-2, RASGEF1A
NRG1		 rs2742234-T
rs16879552-G		 NR
0.39		 4 x 10-18
2 x 10-8 		NR
1.68 [1.40-2.00]		 Affymetrix
[293,836]		 N
03/31/09 Chio
February 04, 2009
Hum Mol Genet
A two-stage genome-wide association study of sporadic amyotrophic lateral sclerosis 		Amyotrophic lateral sclerosis 553 cases, 2,338 controls 3,149 cases, 3,335 controls NR NR NR NR NS NR Illumina
[545,066]		 N
02/27/09 Liu
February 03, 2009
Mol Psychiatry
Genome-wide association analyses suggested a novel mechanism for smoking behavior regulated by IL15 		Smoking behavior 417 Caucasian males, 423 Caucasian females 412 African American males, 839 African American females, 3,491 Caucasian males, 4,132 Caucasian females NR NR NR NR NS NR Affymetrix
[379,319]		 N
02/28/09 Kim
February 01, 2009
Clin Exp Allergy
Alpha-T-catenin (CTNNA3) gene was identified as a risk variant for toluene diisocyanate-induced asthma by genome-wide association analysis 		Asthma (toluene diisocyanate-induced) 84 Korean cases, 263 Korean controls NR 13q12.13
10q21.3
9p21.3		 Intergenic
CTNNA3
Intergenic		 rs9319321-T
rs10762058-G
rs16937883-G		 0.29
0.25
0.02		 3 x 10-6
6 x 10-6
7 x 10-6 		5.2 [2.47-10.92]
5 [2.36-10.6]
5.29 [2.41-11.61]		 Affymetrix
[312,978]		 N
02/27/09 Kim
February 01, 2009
Pharmacogenomics
Genome-wide association study of acute post-surgical pain in humans 		Pain 60 females, 52 males NR 19p12
11q23.3
1p21.3		 LOC400680, ZNF429
NR
NR		 rs2562456-?
rs17122021-?
rs6693882-?		 NR
NR
NR		 2 x 10-10 (onset time of analgesia)
7 x 10-7 (maximum post-operative pain rating)
2 x 10-6 (post-operative pain onset time)		 NR
NR
NR		 Affymetrix
[374,975]		 N
03/30/09 Polasek
February 01, 2009
Croat Med J
Genome-wide association study of anthropometric traits in Korcula Island, Croatia 		Anthropometric traits 898 individuals NR 16p11.2
14q32.13
14q23.3
5q33.3
7q22.1
1p36.32
7q22.1
13q14.3
2q31.1
5q33.3
7q22.1
2p22.3
5q33.2		 SEZ6L2
LOC122509, FAM14B
MAX
SGCD
ZNF498
Intergenic
ZNF498
XTP498
Intergenic
SGCD
ZNF498
CRIM1
AMPA1, GRIA1		 rs4787483-?
rs7157940-?
rs7158173-?
rs157350-?
rs7792939-?
rs7513590-?
rs7792939-?
rs7792939-?
rs7590983-?
rs157350-?
rs7792939-?
rs1863080-?
rs12658202-?		 0.34
0.46
0.48
0.11
0.15
0.10
0.15
0.28
0.05
0.11
0.15
0.10
0.45		 2 x 10-6 (waist cirumference)
3 x 10-6 (weight)
4 x 10-6 (waist circumference)
4 x 10-6 (brachial circumference)
4 x 10-6 (weight)
5 x 10-6 (height)
5 x 10-6 (brachial circumference)
6 x 10-6 (brachial circumference)
6 x 10-6 (BMI)
6 x 10-6 (hip circumference)
6 x 10-6 (hip circumference)
8 x 10-6 (brachial circumference)
9 x 10-6 (height)		 .16 [0.09-0.23] mm increase
.12 [0.07-0.17] kg increase
.11 [0.06-0.16] mm decrease
.31 [0.18-0.44] mm decrease
.26 [0.15-0.37] kg increase
.31 [0.17-0.45] mm decrease
.26 [0.15-0.37] mm increase
.17 [0.10-0.24] mm increase
.46 [0.26-0.66] kg/m2 increase
.31 [0.18-0.44] mm decrease
.26 [0.15-0.37] mm increase
.31 [0.17-0.45] mm increase
.11 [0.06-0.16] mm increase		 Illumina
[316,730]		 N
02/25/09 Stefansson
February 01, 2009
Nat Genet
Variant in the sequence of the LINGO1 gene confers risk of essential tremor 		Essential tremor 452 cases, 14,378 controls 300 cases, 1,419 controls 15q24.3 LINGO1 rs9652490-G 0.23 1 x 10-9 1.55 [1.35-1.79] Illumina
[305,624]		 N
03/31/09 Zemunik
February 01, 2009
Croat Med J
Genome-wide association study of biochemical traits in Korcula Island, Croatia 		Biochemical measures 898 individuals NR 4p16.1
12q24.23
4q12
4q13.1
6q16.3
12q12
4q31.23
Xp22.31
12q21.33
12q24.23
4q23
18q12.3
Xq23
20p12.1
21q22.3
21q22.3
16q13		 SLC2A9
KSR2
USP46
LPHN3
GRIK2
Intergenic
NR3C2
Neuroligin 4
Intergenic
KSR2
RAP1GDS1
SLC14A2
ZCCHC16
PCSK2
PKNOX1
PKNOX1
CETP		 rs13129697-C
rs4767631-A
rs346923-A
rs4599440-A
rs12207601-G
rs871392-A
rs1490453-A
rs7885458-G
rs10777332-A
rs10444502-C
rs10516430-A
rs10502868-G
rs5982533-G
rs6044777-A
rs2839619-G
rs2839619-G
rs7499892-A		 0.25
0.31
0.13
0.23
0.16
0.15
0.17
0.24
0.11
0.28
0.28
0.08
0.22
0.17
0.40
0.40
0.16		 1 x 10-9 (uric acid)
6 x 10-7 (LDL cholesterol)
2 x 10-6 (triglycerides)
2 x 10-6 (HDL cholesterol)
2 x 10-6 (fibrinogen)
3 x 10-6 (HDL cholesterol)
3 x 10-6 (fibrinogen)
3 x 10-6 (fibrinogen)
5 x 10-6 (total cholesterol)
6 x 10-6 (total cholesterol)
6 x 10-6 (triglycerides)
7 x 10-6 (albumin)
7 x 10-6 (triglycerides)
8 x 10-6 (fibrinogen)
8 x 10-6 (total cholesterol)
8 x 10-6 (LDL cholesterol)
9 x 10-6 (HDL cholesterol)		 .29 [0.21-0.37] umol/l decrease
.12 [0.11-0.23] mmol/L decrease
.28 [0.17-0.39] mmol/L decrease
.2 [0.12-0.28] mmol/L increase
.26 [0.15-0.37] g/L decrease
.26 [0.15-0.37] mmol/L decrease
.25 [0.15-0.35] g/L increase
.23 [0.13-0.33] g/L decrease
.24 [0.14-0.34] mmol/L decrease
.17 [0.10-0.24] mmol/L decrease
.16 [0.09-0.23] mmol/L decrease
.04 [0.21-0.51] g/L decrease
.23 [0.13-0.33] mmol/L decrease
.23 [0.13-0.33] g/L increase
.13 [0.07-0.19] mmol/L increase
.13 [0.08-0.18] mmol/L increase
.24 [0.14-0.34] mmol/L decrease		 Illumina
[316,730]		 N
02/25/09 Timpson
January 30, 2009
Hum Mol Genet
Common variants in the region around Osterix are associated with bone mineral density and growth in childhood 		Bone mineral density 1,418 children, 135 adults 3,875 children NR NR NR NR NS NR Illumina
[up to 315,807]		 N
02/28/09 Ferrucci
January 29, 2009
Am J Hum Genet
Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study 		Plasma carotenoid and tocopherol levels 1,191 individuals 2,751 individuals 16q23.2
11q23.3		 BCMO1
APOA5		 rs6564851-G
rs12272004-A		 0.39
0.07		 2 x 10-24 (beta-carotene)
8 x 10-10 (alpha-tocopherol)		 .15 [0.120-0.177] umol/L increase
.07 [0.049-0.095] umol/L increase		 Illumina
[~500,451] (pooled)		 N
02/26/09 Yang
January 28, 2009
JAMA
Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia 		Treatment response for acute lymphoblastic leukemia 487 children NR 10p12.33
2q33.1
4q31.21
20q13.12
7p14.2
7p21.2
10q26.12
11p15.1
6q25.3
5p13.2
10p14
11q21		 ST8SIA6
C2orf47
IL15
NCOA3
ELMO1
DGKB
intergenic
intergenic
intergenic
LMBRD2
Intergenic
MAML2		 rs359312-T
rs1569175-T
rs17007695-C
rs6125048-T
rs4723619-C
rs6971925-T
rs2901286-A
rs7128311-C
rs35229355-T
rs267759-A
rs10508343-A
rs7115578-A		 0.04
0.11
0.10
0.04
0.07
0.02
0.03
0.03
0.03
0.05
0.04
0.64		 9 x 10-8
9 x 10-7
9 x 10-7
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6 		3.91 [1.52-10.10]
2.73 [1.52-4.93]
2.67 [1.53-4.68]
2.73 [1.08-6.88]
3.01 [1.50-6.03]
13.91 [2.72-70.92]
4.66 [1.58-13.7]
13.9 [2.72-71.1]
7.24 [2.46-21.30]
3.23 [1.52-6.87]
3.81 [1.40-10.40]
1.86 [1.23-2.79]		 Affymetrix
[476,796]		 N
02/06/09 Nair
January 25, 2009
Nat Genet
Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways 		Psoriasis 1,359 cases, 1,400 controls 5,048 cases, 5,041 controls 6p21.33
5q33.3
5q33.1
5q31.1
6q23.3
12q13.2
1p31.3
9q34.13		 HLA-C
IL12B
TNIP1
IL13
TNFAIP3
IL23A, STAT2
IL23R
TSC1		 rs12191877-T
rs2082412-G
rs17728338-A
rs20541-G
rs610604-G
rs2066808-A
rs2201841-G
rs1076160-T		 0.15
0.80
0.054
0.79
0.32
0.93
0.30
0.48		 1 x 10-100
2 x 10-28
1 x 10-20
5 x 10-15
9 x 10-12
1 x 10-9
3 x 10-8
6 x 10-6 		2.64 [NR]
1.44 [NR]
1.59 [NR]
1.27 [NR]
1.19 [NR]
1.34 [NR]
1.13 [NR]
1.09 [NR]		 Perlegen
[~2.5 million] (imputed)		 N
02/07/09 Zhang
January 25, 2009
Nat Genet
Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21 		Psoriasis 1,139 Chinese cases, 1,132 Chinese controls 5,721 Chinese cases, 7,340 Chinese controls 1q21.3
5q33.3
6p21.33		 LCE3D, LCE3A
IL12B
MHC		 rs4085613-A
rs3213094-A
rs1265181-?		 0.43
0.45
NR		 7 x 10-30
3 x 10-26
1.32 [1.25-1.39]
1.28 [1.23-1.35]
22.62 		Illumina
[494,902]		 N
02/26/09 Otowa
January 23, 2009
J Hum Genet
Genome-wide association study of panic disorder in the Japanese population 		Panic disorder 200 Japanese cases, 200 Japanese controls NR 12p13.31
1q32.1
17q25.1
12q13.13
13q32.1
6q25.1
8p21.1
1p13.3
3p26.1
12q12
19q13.33
6p12.3
14q23.1
20p13
5q21.1
12q24.33
21q21.1		 TMEM16B
PKP1
SDK2
CALCOCO1
Intergenic
PLEKHG1
CLU
Intergenic
GRM7
Intergenic
Intergenic
TNFRSF21
Intergenic
SMOX
Intergenic
Intergenic
USP25		 rs12579350-?
rs860554-?
rs3816995-?
rs941184-?
rs9302001-?
rs9372078-?
rs17466684-?
rs12061304-?
rs3749380-?
rs2731006-?
rs3810265-?
rs2103868-?
rs4901869-?
rs16989303-?
rs4702982-?
rs7299940-?
rs2823455-?		 0.01
0.05
0.03
0.03
0.20
0.11
0.09
0.10
0.25
0.29
0.07
0.26
0.02
0.21
0.16
0.29
0.03		 4 x 10-9
5 x 10-8
2 x 10-7
3 x 10-7
3 x 10-7
5 x 10-7
7 x 10-7
1 x 10-6
2 x 10-6
4 x10-6
4 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[253,903]		 N
02/25/09 Ling
January 22, 2009
Obesity
Genome-wide Linkage and Association Anaylses to Identify Genes Influencing Adiponectin Levels: The GEMS Study 		Adiponectin levels 997 cases, 989 controls NR 3q27.3
5q35.2		 ADIPOQ
Intergenic		 rs6773957-A
rs7722022-?		 0.37
NR		 5 x 10-8
9 x 10-6 		NR
NR		 Affymetrix
[398,625]		 N
03/03/09 Meyre
January 18, 2009
Nat Genet
Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations 		Obesity 695 obese adults, 685 obese children, 731 lean adults, 685 lean children 1,171 obese adults, 896 obese children, 1,114 lean adults, 1,297 lean children, 4,417 adults, 5,291 children 16q12.2
18q21.32
16q23.2
10p13
18q11.2		 FTO
MC4R
MAF
PTER
NPC1		 rs1421085-C
rs17782313-C
rs1424233-A
rs10508503-C
rs1805081-A		 0.40
0.18
0.43
0.91
0.56		 1 x 10-28 (children)
5 x 10-15 (children)
4 x 10-13 (children)
2 x 10-7 (children)
3 x 10-7 (children)		 1.39 [1.27-1.51]
1.22 [1.05-1.40]
1.12 [1.00-1.24]
1.56 [1.10-2.78]
1.33 [1.08-1.75]		 Illumina
[308,846]		 N
01/21/09 Tanaka
January 16, 2009
PLoS Genet
Genome-wide association study of plasma polyunsaturated fatty acids in the InCHIANTI Study 		Plasma levels of polyunsaturated fatty acids 1,210 individuals 1,076 individuals NR NR NR NR NS NR Illumina
[495,343]		 N
02/27/09 Carrasquillo
January 11, 2009
Nat Genet
Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease 		Alzheimer's disease 844 cases, 1,255 controls 1,547 cases, 1,209 controls Xq21.31 PCDH11X rs2573905-? 0.46 2 x 10-7 1.29 [1.17-1.42] Illumina
[313,504]		 N
01/21/09 Burgner
January 09, 2009
PLoS Genet
A genome-wide association study identifies novel and functionally related susceptibility loci for Kawasaki disease 		Kawasaki disease 107 cases, 134 controls 583 cases, 1,357 family members 3q26.31
16q22.3		 NAALADL2
ZFHX3		 rs17531088-T
rs7199343-T		 0.44
0.30		 1 x 10-6
2 x 10-6 		1.43 [1.32-1.53]
1.56 [1.33-1.92]		 Affymetrix
[223,922]		 N
02/25/09 Feulner
January 07, 2009
Mol Psychiatry
Examination of the current top candidate genes for AD in a genome-wide association study 		Alzheimer's disease 491 cases, 479 controls NR 19q13.32 TOMM40, APOE rs157580-? NR 1 x 10-40 NR Illumina
[~550,000]		 N
01/21/09 Ober
January 07, 2009
J Lipid Res
Genome-wide association study of plasma Lp(a)levels Identifies multiple genes on chromosome 6q 		Plasma Lp (a) levels 357 individuals 1,054 individuals 6q25.3 LPA rs6919346-? 0.16 4 x 10-11 .66 [mg/dl decrease] Affymetrix
[290,327]		 N
01/21/09 Silverberg
January 04, 2009
Nat Genet
Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study 		Ulcerative colitis 1,022 cases, 2,503 controls 1,387 cases, 1,115 controls 6p21.32
1p36.13
12q15
1p36.13
1p31.3
1p31.3
12q15
7q31.1
9q21.32
7q31.1
7q31.1
7q31.1		 BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1
OTUD3, PLA2G2E
IFNG, IL26, IL22
RNF186
IL23R
IL23R
IL26
SLC26A3, DLD, LAMB1
Intergenic
Intergenic
SLC26A3, DLD, LAMB1
SLC26A3, DLD, LAMB1		 rs2395185-?
rs6426833-G
rs1558744-A
rs3806308-?
rs11209026-?
rs10889677-A
rs2870946-G
rs4598195-?
rs668853-G
rs4730273-?
rs2158836-A
rs4730276-?		 0.67
0.54
0.38
0.63
0.93
0.30
0.055
0.54
0.39
0.70
0.35
0.39		 1 x 10-16
5 x 10-13
3 x 10-12
7 x 10-9
1 x 10-8
1 x 10-8
5 x 10-7
1 x 10-6
2 x 10-6
5 x 10-6
7 x 10-6
9 x 10-6 		1.52
1.37
1.35
1.28
1.79
1.29
1.54
1.23
1.2
1.22
1.21
1.22 		Illumina
[280,748]		 N
01/21/09 Beecham
January 03, 2009
Am J Hum Genet
Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease 		Alzheimer's disease 492 cases, 496 controls 238 cases, 220 controls 12q13.11
19q13.31
1q42.2		 FAM113B
ZNF224
DISC1		 rs11610206-?
rs2061333-?
rs12044355-?		 NR
NR
NR		 3 x 10-7
2 x 10-6
9 x 10-6 		NR
NR
NR		 Illumina
[~2.5 million] (imputed)		 N
02/27/09 Hinks
January 01, 2009
Arthritis Rheum
Identification of a novel susceptibility locus for juvenile idiopathic arthritis by genome-wide association analysis 		Juvenile idiopathic arthritis 279 cases, 184 controls up to 654 cases, 1,847 controls 1p13.1 VTCN1 rs12046117-? 0.09 1 x 10-6 1.58 [1.29-1.94] Affymetrix
[88,862]		 N
01/16/09 Limou
January 01, 2009
J Infect Dis
Genomewide Association Study of an AIDS-Nonprogression Cohort Emphasizes the Role Played by HLA Genes (ANRS Genomewide Association Study 02). 		AIDS progression 275 HIV positive patients, 1,438 controls 626 patients 6p21.33
6p21.33
6p21.33		 HCP5, MICB, MCCD1, BAT1, LTB, TNF
HLA-C
ZNRD1, RNF39		 rs2395029-G
rs10484554-T
rs8321-G		 0.03
0.13
NR		 3 x 10-19
6 x 10-8
5 x 10-7 		3.47 [2.39-5.04]
NR
NR		 Illumina
[291,119]		 N
02/26/09 Sun
January 01, 2009
Cancer Res
Sequence variants at 22q13 are associated with prostate cancer risk 		Prostate cancer 1,235 aggressive cases, 1,599 controls 3,629 aggressive cases, 4,255 non-aggressive cases, 5,738 controls 22q13.1 TNRC6B rs9623117-C 0.21 5 x 10-7 1.18 [1.11-1.26] Affymetrix and Illumina
[~2 million] (imputed)		 N
01/14/09 Zhang
December 31, 2008
Mol Psychiatry
Singleton deletions throughout the genome increase risk of bipolar disorder 		Bipolar disorder 1,001 cases, 1,033 controls NR Pending Pending Pending Pending Pending Pending Affymetrix
[51,757 CNVs]		 Y
01/14/09 Wang
December 29, 2008
Proc Natl Acad Sci USA
Whole-genome association study identifies STK39 as a hypertension susceptibility gene 		Blood pressure 542 individuals 6,583 individuals 2q24.3 STK39 rs6749447-G 0.28 2 x 10-7 1.9 [1.2-2.6] mm Hg increase in DBP Affymetrix
[79,447]		 N
01/14/09 Meisinger
December 24, 2008
Am J Hum Genet
A genome-wide association study identifies three loci associated with mean platelet volume 		Mean platelet volume 1,606 individuals 8,617 individuals 12q24.31
17q11.2
3p14.3		 WDR66
TAOK1
ARHGEF3		 rs7961894-A
rs2138852-C
rs12485738-A		 0.11
0.47
0.30		 7 x 10-48
7 x 10-28
4 x 10-27 		.03 [0.03-0.04] per log fl increase
.02 [0.01-0.02] per log fl decrease
.02 [0.01-0.02] per log fl increase		 Affymetrix
[335,152]		 N
02/04/09 Muglia
December 23, 2008
Mol Psychiatry
Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts 		Major depressive disorder 1,359 cases, 1,782 controls NR 12p13.32 CCND2 rs4238010-G 0.02 6 x 10-6 1.72 Illumina and Affymetrix
[494,678] (imputed)		 N
06/22/09 Pare
December 19, 2008
PLoS Genet
Novel association of HK1 with glycated hemoglobin in a non-diabetic population: a genome-wide evaluation of 14,618 participants in the Women's Genome Health Study 		Glycated hemoglobin levels 14,618 Caucasian women 455 Caucasian men and women 10q21.3
7p13
2q24.3
8q24.11		 HK1
GCK
G6PC2
SLC30A8		 rs7072268-A
rs730497-A
rs1402837-A
rs13266634-A		 0.50
0.17
0.23
0.30		 2 x 10-25
6 x 10-12
5 x 10-10
5 x 10-8 		.05 [NR] % increase
.03 [NR] % increase
.02 [NR] % increase
.02 [NR] % decrease		 Illumina
[337,343]		 N
01/14/09 Benyamin
December 17, 2008
Am J Hum Genet
Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels 		Serum markers of iron status 411 family members NR 3q22.1
6q22.33
14q23.2		 TF
RSPO3
Q6ZUR9		 rs1830084-A
rs972275-?
rs973968-?		 0.36
NR
NR		 1 x 10-9 (serum transferrin)
2 x 10-6 (serum ferritin)
3 x 10-6 (transferrin saturation)		 .43 [NR] SD increase
NR
NR		 Affymetrix
[100,846]		 N
01/14/09 " Serum markers of iron status 459 twin pairs NR 3q22.1
6p22.1
6p22.1
6p22.1
6p22.1
6p22.1
6p22.2
6p22.2
6p22.2
3q22.1
6q25.3
11p14.3
3q22.1
Xq24
2p14
6p22.1
3q22.1
6p22.2
22q12.3
7p14.1
18q22.2
5p12
5q14.1
6p22.2		 TF
HFE
HFE
HFE
HIST1H2BJ
BTN1A1
LRRC16
SLC17A1
LRRC16
TOPBP1
WTAP
LUZP2
TF
KLHL13
Q6ZNG6
TRIM38
TF
LRRC16A
TMPRSS6
Q4KMW4
Intergenic
GHR
ARSB
SCGN		 rs3811647-?
rs1800562-?
rs1800562-?
rs1800562-?
rs13194491-?
rs13194984-?
rs2274089-?
rs17270561-?
rs2274089-?
rs2718812-?
rs4516970-?
rs10500991-?
rs1867504-?
rs2430212-?
rs1457451-?
rs12216125-?
rs1799852-?
rs2274089-?
rs4820268-?
rs29880-?
rs2660917-?
rs13188386-?
rs2052550-?
rs932316-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
0.09
NR
NR
NR
NR
NR
NR
NR		 3 x 10-15 (serum transferrin)
4 x 10-15 (transferrin saturation)
4 x 10-11 (serum iron)
1 x 10-10 (serum transferrin)
1 x 10-8 (transferrin saturation)
6 x 10-8 (transferrin saturation)
3 x 10-7 (serum transferrin)
5 x 10-7 (transferrin saturation)
8 x 10-7 (transferrin saturation)
1 x 10-6 (serum transferrin)
1 x 10-6 (serum ferritin)
2 x 10-6 (serum transferrin)
2 x 10-6 (serum transferrin)
2 x 10-6 (serum transferrin)
3 x 10-6 (transferrin saturation)
4 x 10-6 (transferrin saturation)
5 x 10-6 (serum transferrin)
5 x 10-6 (serum iron)
6 x 10-6 (serum iron)
7 x 10-6 (serum ferritin)
8 x 10-6 (serum ferritin)
8 x 10-6 (transferrin saturation)
8 x 10-6 (serum ferritin)
9 x 10-6 (transferrin saturation)		 .46 [0.34-0.58] SD decrease
NR
.66 [0.46-0.86] SD increase
.68 [0.48-0.88] SD decrease
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
.43 [0.25-0.61] SD decrease
NR
NR
NR
NR
NR
NR
NR		 Illumina
[315,887]		 N
01/14/09 Pollin
December 17, 2008
Science
A null mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection 		Triglycerides 809 individuals 698 individuals 11q23.3 APOA1, APOC3, APOA4, APOA5, DSCAML1 rs10892151-A 0.028 3 x 10-29 NR Affymetrix
[381,934]		 N
01/16/09 Styrkarsdottir
December 14, 2008
Nat Genet
New sequence variants associated with bone mineral density 		Bone mineral density (hip) 6,865 individuals 8,510 individuals 1p36.12
6q25.1
17q21.31
11p11.2
17q21.31
Xq21.2
2q12.1
3p22.1		 Intergenic
ESR1
SOST
LRP4
C17orf53
NR
NR
NR		 rs7524102-A
rs1038304-G
rs1513670-A
rs1007738-A
rs227584-T
rs2710057-T
rs6735786-C
rs10490823-G		 0.82
0.47
0.37
0.77
0.73
0.67
0.64
0.46		 1 x 10-16
4 x 10-10
2 x 10-8
7 x 10-7
9 x 10-7
1 x 10-6
2 x 10-6
9 x 10-6 		.15 [0.11-0.18] SD decrease
.08 [0.06-0.11] SD decrease
.08 [0.05-0.10] SD decrease
.08 [0.05-0.11] SD decrease
.07 [0.04-0.10] SD decrease
.07 [0.04-0.09] SD decrease
.07 [0.04-0.09] SD decrease
.06 [0.03-0.09] SD decrease		 Illumina
[305,051]		 N
01/16/09 " Bone mineral density (spine) 6,865 individuals 8,510 individuals 13q14.11
6q25.1
1p36.12
12q13.13
2p16.2
2p22.2
21q11.2		 RANKL
C6orf97, ESR1
Intergenic
OSX
SPTBN1
LOC344382
NR		 rs9594759-T
rs6929137-A
rs6696981-G
rs10876432-A
rs11898505-G
rs4670779-T
rs1006899-A		 0.62
0.30
0.86
0.73
0.68
0.32
0.84		 2 x 10-17
2 x 10-10
2 x 10-8
1 x 10-7
4 x 10-6
4 x 10-6
6 x 10-6 		.12 [0.09-0.15] SD decrease
.1 [0.07-0.13] SD decrease
.12 [0.08-0.16] SD decrease
.08 [0.05-0.11] SD decrease
.07 [0.04-0.10] SD decrease
.07 [0.04-0.10] SD decrease
.09 [0.05-0.13] SD decrease		 Illumina
[305,051]		 N
01/15/09 Thorleifsson
December 14, 2008
Nat Genet
Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity 		Body mass index 80,969 individuals 11,036 individuals 16q12.2
2p25.3
16q12.2
18q21.32
19q13.11
1p31.1
3q27.2
16p11.2
11p14.1
11p14.1
1q25.2
12q13.13
1p21.3
11p14.1		 FTO
TMEM18
FTO
MC4R
KCTD15, CHST8
NEGR1
SFRS10, ETV5, DGKG
SH2B1, ATP2A1
BDNF
BDNF
SEC16B, RASAL2
BCDIN3D, FAIM2
NR
BDNF		 rs8050136-A
rs7561317-G
rs6499640-A
rs12970134-A
rs29941-C
rs2568958-A
rs7647305-C
rs7498665-G
rs6265-G
rs925946-T
rs10913469-C
rs7138803-A
rs10783050-C
rs7481311-T		 0.41
0.84
0.41
0.30
0.69
0.58
0.77
0.44
0.85
0.34
0.20
0.37
0.36
0.24		 1 x 10-47
4 x 10-17
4 x 10-13
1 x 10-12
7 x 10-12
1 x 10-11
7 x 10-11
3 x 10-10
5 x 10-10
9 x 10-10
6 x 10-8
1 x 10-7
4 x 10-6
8 x 10-6 		8.04 [6.96-9.12] % SD
6.12 [4.69-7.55] % SD
5.25 [3.82-6.68] % SD
4.38 [3.16-5.60] % SD
4.18 [2.98-5.38] % SD
3.77 [2.67-4.87] % SD
4.42 [3.09-5.75] % SD
3.63 [2.49-4.77] % SD
4.58 [3.07-6.09] % SD
3.85 [2.62-5.08] % SD
3.36 [2.14-4.58] % SD
3.28 [2.06-4.50] % SD
2.6 [1.50-3.70] % SD
3.15 [1.78-4.52] % SD		 Illumina
[305,846]		 N
01/15/09 " Weight 80,969 individuals 11,036 individuals 16q12.2
2p25.3
16q12.2
18q21.32
16p11.2
11p14.1
3q27.2
19q13.11
1q25.2
1p31.1
6p21.33
11p14.1
12q13.13
13q12.2
1p21.3
5q23.2
11p14.1		 FTO
TMEM18
FTO
MC4R
SH2B1, ATP2A1
BDNF
SFRS10, ETV5, DGKG
KCTD15, CHST8
SEC16B, RASAL2
NEGR1
AIF1, NCR3
BDNF
BCDIN3D, FAIM2
NR
NR
NR
BDNF		 rs8050136-A
rs7561317-G
rs6499640-A
rs12970134-A
rs7498665-G
rs925946-T
rs7647305-C
rs29941-C
rs10913469-C
rs2568958-A
rs2844479-T
rs6265-G
rs7138803-A
rs7336332-G
rs1973993-C
rs2115172-A
rs7481311-T		 0.41
0.84
0.65
0.30
0.44
0.34
0.77
0.69
0.20
0.58
0.68
0.85
0.37
0.15
0.63
0.57
0.24		 5 x 10-36
2 x 10-18
6 x 10-14
5 x 10-13
1 x 10-9
4 x 10-9
4 x 10-9
5 x 10-9
1 x 10-8
2 x 10-8
2 x 10-8
2 x 10-7
2 x 10-7
1 x 10-6
1 x 10-6
2 x 10-6
3 x 10-6 		7.05 [5.95-8.15] % SD
6.47 [5.02-7.92] % SD
5.5 [4.07-6.93] % SD
4.66 [3.41-5.91] % SD
3.69 [2.51-4.87] % SD
3.8 [2.55-5.05] % SD
4 [2.67-5.33] % SD
3.73 [2.48-4.98] % SD
3.82 [2.51-5.13] % SD
3.37 [2.19-4.55] % SD
3.58 [2.33-4.83] % SD
4 [2.47-5.53] % SD
3.27 [2.05-4.49] % SD
4.01 [2.40-5.62] % SD
2.71 [1.61-3.81] % SD
2.71 [1.59-3.83] % SD
3.5 [2.03-4.97] % SD		 Illumina
[305,846]		 N
01/12/09 Willer
December 14, 2008
Nat Genet
Six new loci associated with body mass index highlight a neuronal influence on body weight regulation 		Body mass index 32,387 individuals 59,092 individuals 16q12.2
2p25.3
18q21.32
4p13
16p11.2
11p11.2
19q13.11
1p31.1
11p15.4
20p12.3
15q25.2		 FTO
TMEM18
MC4R
GNPDA2
SH2B1
MTCH2
KCTD15
NEGR1
STK33
BMP2
RKHD3		 rs9939609-A
rs6548238-C
rs17782313-C
rs10938397-G
rs7498665-G
rs10838738-G
rs11084753-G
rs2815752-A
rs10769908-C
rs2145270-T
rs12324805-C		 0.41
0.84
0.21
0.45
0.41
0.34
0.67
0.62
0.53
0.65
0.31		 4 x 10-51
1 x 10-18
5 x 10-18
3 x 10-16
5 x 10-11
5 x 10-9
2 x 10-8
6 x 10-8
1 x 10-6
6 x 10-6
7 x 10-6 		.33 [0.27-0.39] kg/m2 increase
.26 [0.19-0.34] kg/m2 increase
.2 [0.12-0.28] kg/m2 increase
.19 [0.13-0.25] kg/m2
.15 [0.08-0.21] kg/m2 increase
.07 [0.01-0.13] kg/m2 increase
.06 [-0.01-0.13] kg/m2 increase
.1 [0.04-0.16] kg/m2 increase
NR
NR
NR		 Illumina and Affymetrix
[2,399,588] (imputed)		 N
02/05/09 Mead
December 11, 2008
Lancet Neurol
Genetic risk factors for variant Creutzfeldt-Jakob disease: a genome-wide association study 		Creutzfeldt-Jakob disease 117 CJD cases, 3,083 controls 506 sCJD cases, 28 iCJD cases, 151 Kuru cases, 125 Kuru-resistant cases, up to 1,137 controls 20p13
8q21.13		 PRNP
STMN2		 rs1799990-A
rs1460163-A		 NR
NR		 2 x 10-21
6 x 10-8 		NR
NR		 Affymetrix
[288,908]		 N
01/06/09 Sullivan
December 09, 2008
Mol Psychiatry
Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo 		Major depressive disorder 1,738 cases, 1,802 controls 6,079 cases, 5,893 controls NR NR NR NR NS NR Perlegen
[435,291]		 N
01/12/09 Aulchenko
December 07, 2008
Nat Genet
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts 		Cholesterol, total 22,562 individuals NR 19p13.2
2p24.1
1p13.3
19q13.32
5q13.3
19p13.11
1p31.3
18q21.1
2p21
11q12.2
1p36.11
8q24.13
15q22.1
11q23.3
7p15.3		 LDLR
APOB
CELSR2
TOMM40, APOE
HMGCR
NCAN
DOCK7
LIPG
ABCG5
FADS2, FADS3
TMEM57
TRIB1
LIPC
APOA1, APOA4, APOA5, APOC3
DNAH11		 rs2228671-G
rs693-G
rs646776-G
rs2075650-G
rs3846662-G
rs2304130-G
rs10889353-C
rs4939883-G
rs6756629-G
rs174570-G
rs10903129-G
rs6987702-G
rs1532085-G
rs12272004-C
rs12670798-G		 0.88
0.52
0.22
0.15
0.44
0.07
0.32
0.83
0.92
0.83
0.54
0.29
0.59
0.93
0.24		 9 x 10-24
9 x 10-23
9 x 10-22
3 x 10-19
3 x 10-19
2 x 10-15
4 x 10-12
2 x 10-11
2 x 10-11
2 x 10-10
5 x 10-10
3 x 10-9
4 x 10-7
7 x 10-7
9 x 10-7 		.16 [NR] SD increase
.1 [NR] SD decrease
.13 [NR] SD decrease
.14 [NR] SD increase
.09 [NR] SD increase
.15 [NR] SD decrease
.08 [NR] SD decrease
.07 [NR] SD increase
.15 [NR] SD increase
.09 [NR] SD increase
.06 [NR] SD increase
.07 [NR] SD increase
.05 [NR] SD decrease
.11 [NR] SD decrease
.06 [NR] SD increase		 Illumina and Affymetrix
[up to ~600,000]		 N
01/12/09 " HDL cholesterol 21,412 individuals NR 16q13
15q22.1
8p21.3
16q22.1
9q31.1
18q21.1
11p11.2
2p24.1
19q13.32
11q12.2		 CETP
LIPC
LPL
CTCF, PRMT8
ABCA1
LIPG
MADD, FOLH1
APOB
TOMM40, APOE
FADS2, FADS3		 rs1532624-C
rs1532085-G
rs2083637-G
rs2271293-G
rs3905000-G
rs4939883-G
rs7395662-G
rs6754295-C
rs157580-G
rs174570-G		 0.57
0.59
0.26
0.87
0.86
0.83
0.61
0.25
0.33
0.83		 9 x 10-94
1 x 10-35
6 x 10-18
8 x 10-16
9 x 10-13
2 x 10-11
6 x 10-11
4 x 10-8
4 x 10-7
4 x 10-6 		.21 [NR] SD decrease
.13 [NR] SD decrease
.11 [NR] SD increase
.13 [NR] SD decrease
.11 [NR] SD increase
.1 [NR] SD increase
.07 [NR] SD decrease
.07 [NR] SD increase
.06 [NR] SD increase
.06 [NR] SD increase		 Illumina and Affymetrix
[up to ~600,000]		 N
01/12/09 " LDL cholesterol 17,797 individuals NR 1p13.3
19q13.32
2p24.1
19p13.2
11q12.2
11q23.3
5q13.3
2p21
7p15.3
19p13.11
8q24.13
1p31.3		 CELSR2
TOMM40, APOE
APOB
LDLR
FADS2, FADS3
APOA1, APOA4, APOA5, APOC3
HMGCR
ABCG5
DNAH11
NCAN
TRIB1
DOCK7		 rs646776-G
rs157580-G
rs693-G
rs2228671-G
rs174570-G
rs12272004-C
rs3846662-G
rs6756629-G
rs12670798-G
rs2304130-G
rs6987702-G
rs10889353-C		 0.22
0.33
0.52
0.88
0.83
0.93
0.44
0.92
0.24
0.07
0.29
0.32		 8 x 10-23
2 x 10-19
4 X 10-17
4 x 10-14
4 x 10-13
5 X 10-13
2 x 10-11
3 x 10-10
6 x 10-9
3 x 10-6
3 x 10-6
8 x 10-6 		.16 [NR] SD decrease
.11 [NR] SD decrease
.1 [NR] SD decrease
.14 [NR] SD increase
.11 [NR] SD increase
.18 [NR] SD decrease
.08 [NR] SD increase
.16 [NR] SD increase
.09 [NR] SD increase
.12 [NR] SD decrease
.07 [NR] SD increase
.06 [NR] SD decrease		 Illumina and Affymetrix
[up to 600,000]		 N
01/12/09 " Triglycerides 17,815 individuals NR 2p23.3
8p21.3
11q23.3
7q11.23
1p31.3
19q13.32
2p24.1
19p13.11		 GCKR
LPL
APOA1, APOA4, APOA5, APOC3
MLXIPL
DOCK7
TOMM40, APOE
APOB
NCAN		 rs780094-G
rs10096633-G
rs12272004-C
rs2240466-G
rs1167998-C
rs439401-G
rs6754295-C
rs2304130-G		 0.63
0.88
0.93
0.87
0.32
0.68
0.25
0.07		 3 x 10-20
2 x 10-18
5 X 10-13
1 x 10-12
2 x 10-12
2 x 10-9
3 x 10-8
3 x 10-6 		.1 [NR] SD decrease
.17 [NR] SD increase
.18 [NR] SD decrease
.14 [NR] SD increase
.09 [NR] SD decrease
.09 [NR] SD increase
.08 [NR] SD decrease
.1 [NR] SD decrease		 Illumina and Affymetrix
[up to 600,000]		 N
01/07/09 Bouatia-Naji
December 07, 2008
Nat Genet
A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk 		Fasting plasma glucose 2,151 individuals 6,332 cases, 9,132 controls 11q21 MTNR1B rs1387153-T 0.29 2 x 10-36 .07 [0.05-0.08] mmol/l increase Illumina
[308,846]		 N
01/12/09 Kathiresan
December 07, 2008
Nat Genet
Common variants at 30 loci contribute to polygenic dyslipidemia 		HDL cholesterol 19,840 individuals Up to 20,623 individuals 16q13
8p21.3
15q22.1
18q21.1
16q22.1
11q23.3
11q12.2
12q24.11
9p22.3
20q13.2
9q31.1
20q13.12
19p13.2
1q42.13		 CETP
LPL
LIPC
LIPG
LCAT
APOA1, APOC3, APOA4, APOA5
FADS1, FADS2, FADS3
MMAB,MVK
TTC39B
HNF4A
ABCA1
PLTP
ANGPTL4
GALNT2		 rs173539-T
rs12678919-G
rs10468017-T
rs4939883-T
rs2271293-A
rs964184-G
rs174547-C
rs2338104-C
rs471364-C
rs1800961-T
rs1883025-T
rs7679-C
rs2967605-T
rs4846914-G		 0.32
0.10
0.30
0.17
0.11
0.14
0.33
0.45
0.12
0.03
0.26
0.19
0.16
0.40		 4 x 10-75
2 x 10-34
8 x 10-23
7 x 10-15
9 x 10-13
1 x 10-12
2 x 10-12
1 x 10-10
3 x 10-10
8 x 10-10
1 x 10-9
4 x 10-9
1 x 10-8
4 x 10-8 		.25 [0.21-0.29] SD increase
.23 [0.17-0.29] SD increase
.1 [0.06-0.14] SD increase
.14 [0.10-0.18] SD decrease
.07 [0.01-0.13] SD increase
.17 [0.11-0.23] SD decrease
.09 [0.05-0.13] SD decrease
.07 [0.03-0.11] SD decrease
.08 [0.02-0.14] SD decrease
.19 [0.09-0.29] SD decrease
.08 [0.04-0.12] SD decrease
.07 [0.03-0.11] SD decrease
.12 [0.04-0.20] SD decrease
.05 [0.01-0.09] SD decrease		 Affymetrix and Illumina
[~2,600,000] (imputed)		 N
01/12/09 " LDL cholesterol 19,840 individuals Up to 20,623 individuals 1p13.3
2p24.1
19q13.32
19p13.2
2p21
5q13.3
5q33.3
20q12
12q24.31
19p13.11
1p32.3		 CELSR2, PSRC1, SORT1
APOB
APOE, APOC1, APOC4, APOC2
LDLR
ABCG8
HMGCR
TIMD4, HAVCR1
MAFB
HNF1A
NCAN, CILP2, PBX4
PCSK9		 rs12740374-T
rs515135-T
rs4420638-G
rs6511720-T
rs6544713-T
rs3846663-T
rs1501908-G
rs6102059-T
rs2650000-A
rs10401969-C
rs11206510-C		 0.21
0.20
0.16
0.10
0.32
0.38
0.37
0.32
0.36
0.06
0.19		 2 x 10-42
5 x 10-29
4 x 10-27
2 x 10-26
2 x 10-20
8 x 10-12
1 x 10-11
4 x 10-9
2 x 10-8
2 x 10-8
4 x 10-8 		.23 [0.19-0.27] SD decrease
.16 [0.12-0.20] SD decrease
.29 [0.17-0.41] SD increase
.26 [0.18-0.34] SD increase
.15 [0.11-0.19] SD increase
.07 [0.03-0.11] SD increase
.07 [0.03-0.11] SD decrease
.06 [0.03-0.10] SD decrease
.07 [0.03-0.11] SD increase
.05 [-0.03-0.13] SD decrease
.09 [0.05-0.13] SD decrease		 Affymetrix and Illumina
[~2,600,000] (imputed)		 N
01/12/09 " Triglycerides 19,840 individuals Up to 20,623 individuals 11q23.3
8p21.3
2p23.3
8q24.13
7q11.23
11q12.2
2p24.1
19p13.11
20q13.12
8p23.1
1p31.3		 APOA1, APOC3, APOA4, APOA5
LPL
GCKR
TRIB1
MLXIPL
FADS1, FADS2, FADS3
APOB
NCAN,CILP2,PBX4
PLTP
XKR6, AMAC1L2
ANGPTL3		 rs964184-G
rs12678919-G
rs1260326-T
rs2954029-T
rs714052-G
rs174547-C
rs7557067-G
rs17216525-T
rs7679-C
rs7819412-G
rs10889353-C		 0.14
0.10
0.45
0.44
0.12
0.33
0.22
0.07
0.19
0.48
0.33		 4 x 10-62
2 x 10-41
2 x 10-31
3 x 10-19
3 x 10-15
2 x 10-14
9 x 10-12
4 x 10-11
7 x 10-11
3 x 10-8
3 x 10-7 		.3 [0.24-0.36] SD increase
.25 [0.19-0.31] SD decrease
.12 [0.08-0.16] SD increase
.11 [0.07-0.15] SD decrease
.16 [0.10-0.22] SD decrease
.06 [0.02-0.10] SD increase
.08 [0.04-0.12] SD decrease
.11 [0.05-0.17] SD decrease
.07 [0.03-0.11] SD increase
.04 [0.001-0.08] SD decrease
.05 [0.01-0.09] SD decrease		 Affymetrix and Illumina
[~2,600,000] (imputed)		 N
01/12/09 Sabatti
December 07, 2008
Nat Genet
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population 		HDL cholesterol 4,763 individuals NR 16q13
15q22.1
16q22.1
11p11.2
17p13.3		 CETP
LIPC
LCAT
NR1H3
Intergenic		 rs3764261-A
rs1532085-A
rs255049-G
rs7120118-G
rs9891572-A		 0.28
0.44
0.22
0.42
0.16		 7 x 10-29
2 x 10-10
3 x 10-8
4 x 10-8
2 x 10-7 		.09 [0.08-0.11] mmol/l increase
.05 [0.03-0.06] mmol/l increase
.05 [0.03-0.07] mmol/l increase
.04 [0.03-0.05] mmol/l increase
.05 [0.048-0.051] mmol/l increase		 Illumina
[329,091]		 N
01/12/09 " LDL cholesterol 4,763 individuals NR 1p13.3
2p24.1
19q13.32
11q12.2
19p13.2
1q32.2
Xq12		 CELSR2, PSRC1, SORT1
APOB
APO cluster
FADS1, FADS2
LDLR
CR1L
AR		 rs646776-G
rs693-A
rs157580-G
rs174546-A
rs11668477-G
rs4844614-A
rs5031002-A		 0.21
0.41
0.29
0.44
0.18
0.32
0.02		 2 x 10-12
3 x 10-11
5 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
2 x 10-7 		.16 [0.11-0.20] mmol/l decrease
.12 [0.09-0.16] mmol/l increase
.11 [0.07-0.15] mmol/l decrease
.1 [0.06-0.13] mmol/l decrease
.13 [0.08-0.17] mmol/l decrease
.1 [0.06-0.14] mmol/l increase
.3 [0.18-0.41] mmol/l increase		 Illumina
[329,091]		 N
01/12/09 " Other metabolic traits 4,763 individuals NR 1q23.2
12q24.31
2p23.3
2q24.3
2p24.1
8p21.3
11q21
7p21.2
10q23.31
15q14
1p31.3		 CRP
LEF1
GCKR
G6PC2, ABCB11
APOB
LPL
MTNR1B
Intergenic
PANK1
Intergenic
LEPR		 rs2794520-A
rs2650000-A
rs1260326-A
rs560887-A
rs673548-A
rs10096633-A
rs1447352-G
rs10244051-C
rs11185790-A
rs2624265-G
rs12753193-G		 0.36
0.45
0.35
0.31
0.27
0.098
0.42
0.46
0.21
0.42
0.45		 3 x 10-22 (CRP)
3 x 10-11 (CRP)
4 x 10-10 (TG)
6 x 10-10 (GLU)
2 x 10-8 (TG)
5 x 10-8 (TG)
6 x 10-8 (GLU)
1 x 10-7 (GLU)
3 x 10-7 (INS)
4 x 10-7 (TG)
4 x 10-7 (CRP)		 .47 [0.32-0.62] mmol/l decrease
.4 [0.25-0.55] mmol/l decrease
.09 [0.06-0.12] mmol/l increase
.06 [0.04-0.07] mmol/l decrease
.08 [0.05-0.11] mmol/l decrease
.12 [0.07-0.17] mmol/l decrease
.05 [0.03-0.06] mmol/l decrease
.05 [0.03-0.06] mmol/l increase
.31 [0.18-0.44] mmol/l decrease
.07 [0.04-0.10] mmol/l increase
.13 [-0.02-0.27] mmol/l decrease		 Illumina
[329,091]		 N
05/07/09 Lasky-Su
December 05, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations 		Attention deficit hyperactivity disorder 909 trios NR 12p11.22
3p24.3
14q23.2
2q21.2
16q22.1
13q32.3
1q41
22q12.3
2q24.1
1p31.2
2p21
3p14.1
11p13
19q13.43
3p14.2
4q13.3
2q14.1
2q14.3
8q24.3		 Intergenic
Intergenic
Intergenic
FLJ34870
HAS3
CLYBL
Intergenic
Intergenic
Intergenic
Intergenic
OXER1
FOXP1
Intergenic
ZNF544
FHIT
EREG
Intergenic
Intergenic
NAPRT1		 rs522958-?
rs11719664-?
rs1514928-?
rs7577925-?
rs8047014-?
rs7992643-?
rs1018040-?
rs130575-?
rs1918172-?
rs4147141-?
rs930421-?
rs17651978-?
rs10767942-?
rs260461-?
rs6791644-?
rs1350666-?
rs272000-?
rs17367118-?
rs2290416-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-6 (binary)
2 x 10-6 (count)
3 x 10-6 (binary)
3 x 10-6 (binary)
4 x 10-6 (binary)
5 x 10-6 (count)
5 x 10-6 (binary)
5 x 10-6 (binary)
5 x 10-6 (count)
6 x 10-6 (count)
6 x 10-6 (binary)
6 x 10-6 (count)
8 x 10-6 (count)
8 x 10-6 (binary)
8 x 10-6 (count)
8 x 10-6 (binary)
9 x 10-6 (count)
9 x 10-6 (count)
9 x 10-6 (count)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
05/07/09 " Hyperactive-impulsive symptoms 909 trios NR 12p11.22
6p22.3
2p21
8p21.3
1p13.2
15q14
21q21.3
3q26.1
9p24.3
19q13.43
1q41
3q26.1
18q22.1
6p22.3		 Intergenic
Intergenic
OXER1
LPL
Intergenic
MEIS2
GRIK1
Intergenic
DMRT2
LOC390980
Intergenic
Intergenic
Intergenic
Intergenic		 rs522958-?
rs41441749-?
rs6719977-?
rs7816032-?
rs11590090-?
rs8041675-?
rs363512-?
rs6808138-?
rs17641078-?
rs2014572-?
rs1018040-?
rs6808138-?
rs13353224-?
rs1202199-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 8 x 10-7 (binary)
1 x 10-6 (binary)
2 x 10-6 (binary)
2 x 10-6 (count)
3 x 10-6 (count)
4 x 10-6 (count)
4 x 10-6 (binary)
5 x 10-6 (binary)
5 x 10-6 (binary)
7 x 10-6 (count)
8 x 10-6 (binary)
8 x 10-6 (binary)
9 x 10-6 (count)
9 x 10-6 (count)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
05/07/09 " Inattentive symptoms 909 trios NR 9q22.32
8q21.11
11q22.3
15q26.1
16q12.1
9q21.31
15q25.1
7q36.3
13q12.12
1p31.2
12q24.22
15q13.1
1p31.2
16q23.1
8p11.21		 Intergenic
Intergenic
Intergenic
SLCO3A1
ZNF423
Intergenic
IL16
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic		 rs11790994-?
rs12679254-?
rs10895959-?
rs7495052-?
rs17281813-?
rs2769967-?
rs7172689-?
rs10227331-?
rs17079773-?
rs4650135-?
rs478597-?
rs1471225-?
rs4147141-?
rs13330107-?
rs11786458-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7 (binary)
2 x 10-6 (binary)
3 x 10-6 (binary)
3 x 10-6 (binary)
3 x 10-6 (binary)
3 x 10-6 (count)
4 x 10-6 (count)
4 x 10-6 (count)
5 x 10-6 (binary)
5 x 10-6 (binary)
8 x 10-6 (binary)
8 x 10-6 (count)
8 x 10-6 (binary)
9 x 10-6 (binary)
9 x 10-6 (binary)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
05/07/09 Lasky-Su
December 05, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association scan of the time to onset of attention deficit hyperactivity disorder 		Attention deficit hyperactivity disorder (time to onset) 930 trios NR 6q15
2q36.3
7q31.1
11p15.1
3p22.3
9p23
3q29
20q13.13
14q23.1
5q35.3
8q23.3		 Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
SULF2
Intergenic
ADAMTS2
Intergenic		 rs806276-A
rs1517484-C
rs6968385-T
rs874426-C
rs9845475-G
rs1325154-C
rs3892715-C
rs4810685-C
rs1335515-C
rs10039254-A
rs17658378-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-7 (later onset)
5 x 10-7 (earlier onset)
2 x 10-6 (earlier onset)
4 x 10-6 (earlier onset)
4 x 10-6 (later onset)
5 x 10-6 (later onset)
6 x 10-6 (earlier onset)
7 x 10-6 (earlier onset)
8 x 10-6 (earlier onset)
8 x 10-6 (later onset)
9 x 10-6 (later onset)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
01/15/09 Timpson
December 03, 2008
Diabetes
Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome wide association data 		Type 2 diabetes 1,924 cases, 2,938 controls 3,757 cases, 5,346 controls 10q25.2
16q12.2
10q25.2
11p15.1
11p15.1
6p22.3
9p21.3
8q24.11		 TCF7L2
FTO
TCF7L2
KCNJ11
KCNJ11
CDKAL
CDKN2B
SLC30A8		 rs7903146-?
rs8050136-?
rs7903146-?
rs5219-?
rs5219-?
rs10946398-?
rs10811661-?
rs13266634-?		 NR
NR
NR
NR
NR
NR
NR
NR		 9 x 10-30 (non-obese)
2 x 10-17 (obese)
6 x 10-16 (obese)
1 x 10-9 (non-obese)
5 x 10-7 (obese)
7 x 10-7 (non-obese)
7 x 10-7 (non-obese)
7 x 10-6 (non-obese)		 1.49 [1.39-1.59]
1.3 [1.23-1.39]
1.31 [1.23-1.40]
1.25 [1.16-1.34]
1.19 [1.11-1.27]
1.18 [1.11-1.26]
1.26 [1.15-1.38]
1.18 [1.10-1.27]		 Affymetrix
[393,453]		 N
01/12/09 Friedman
December 01, 2008
Hum Mol Genet
grm7 variants confer susceptibility to age-related hearing impairment 		Hearing impairment 846 cases, 846 controls 63 cases, 67 controls NR NR NR NR NS NR Affymetrix
[506,627] (pooled)		 N
02/26/09 Prokopenko
December 01, 2008
Nat Genet
Variants in MTNR1B influence fasting glucose levels 		Fasting plasma glucose 35,812 individuals NR 2q24.3
11q21
7p13		 G6PC2
MTNR1B
GCK		 rs560887-C
rs10830963-G
rs4607517-A		 0.70
0.28
0.18		 1 x 10-57
3 x 10-50
1 x 10-25 		.06 [0.05-0.07] mmol/l increase
.07 [0.06-0.08] mmol/l increase
.06 [0.05-0.07] mmol/l increase		 Affymetrix, Illumina and Perlegen
[up to 2,557,249] (imputed)		 N
12/24/08 Gieger
November 28, 2008
PLoS Genet
Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum 		Serum metabolites 284 males NR 2p14
10p11.21
11q12.2
13q31.3
15q22.1
3p25.3
6q25.1
6q26
15q26.1
4q13.1
7q31.1
12q24.21
6q12
3q28
16p13.2
3q22.3		 PLEK
ANKRD30A
FADS1
GPC5
LIPC
ATP2B2
C6orf71
PARK2
SV2B
Intergenic
Intergenic
Intergenic
Intergenic
FGF12
A2BP1
Intergenic		 rs9309413-?
rs1148259-?
rs174548-?
rs17267292-?
rs4775041-?
rs6807064-?
rs1591830-?
rs992037-?
rs886144-?
rs10517480-?
rs10953730-?
rs2194980-?
rs9354308-?
rs4453795-?
rs9924951-?
rs1382269-?		 0.45
0.42
0.28
0.28
0.28
0.29
0.32
0.35
0.38
0.31
0.35
0.33
0.37
0.41
0.41
0.47		 2 x 10-9 (SM)
3 x 10-9 (SM)
5 x 10-8 (PC)
1 x 10-7 (Docosahexaonic acoid)
1 x 10-7 (PE)
1 x 10-7 (phenylalanine)
1 x 10-7 (sugar)
1 x 10-7 (Lysine)
2 x 10-7 (SM)
2 x 10-7 (PC)
2 x 10-7 (acylcarnitine)
3 x 10-7 (Tyrosine)
3 x 10-7 (serotonin)
4 x 10-7 (PC)
5 x 10-7 (PC)
5 x 10-7 (SM)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[187,454]		 N
12/09/08 Terracciano
November 24, 2008
Mol Psychiatry
Genome-wide association scan for five major dimensions of personality 		Personality dimensions 3,972 individuals 3,903 individuals 19q13.31
4q12
2p22.1
Xp11.3
19q13.31		 ZNF180
CLOCK
THUMPD2
FUNDC1
ZNF180		 rs644148-G
rs6832769-A
rs2540226-T
rs6610953-G
rs644148-G		 0.50
0.73
0.53
0.85
0.50		 9 x 10-7 (openness)
2 x 10-6 (agreeableness)
3 x 10-6 (agreeableness)
6 x 10-6 (openness)
8 x 10-6 (extraversion)		 .15 [NR] SD increase
.14 [NR] SD decrease
.13 [NR] SD increase
.15 [NR] SD increase
.14 [NR] SD increase		 Affymetrix
[362,129]		 N
01/07/09 Lei
November 23, 2008
Hum Genet
Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci 		Height 618 Chinese individuals 2,953 Chinese individuals 9q22.23 ZNP510 rs10816533-C 0.29 2 x 10-6 NR Affymetrix
[281,533]		 N
01/06/09 Potkin
November 20, 2008
Schizophr Bull
A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype 		Brain imaging in schizophrenia (interaction) 64 cases, 74 cases NR 5q23.2
2q37.3
3p12.3
14q32.32
3q26.2
6q16.2		 CTXN3, SLC12A2
GPC1
ROBO2, ROBO1
TRAF3
TNIK
POU3F2		 rs245201-?
rs1574192-?
rs9836484-?
rs10133111-?
rs2088885-?
rs9491640-?		 0.32
0.38
0.32
0.20
0.47
0.06		 9 x 10-8
4 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR		 Illumina
[302,783]		 N
12/01/08 COGENT Study
November 16, 2008
Nat Genet
Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer 		Colorectal cancer 1,902 cases, 1,929 controls 4,878 cases, 4,914 controls 20p12.3
14q22.2
19q13.11
16q22.1		 Intergenic
BMP4
RHPN2
CDH1		 rs961253-A
rs4444235-C
rs10411210-C
rs9929218-A		 0.36
0.46
0.90
0.29		 2 x 10-10
8 x 10-10
5 x 10-9
1 x 10-8 		1.12 [1.08-1.16]
1.11 [1.08-1.15]
1.15 [1.10-1.20]
1.1 [1.06-1.12]		 Illumina
[up to 548,586]		 N
01/16/09 Baranzini
November 14, 2008
Hum Mol Genet
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis 		Brain lesion load 791 cases, 883 controls NR 2q37.1
14q12
19p13.11
6q25.3		 CHRND
NUBPL
CPAMD8
IGF2R		 rs2602397-?
rs2039485-?
rs11666377-?
rs6917747-?		 0.45
0.22
0.14
0.15		 4 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6 		NR
NR
NR
NR		 Illumina
[551,642]		 N
01/16/09 " Multiple sclerosis 978 cases, 883 controls NR 20p13
13q31.3
12q12
8p23.2
3q23
9p22.2
2q14.2
3q24
4q35.1
2p25.1		 C20orf46
GPC5
PDZRN4
CSMD1
SLC25A36
SH3GL2
EN1
ZIC1
MGC45800
DDEF2		 rs397020-?
rs9523762-?
rs1458175-?
rs1529316-?
rs908821-?
rs1755289-?
rs651477-?
rs1841770-?
rs7672826-?
rs1109670-?		 0.52
0.35
0.49
0.47
0.71
0.61
0.26
0.53
0.34
0.26		 8 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		1.41 [NR]
1.36 [NR]
1.34 [NR]
1.36 [NR]
1.37 [NR]
1.35 [NR]
1.38 [NR]
1.34 [NR]
1.37 [NR]
1.38 [NR]		 Illumina
[551,642]		 N
01/16/09 " Multiple sclerosis (age of onset) 978 cases, 883 controls NR 11q14.2
7q22.1
8q13.3
18q21.31
9q21.13
1q25.2
5q33.2
2q21.2		 RAB38
RELN
KCNB2
WDR7
RFK
C1orf125
SGCD
FLJ34870		 rs1386330-?
rs17157903-?
rs2116078-?
rs1557351-?
rs2842483-?
rs12047808-?
rs4704970-?
rs1437898-?		 0.13
0.14
0.48
0.22
0.29
0.13
0.20
0.40		 2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[551,642]		 N
01/16/09 " Multiple sclerosis (severity) 794 cases, 883 controls NR 3q25.32
4q28.3
19q13.42
4q13.2
7p21.3
11q23.3
16q22.3
6p23
7q31.2
18q22.3
19p13.2		 FLJ16641
LOC132321
NLRP11
CENPC1
C1GALT1
MGC13125
C16orf47
JARID2
MET
CBLN2
ACP5		 rs12638253-?
rs1478091-?
rs299175-?
rs10518025-?
rs10259085-?
rs180358-?
rs7191888-?
rs6941421-?
rs10243024-?
rs337718-?
rs7253363-?		 0.47
0.06
0.46
0.14
0.46
0.23
0.17
0.24
0.23
0.29
0.05		 2 x 10-6
2 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[551,642]		 N
01/16/09 " Normalized brain volume 753 cases, 883 controls NR 12p11.21
6q21
10p11.23
10q25.2
5q35.1		 BICD1
FOXO3
SVIL
MXI1
KCNIP1		 rs261902-?
rs9480865-?
rs1927457-?
rs716595-?
rs11957313-?		 0.16
0.16
0.31
0.08
0.13		 4 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR		 Illumina
[551,642]		 N
12/09/08 Aulchenko
November 09, 2008
Nat Genet
Genetic variation in the KIF1B locus influences susceptibility to multiple sclerosis 		Multiple sclerosis 45 cases, 195 controls 2,634 cases, 2,930 controls 1p36.22 KIF1B rs10492972-C 0.27 3 x 10-10 1.34 [1.23-1.48] Affymetrix
[~250,000]		 N
12/01/08 Bilguvar
November 09, 2008
Nat Genet
Susceptibility loci for intracranial aneurysm in European and Japanese populations 		Intracranial aneurysm 1,580 European cases, 6,276 European controls 495 Japanese cases, 676 Japanese controls 8q11.23
9q21.3
8q11.23-q12.1
2q33.1		 SOX17
CDKN2A, CDKN2B
SOX17
BOLL, PLCL1		 rs10958409-A
rs1333040-T
rs9298506-A
rs700651-G		 0.15
0.55
0.81
0.35		 1 x 10-10
1 x 10-10
2 x 10-9
4 x 10-8 		1.36 [1.24-1.49]
1.29 [1.19-1.40]
1.35 [1.22-1.49]
1.24 [1.15-1.34]		 Illumina
[289,271]		 N
12/30/08 Drgon
November 09, 2008
Mol Med
Genome wide association for nicotine dependence and smoking cessation success in NIH research volunteers 		Nicotine dependence 220 cases, 260 controls 2,271 cases, 1,868 controls NR NR NR NR NS NR Affymetrix
[~600,00] (pooled)		 N
12/09/08 Pankratz
November 06, 2008
Nat Genet
Genomewide association study for susceptibility genes contributing to familial Parkinson disease 		Parkinson disease (familial) 857 cases, 867 controls 262 cases, 260 controls 4p16.3 GAK, DGKQ rs1564282-T 0.09 7 x 10-7 1.7 [NR] Illumina
[328,189]		 N
12/09/08 Cronin
November 05, 2008
Eur J Hum Genet
Screening for replication of genome-wide SNP associations in sporadic AL 		Amyotrophic lateral sclerosis 958 cases, 932 controls 309 cases, 404 controls 7q36.2 DPP6 rs10260404-C 0.35 3 x 10-6 1.37 [1.20-1.56] Illumina
[287,522]		 N
12/01/08 Neale
November 03, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association scan of attention deficit hyperactivity disorder 		Attention deficit hyperactivity disorder 909 trios NR NR NR NR NR NS NR Perlegen
[438,784]		 N
11/25/08 Cooper
November 02, 2008
Nat Genet
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci 		Type 1 diabetes 3,561 cases, 4,646 controls 6,225 cases, 6,946 controls, 3,064 trios 6p21.32
1p13.2
12q24.13
12q13.2
15q25.1
16p13.13
6q15
2q33.2
10p15.1
22q13.1
18p11.21
10p15.1
16p13.13
2p23.3		 HLA
PTPN22
C12orf30
ERBB3
CTSH
CLEC16A
BACH2
CTLA4
PRKCQ
C1QTNF6
PTPN2
IL2RA
C16orf75, PRM3, TNP2
Intergenic		 rs9272346-G
rs6679677-A
rs17696736-G
rs2292239-A
rs3825932-C
rs12708716-G
rs11755527-G
rs3087243-A
rs947474-G
rs229541-T
rs2542151-C
rs12251307-T
rs416603-T
rs2165738-C		 NR
NR
NR
NR
0.32
NR
0.47
NR
0.19
0.43
NR
NR
0.44
0.27		 6 x 10-129
1 x 10-40
6 x 10-18
3 x 10-16
3 x 10-15
7 x 10-13
5 x 10-12
8 x 10-11
4 x 10-9
2 x 10-8
9 x 10-8
2 x 10-6
3 x 10-6
4 x 10-6 		NR
NR
NR
NR
1.16 [1.10-1.22]
NR
1.13 [1.08-1.19]
NR
1.1 [1.03-1.18]
1.04 [0.97-1.12]
NR
NR
1.06 [1.01-1.12]
1.07 [1.01-1.13]		 Affymetrix
[up to 335,565]		 N
12/09/08 McKay
November 02, 2008
Nat Genet
Lung cancer susceptibility locus at 5p15.33 		Lung cancer 2,971 cases, 3,746 controls 2,899 cases, 5,573 controls 15q25.1
5p15.33		 Intergenic
TERT, CLPTM1		 rs1051730-A
rs402710-C		 NR
NR		 1 x 10-15
4 x 10-6 		1.35 [1.25-1.45]
1.18 [1.12-1.24]		 Illumina
[315,194]		 N
11/25/08 Wang
November 02, 2008
Nat Genet
Common 5p15.33 and 6p21.33 variants influence lung cancer risk 		Lung cancer 1,952 cases, 1,438 controls 7,579 cases, 8,236 controls 15q25.1
6p21.33
5p15.33		 NR
BAT3,MSH5
CLPTM1L		 rs8042374-?
rs3117582-C
rs401681-G		 NR
NR
NR		 8 x 10-12
5 x 10-10
8 x 10-9 		NR
1.24 [1.16-1.33]
1.15 [1.09-1.19]		 Illumina
[223,891]		 N
12/09/08 Bertram
October 29, 2008
Am J Hum Genet
Genome-wide Association Analysis Reveals Putative Alzheimer's Disease Susceptibility Loci in Addition to APOE 		Alzheimer's disease 941 affected individuals, 404 unaffected individuals 1,767 affected individuals, 838 unaffected individuals 14q31.2
19q13.33		 Intergenic
CD33		 rs11159647-?
rs3826656-?		 NR
NR		 2 x 10-6
6 x 10-6 		NR
NR		 Affymetrix
[484,522]		 N
12/09/08 Anney
October 24, 2008
Am J Med Genet B Neuropsychiatr Genet
Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study 		Attention deficit hyperactivity disorder and conduct disorder 938 affected trios NR 13q33.3
21q21.1
4q13.3
12q21.2
15q26.2
1q42.13
2p22.3
11q24.2
14q12
7q31.1
8q22.3
16q21
18q21.31
9p24.1
12q15
16q22.3
16q23.2
2p12
1q23.1
2q33.1
5q31.1
10p14
10p15.2
13q12.2
1p35.2
1q25.3		 LIG4, ABHD13
Intergenic
AMOTL1, CWC15, JMJD2D
PAWR
SPATA8
LOC729257
Intergenic
KIRREL3
Intergenic
FLJ31818, GPR85
YWHAZ
Intergenic
ATP8B1
PTPRD
C12orf28
PKD1L3, KIAA0174, DHODH
PKD1L2, C16orf46
Intergenic
ETV3L, ETV3
FLJ39061, FZD7
C5orf15
A2BP1
PITRM1
GSX1, PDX1
Intergenic
RGL1, GLT25D2		 rs10492664-C
rs2826340-T
rs10831284-G
rs7297018-A
rs4533251-T
rs701157-C
rs6733379-G
rs1557488-T
rs1951082-T
rs10229603-C
rs931812-C
rs1381102-A
rs7236632-A
rs10815798-A
rs789560-G
rs16973500-C
rs4889240-T
rs7595103-A
rs6427356-G
rs1521882-A
rs1644305-A
rs1291846-T
rs2764980-A
rs9512900-C
rs2180233-C
rs10797919-G		 0.84
0.17
0.13
0.19
0.15
0.45
0.28
0.18
0.43
0.31
0.74
0.40
0.86
0.48
0.87
0.86
0.45
0.64
0.28
0.82
0.41
0.19
0.51
0.37
0.31
0.59		 1 x 10-6
2 X 10-6
2 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
7 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[378,332]		 N
12/01/08 Johansson
October 24, 2008
Hum Mol Genet
Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis 		Height 3,925 individuals 38,091 individuals 7p15.1 JAZF1 rs1635852-A NR 9 x 10-10 .25 [0.17-0.33] cm taller Illumina
[NR]		 N
12/09/08 Comabella
October 22, 2008
PLoS ONE
Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms 		Multiple sclerosis 242 cases, 242 controls 375 cases, 375 controls 6p21.32 HLA-DRB1 rs3129934-T NR 9 x 10-11 3.3 [2.3-4.9] Affymetrix
[428,867] (pooled)		 N
11/25/08 Hillmer
October 12, 2008
Nat Genet
Susceptibility variants for male-pattern baldness on chromosome 20p11 		Male-pattern baldness 296 cases, 347 controls 319 cases, 234 controls 20p11.22 PAX1, BQ013595, BE789145 rs2180439-C 0.43 3 x 10-15 1.82 [1.45-2.30] Illumina
[531,695]		 N
11/25/08 Richards
October 12, 2008
Nat Genet
Male-pattern baldness susceptibility locus at 20p11 		Male-pattern baldness 578 cases, 547 controls 1,351 cases, 2,485 controls 20p11.22
Xq12		 PAX1
AR		 rs1160312-A
rs6625163-A		 0.43
NR		 1 x 10-14 (males)
5 x 10-11 		1.6 [1.42-1.80] (males)
3.3 [2.31-4.71]		 Affymetrix
[370,102]		 N
11/25/08 Stacey
October 12, 2008
Nat Genet
Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits 		Basal cell carcinoma (cutaneous) 930 cases, 33,117 controls 1,216 cases, 2,844 controls 1p36.13
1q42.13		 PADI4, PADI6,RCC2, ARHGEF10L
RHOU		 rs7538876-A
rs801114-G		 0.35
0.33		 4 x 10-12
6 x 10-12 		1.28 [1.19-1.37]
1.28 [1.19-1.37]		 Illumina
[304,083]		 N
12/01/08 Yuan
October 10, 2008
Am J Hum Genet
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes 		Plasma levels of liver enzymes 7,751 European white individuals 4,704 European white and Indian Asian individua 9p34.2
9q34.2
22q13.31
1p36.12
6p22.2
22q11.23
12q24.2
10q24.31
10q21.2
10q24.2q
10q21.3		 ABO
ADAMTS13
PNPLA3, SAMM50
NBPF3, ALPL, RAP1GAP
GPLD1
GGT1, C22orf36
HNF1A, C12orf27, C12orf43
JMJD1C
REEP3
CPN1, CHUK, ERLIN1
POU2F1		 rs657152-T
rs4962153-A
rs2281135-T
rs1780324-T
rs9467160-A
rs4820599-G
rs1169313-C
rs12355784-A
rs10761779-G
rs11597390-A
rs9803659-Cq		 0.39
NR
0.18
0.43
0.24
0.31
0.38
0.48
0.49
0.36
NR		 2 x 10-30 (ALP)
8 x 10-21 (ALP)
8 x 10-16 (ALT)
7 x 10-15 (ALP)
1 x 10-11 (ALP)
4 x 10-11 (GGT)
2 x 10-10 (GGT)
5 x 10-10 (ALP)
7 x 10-10 (ALP)
2 x 10-8 (ALT)
4 x 10-6 (ALT)		 .05 [0.039-0.055] U/L decrease
.06 [0.048-0.072] U/L decrease
.06 [0.046-0.074] U/L increase
.03 [0.023-0.039] U/L increase
.03 [0.024-0.044] U/L increase
.01 [0.005-0.009] U/L increase
.01 [0.003-0.007] U/L decrease
.03 [0.017-0.033] U/L increase
.03 [0.017-0.033] U/L increase
.04 [0.025-0.053] U/L decrease
.03 [0.018-0.042] U/L decrease		 Affymetrix and Illumina
[up to 496,032]		 N
11/25/08 Grant
October 07, 2008
Diabetes
Follow up analysis of genome-wide association data identifies novel loci for type 1 diabetes 		Type 1 diabetes 563 cases, 1,146 controls, 483 case-parents trios 636 families, 3,303 cases, 4,673 controls 21q22.3
6q15
1p22.3
9p24.2
15q14		 UBASH3A
BACH2
EDG7
GLIS3
RASGRP1		 rs9976767-C
rs3757247-A
rs1983853-?
rs10758593-A
rs8035957-C		 NR
NR
NR
NR
NR		 2 x 10-8
1 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6 		1.16 [1.10-1.22]
1.13 [1.08-1.19]
1.2 [1.11-1.29]
1.13 [1.07-1.19]
1.14 [1.08-1.21]		 Illumina
[up to 1,000,000]		 N
05/07/09 Lesch
October 07, 2008
J Neural Transm
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies 		Attention deficit hyperactivity disorder 343 cases, 304 controls NR 13q31.3
3p22.1
9q34.13
15q23
17p13.2
9q33.1
2q14.2
1p35.1
15q26.1
16q24.1
15q26.1
10q24.1
5q13.2
9q34.11
6p21.1
10q22.1
10q25.1
20q11.22
12q23.3
6p21.1
7p15.1
22q11.22
16q23.3
2p25.3
2q33.3
5q22.2		 GPC6
MOBP
C9orf98
ITGA11
ITGAE
ASTN2
MGC33657
CSMD2
AK094352
ATP2C2
MAN2A2
TLL2
MAP1B
DNM1
TFEB
UNC5B
C10orf79
MMP24
NT5DC3
SUPT3H
CREB5
PPM1F
CDH13
MYT1L
CRYGC
REEP5		 rs7995215-?
rs864643-?
rs11243897-?
rs7164335-?
rs220470-?
rs10983238-?
rs2587695-?
rs2281597-?
rs7175404-?
rs10514604-?
rs2677744-?
rs10786284-?
rs2199161-?
rs2502731-?
rs2842643-?
rs16928529-?
rs515910-?
rs1555322-?
rs4964805-?
rs3799977-?
rs2237349-?
rs412050-?
rs11646411-?
rs2241685-?
rs2242073-?
rs469727-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-8
1 x 10-8
6 x 10-8
1 x 10-7
1 x 10-7
1 x 10-7
3 x 10-7
5 x 10-7
6 x 10-7
8 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[504,219](pooled)		 N
12/09/08 Sonuga-Barke
October 07, 2008
Am J Med Genet B Neuropsychiatr Genet
Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan 		Conduct disorder (interaction) 909 trios NR 5q21.1
16p13.3
4q23
2p21
10q22.3
3p25.3
8p23.1
15q26.2
18q12.3
1q22
4q22.1
17q22
2p22.2
11q23.2
6p15		 Intergenic
A2BP1
ADH1C
Intergenic
Intergenic
SLC6A1
MFHAS1
Intergenic
Intergenic
RIT1
PPM1K
Intergenic
Intergenic
ZBTB16
Intergenic		 rs13188771-A
rs6500744-C
rs1789891-A
rs719593-T
rs2395528-T
rs9990174-T
rs332034-A
rs4321143-G
rs17664267-T
rs2282301-A
rs893971-T
rs8073783-C
rs604381-A
rs17116334-T
rs16880441-G		 0.17
0.53
0.14
0.86
0.23
0.33
0.85
0.28
0.19
0.23
0.60
0.49
0.32
0.16
0.08		 2 x 10-6 (int, MW)
3 x 10-6 (int, MW)
3 x 10-6 (int, MW)
5 x 10-6 (int, MC)
6 x 10-6 (int, MW)
6 x 10-6 (int, MW)
6 x 10-6 (int, MW)
7 x 10-6 (int, MC)
7 x 10-6 (int, MW)
7 x 10-6 (int, MW)
7 x 10-6 (int, MC)
8 x 10-6 (int, MW)
8 x 10-6 (int, MW)
9 x 10-6 (int, MC)
9 x 10-6 (int, MC)		 4.24 [NR] unit decrease
.91 [NR] unit increase
1.47 [NR] unit increase
2.05 [NR] unit decrease
1.46 [NR] unit decrease
2.52 [NR] unit decrease
1.05 [NR] unit increase
1.13 [NR] unit increase
1.39 [NR] unit increase
2.88 [NR] unit increase
1.15 [NR] unit decrease
1.76 [NR] unit decrease
1.26 [NR] unit increase
1.3 [NR] unit increase
1.63 [NR] unit increase		 Perlegen
[429,901)		 N
12/09/08 " Attention deficit hyperactivity disorder symptoms (interaction) 909 trios NR 11q21
13q12.3
6p21.2
14q24.3
21q21.1
3q27.2
8p23.2		 PIWIL4
Intergenic
KIF6
Intergenic
Intergenic
Intergenic
Intergenic		 rs2212361-C
rs1161463-C
rs4714261-T
rs2360997-C
rs2825388-A
rs10049246-G
rs4875598-G		 0.26
0.79
0.17
0.86
0.40
0.59
0.34		 9 x 10-7 (int, MW)
2 x 10-6 (int, MW)
2 x 10-6 (int, MW)
8 x 10-6 (int, MW)
8 x 10-6 (int, MC)
8 x 10-6 (int, MW)
9 x 10-6 (int, MW)		 .97 [NR] unit decrease
1.72 [NR] unit decrease
.95 [NR] unit increase
1.3 [NR] unit decrease
1.06 [NR] unit increase
.6 [NR] unit increase
.94 [NR] unit decrease		 Perlegen
[429,981]		 N
11/25/08 Franke
October 05, 2008
Nat Genet
Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility 		Ulcerative colitis 1,167 cases, 777 controls 1,855 cases, 3,091 controls 6p21.32
1q32.1		 HLA-DRA, BTNL2
IL10		 rs9268877-T
rs3024505-T		 0.45
0.15		 6 x 10-18
1 x 10-12 		1.45 [1.33-1.58]
1.46 [1.31-1.62]		 Affymetrix
[355,262]		 N
11/25/08 Dehghan
October 01, 2008
Lancet
Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study 		Serum urate 11,847 individuals 14,867 individuals 4p16.1
4q22.1
6p22.2		 SLC2A9
ABCG2
SLC17A3		 rs16890979-T
rs2231142-?
rs1165205-?		 0.23
0.11
0.47		 7 x 10-168 (whites)
3 x 10-60 (whites)
4 x 10-29 (whites)		 .34 [0.30-0.38] SD decrease in serum uric acid level
.24 [0.20-0.28] SD increase in serum uric acid level
.09 [0.07-0.11] SD decrease in serum uric acid level		 Affymetrix and Illumina
[up to 530,683]		 N
12/09/08 Gretarsdottir
October 01, 2008
Ann Neurol
Risk variants for atrial fibrillation on chromosome 4q25 associate with ischemic stroke 		Ischemic stroke 1,661 cases, 10,815 controls 4,576 cases, 19,343 controls 4q25 NR rs2200733-T 0.11 2 x 10-10 1.26 [1.17-1.35] Illumina
[310,881]		 N
11/25/08 Mushiroda
October 01, 2008
J Med Genet
A genome-wide association study identifies an association of a common variant in TERT with susceptibility to idiopathic pulmonary fibrosis 		Idiopathic pulmonary fibrosis 159 Japanese cases, 934 Japanese controls 83 Japanese cases, 535 Japanese controls 5p15.33 TERT rs2736100-A 0.41 3 x 10-8 2.11 [1.61-2.78] Illumina
[214,508]		 N
11/25/08 Abraham
September 29, 2008
BMC Med Genomics
A genome-wide association study for late-onset Alzheimer's disease using DNA pooling 		Alzheimer's disease 1,082 cases, 1,239 controls 1,400 additional controls 19q13.32
22q13.33		 PVRL2, TOMM40, APOE
CPT1B		 rs6859-A
rs727153-C		 NR
0.17		 6 x 10-14
3 x 10-6 		NR
1.63 [1.37-1.95]		 Illumina
[561,494] (pooled)		 N
11/25/08 Miyagawa
September 28, 2008
Nat Genet
Variant between CPT1B and CHKB associated with susceptibility to narcolepsy 		Narcolepsy 222 Japanese cases, 389 Japanese controls 748 cases, 994 controls 22q13.33 CPT1B rs5770917-C 0.17 6 x 10-8 1.63 [1.37-1.95] Affymetrix
[249,133]		 N
11/25/08 Mick
September 26, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association study of response to methylphenidate in 187 children with attention-deficit/hyperactivity disorder 		Attention deficit hyperactivity disorder 187 children NR 22q13.31
5p15.31		 Intergenic
Intergenic		 rs9627183-C
rs11134178-T		 0.03
0.05		 3 x 10-6
3 x 10-6 		NR
NR		 Affymetrix
[319,722]		 N
12/09/08 Burkhardt
September 18, 2008
Arterioscler Thromb Vasc Biol
Common SNPs in HMGCR in Micronesians and Whites Associated With LDL-Cholesterol Levels Affect Alternative Splicing of Exon13 		LDL cholesterol 2,346 Micronesian individuals 1,464 European white cases, 1,467 European white controls 5q13.3
19q13.32		 HMGCR
APOE, APOC1, APOC4, APOC2		 rs7703051-A
rs4420638-?		 0.41
NR		 1 x 10-8
2 x 10-7 		18 [NR] % SD increase
NR		 Affymetrix
[~500,000]		 N
11/25/08 Liu
September 17, 2008
J Natl Cancer Inst
Familial Aggregation of Common Sequence Variants on 15q24-25.1 in Lung Cancer 		Lung cancer 194 cases, 219 controls 3,878 cases, 4,831 controls 15q25.1 LOC123688, PSMA4, CHRNA3, CHRNA5, CHRNB4 rs8034191-G NR 1 x 10-8 1.38 [1.17-1.64] Affymetrix
[up to 722,376]		 N
11/25/08 Kiemeney
September 14, 2008
Nat Genet
Sequence variant on 8q24 confers susceptibility to urinary bladder cancer 		Urinary bladder cancer 1,803 cases, 34,336 controls 2,165 cases, 3,800 controls 8q24.21
3q28		 MYC, BC042052
TP63		 rs9642880-T
rs710521-A		 0.45
0.73		 9 x 10-12
1 x 10-7 		1.22 [1.15-1.29]
1.19 [1.12-1.27]		 Illumina
[302,140]		 N
11/25/08 Raychaudhuri
September 14, 2008
Nat Genet
Common variants at CD40 and other loci confer risk of rheumatoid arthritis 		Rheumatoid arthritis 3,393 cases, 12,460 controls 3,929 cases, 5,807 controls 6p21.32
1p13.2
6q23.3
20q13.12
9p13.3
12q13.3
1p36.32
10p15.1
7q21.2		 HLA-DRB1
PTPN22
OLIG3, TNFIP3
CD40
CCL21
KIF5A-PIP4K2C
MMEL1-TNFRSF14
PRKCQ
CDK6		 rs6457620-?
rs6679677-?
rs6920220-?
rs4810485-G
rs2812378-G
rs1678542-C
rs3890745-T
rs4750316-G
rs42041-G		 0.50
0.10
0.22
0.25
0.34
0.37
0.33
0.20
0.24		 4x10-186
6 x 10-42
2 x 10-9
8 x 10-9
3 x 10-8
9 x 10-8
1 x 10-7
4 x 10-6
4 x 10-6 		2.55 [2.40-2.71]
1.79 [1.65-1.94]
1.24 [1.16-1.32]
1.15 [NR]
1.12 [NR]
1.12 [NR]
1.12 [NR]
1.14 [NR]
1.11 [NR]		 Illumina
[818,728] Affymetrix
[~340,000] (imputed)		 N
11/25/08 Huyghe
September 12, 2008
Am J Hum Genet
Genome-wide SNP-based linkage scan identifies a locus on 8q24 for an age-related hearing impairment trait 		Hearing impairment 1,081 individuals NR NR NR NR NR NS NR Affymetrix
[169,154]		 N
11/25/08 Liu
September 08, 2008
PLoS ONE
Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study 		Hip bone size 501 women, 499 men 1,216 women 2q33.1 PLCL1 rs7595412-A 0.89 2 x 10-6 5 [NR] cm2 increase in hip bone size on women Affymetrix
[306,823]		 N
11/25/08 Hazra
September 07, 2008
Nat Genet
Common variants of FUT2 are associated with plasma vitamin B12 levels 		Plasma level of vitamin B12 1,658 women 1,059 women 19q13.3 FUT2 rs492602-G 0.49 5 x 10-17 .09 [0.07-0.11] pg/ml decrease Illumina
[528,134]		 N
11/25/08 McArdle
September 01, 2008
Arthritis Rheum
Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish 		Serum uric acid 408 women, 460 men NR 4p16.1
13q33.1
2q31.1
13q14.11
3p24.3
20p12.3
5q31.3		 GLUT9, WDR1
NR
NR
NR
NR
NR
NR		 rs16890979-?
rs4771450-?
rs4668338-?
rs17065323-?
rs6442522-?
rs6085920-?
rs3776331-?		 NR
NR
NR
NR
NR
NR
NR		 1 x 10-11
2 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
8 x 10-6 		.44 [0.32-0.56] mg/dl decrease in uric serum levels
.23 [NR] mg/dl decrease in uric acid levels
4.29 [NR] mg/dl decrease in uric acid levels
4.29 [NR] mg/dl decrease in uric acid levels
.05 [NR] mg/dl increase in uric acid levels
.4 [NR] mg/dl decrease in uric acid levels
.3 [NR] mg/dl increase in uric acid levels		 Affymetrix
[361,034]		 N
11/25/08 van den Oord
September 01, 2008
Arch Gen Psychiatry
Genomewide Association Analysis Followed by a Replication Study Implicates a Novel Candidate Gene for Neuroticism 		Neuroticism 1,227 individuals 1,880 individuals 14q21.3
8q24.23
7p21.3		 MAMDC1
AK127771
NXPH1		 rs12883384-?
rs2705293-?
rs2349775-?		 NR
NR
NR		 7 x 10-7
6 x 10-6
7 x 10-6 		NR
NR
NR		 Affymetrix
[420,287]		 N
11/25/08 Di Bernardo
August 31, 2008
Nat Genet
A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia 		Chronic lymphocytic leukemia 505 cases, 1,438 controls 1,024 cases, 1,677 controls 6p25.3
11q24.1
15q23
2q13
2q37.1
19q13.32		 IRF4
GRAMD1B
Intergenic
ACOXL,BCL2L11
SP140, SP110
PRKD2,STRN4		 rs872071-G
rs735665-A
rs7176508-A
rs17483466-G
rs13397985-G
rs11083846-A		 0.54
0.21
0.37
0.20
0.19
0.22		 2 x 10-20
4 x 10-12
5 x 10-12
2 x 10-10
6 x 10-10
4 x 10-9 		1.54 [1.41- 1.69]
1.45 [1.31-1.61]
1.37 [1.26-1.50]
1.39 [1.25-1.53]
1.41 [1.26-1.57]
1.35 [1.22-1.49]		 Illumina
[345,665]		 N
11/25/08 Kugathasan
August 31, 2008
Nat Genet
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease 		Inflammatory bowel disease 1,011 cases, 4,250 controls 1,922 cases, 14,124 controls 20q13.33
21q22.2
1p31.3
16q12.1
6p21.32
9q32		 TNFRSF6B
PSMG1
IL23R
NOD2
HLA-DQA1
TNFSF15		 rs2315008-G
rs2836878-?
rs11209026-?
rs5743289-T
rs477515-?
rs6478109-?		 0.69
0.72
0.94
0.17
0.69
0.69		 9 x 10-15
4 x 10-12
7 x 10-11
4 x 10-10
1 x 10-8
3 x 10-8 		1.36 [1.05-1.76]
1.41 [1.08-1.84]
2.56 [1.92-3.45]
1.46 [1.29-1.64]
1.38 [1.23-1.54]
1.36 [1.22-1.52]		 Illumina
[NR]		 N
11/25/08 Galvan
August 26, 2008
Int J Cancer
A polygenic model with common variants may predict lung adenocarcinoma risk in humans 		Lung adenocarcinoma 482 cases, 522 controls NR NR NR NR NR NS NR Illumina
[~318,000] (pooled)		 N
11/25/08 Weidinger
August 22, 2008
PLoS Genet
Genome-Wide Scan on Total Serum IgE Levels Identifies FCER1A as Novel Susceptibility Locus 		Serum IgE levels 1,530 individuals 9,769 individuals 1q23.2
5q31.1		 FCER1A
RAD50		 rs2251746-C
rs2040704-?		 0.26
0.23		 2 x 10-20
4 x 10-8 		19.2 [NR] % decrease
13.9 [NR] % increase		 Affymetrix
[353,569]		 N
11/25/08 Ferreira
August 17, 2008
Nat Genet
Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder 		Bipolar disorder 4,387 cases, 6,209 controls NR 10q21.2
12q13.12
15q14
2q11.2
9q33.3
11q14.1
15q14
3p22.3
6q25.2
9p13.3
14q11.2
14q13.1
3p24.3
3p24.3
11q24.2
15q25.1
1p21.2
9q31.3
18p11.32
3p26.2
10q22.3		 ANK3
CACNA1C
C15orf53, RASGRP1
Intergenic
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 rs10994336-T
rs1006737-A
rs12899449-?
rs2314398-?
rs4130590-?
rs12290811-A
rs16966460-G
rs4380451-?
rs17082664-G
rs216345-T
rs12436436-C
rs8015959-T
rs11720452-?
rs3821396-A
rs544368-T
rs2278702-?
rs1948368-?
rs7042161-?
rs7226677-G
rs1601875-?
rs703965-?		 0.05
0.32
0.72
0.69
0.56
0.15
0.10
0.73
0.13
0.37
0.08
0.02
0.58
0.11
0.12
0.83
0.51
0.65
0.12
0.50
0.54		 9 x 10-9
7 x 10-8
4 x 10-7
3 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
8 x 10-6 		1.45 [NR]
1.18 [NR]
1.2 [NR]
1.17 [NR]
1.16 [NR]
1.2 [NR]
1.26 [NR]
1.18 [NR]
1.22 [NR]
1.15 [NR]
1.3 [NR]
1.59 [NR]
1.15 [NR]
1.23 [NR]
1.22 [NR]
1.21 [NR]
1.15 [NR]
1.15 [NR]
1.24 [NR]
1.14 [NR]
1.15 [NR]		 Affymetrix
[1,769,948] imputed		 N
04/10/09 Unoki
August 17, 2008
Nat Genet
SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations 		Type 2 diabetes 194 Japanese cases, 1,558 Japanese controls 4,924 cases, 2,618 controls (Japanese), 1433 cases, 1,735 controls (Singaporean), 3,891 cases, 4,888 controls (Danish) 11p15.4
6p22.3
3q27.2		 KCNQ1
CDKAL1
IGF2BP2		 rs2237897-C
rs4712524-G
rs6769511-C		 0.61
0.42
0.32		 1 x 10-16
3 x 10-10
1 x 10-9 		1.33 [1.24-1.41]
1.22 [1.15-1.31]
1.23 [1.15-1.31]		 Affymetrix
[207,097]		 N
04/03/09 Yasuda
August 17, 2008
Nat Genet
Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus 		Type 2 diabetes 187 Japanese cases, 1,504 Japanese controls 6,552 Asian cases, 6,621 Asian controls, 2,830 cases, 3,740 controls (Swedish) 11p15.5 KCNQ1 rs2237892-C 0.61 2 x 10-42 1.4 [1.34-1.47] Invader
[82,343]		 N
11/25/08 Shlien
August 12, 2008
Proc Natl Acad Sci USA
Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome 		TP53 carriage 53 carriers, 70 controls 770 individuals Pending Pending Pending Pending Pending Pending Affymetrix
[3,884 CNVs]		 Y
11/25/08 Hofmann
August 10, 2008
Nat Genet
Genome-wide association study identifies ANXA11 as a new susceptibility locus for sarcoidosis 		Sarcoidosis 499 cases, 490 controls 1,649 cases, 1,832 controls NR NR NR NR NS NR Affymetrix
[375,771]		 N
11/25/08 Graham
August 01, 2008
Nat Genet
Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus 		Systemic lupus erythematosus 431 cases, 2,155 controls 740 trios 6q23.3
2q32.3
8p23.1
16p11.2
10q11.22
17p12
4q28.3
2p16.3		 TNFAIP3
STAT4
BLK
ITGAM
c10orf64
Intergenic
Intergenic
Intergenic		 rs5029939-?
rs3821236-?
rs2618476-?
rs11150610-?
rs11101442-?
rs12949531-?
rs2313132-?
rs17039212-?		 0.03
0.19
0.26
0.42
0.32
0.22
0.12
0.10		 3 x 10-12
8 x 10-11
2 x 10-8
2 x 10-6
3 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		2.28 [NR]
1.49 [NR]
1.29 [NR]
NR
NR
NR
NR
NR		 Affymetrix
[313,238]		 N
11/25/08 Julia
August 01, 2008
Arthritis Rheum
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility 		Rheumatoid arthritis 400 cases, 400 controls 410 cases, 394 controls 6p21.32
18q23		 HLA-DQA1, HLA-DQA2
SALL3		 rs6457617-?
rs2002842-A		 NR
0.49		 1 x 10-9
6 x 10-6 		NR
1.61 [NR]		 Illumina
[299,918]		 N
11/25/08 O'Donovan
July 30, 2008
Nat Genet
Identification of loci associated with schizophrenia by genome-wide association and follow-up 		Schizophrenia 479 cases, 2,937 controls 6,666 cases, 9,897 controls 2q32.1
11p14.1
16p13.12		 ZNF804A
Intergenic
Intergenic		 rs1344706-T
rs1602565-C
rs7192086-T		 0.59
0.11
0.24		 2 x 10-7
3 x 10-6
6 x 10-6 		1.12 [NR]
1.16 [NR]
1.12 [NR]		 Affymetrix
[362,532]		 N
11/25/08 Schormair
July 27, 2008
Nat Genet
PTPRD (protein tyrosine phosphatase receptor type delta) is associated with restless legs syndrome 		Restless legs syndrome 628 cases, 1,644 controls 1,835 cases, 3,111 controls 9p23
9p24.1		 PTPRD
PTPRD		 rs4626664-A
rs1975197-T		 0.12
0.16		 6 x 10-10
6 x 10-9 		1.44 [1.31-1.59]
1.31 [1.20-1.44]		 Affymetrix
[208,733]		 N
11/25/08 The SEARCH Collaborative Group
July 23, 2008
N Engl J Med
SLCO1B1 Variants and Statin-Induced Myopathy--A Genomewide Study 		Myopathy 85 cases, 90 controls 19,856 individuals 12p12.1 SLCO1B1 rs4149056-C 0.13 2 x 10-9 4.5 [2.60-7.70] Illumina
[316,184]		 N
11/25/08 Franke
July 21, 2008
Gastroenterology
Genome-wide association study anaylsis in sarcoidosis and Crohn disease unravels a common susceptibility locus on 10p12.2 		Crohn's disease and Sarcoidosis (combined) 382 CD cases, 398 SA cases, 394 controls 660 CD cases, 657 SA cases, 1,091 controls 10p12.2 C10orf67 rs1398024-A 0.25 4 x 10-6 1.23 [1.04-1.45] Affymetrix
[83,360]		 N
11/25/08 Liu
July 10, 2008
Mol Med
Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in Rheumatoid Arthritis 		Treatment respo