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A Catalog of Published Genome-Wide Association Studies

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.

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Published Genome-Wide Associations
Credit: Darryl Leja and Teri Manolio

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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 (see full methods for additional details). 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. For quantitative traits, information on % variance explained, SD increment, or unit difference is reported where available. 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 and risk alleles 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 11/05/09, this table includes 425 publications and 1974 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
11/05/09 Benyamin
October 11, 2009
Nat Genet
Common variants in TMPRSS6 are associated with iron status and erythrocyte volume 		Serum markers of iron status 4,818 Australian siblings 3,470 Dutch individuals 22q12.3
6p22.1
22q12.3
6p22.1		 TMPRSS6
HFE
TMPRSS6
HFE		 rs855791-T
rs1800562-A
rs855791-T
rs1800562-A		 0.42
0.08
0.42
0.08		 1 x 10-10 (MCV)
2 x 10-8 (MCV)
5 x 10-7 (Hgb)
5 x 10-7 (Hgb)		 .13 [0.09-0.17] SD decrease
.22 [0.14-0.30] SD increase
.1 [0.06-0.14] SD decrease
.2 [0.12-0.28] SD increase		 Illumina & Perlegen
[427,037]		 N
11/05/09 Chambers
October 11, 2009
Nat Genet
Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels 		Hemoglobin levels 6,316 Europeans, 9,685 Indian Asians 5,187 Europeans, 6,721 Indian Asians 22q12.3
6p22.1		 TMPRSS6
HFE		 rs855791-A
rs198846-A		 0.53
NR		 2 x 10-13
1 x 10-8 		.13 [0.09-0.17] g/dl decrease
NS		 Affymetrix, Illumina & Perlegen
[NR]		 N
11/03/09 Ganesh
October 11, 2009
Nat Genet
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium 		Hematocrit 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
2p21
7q36.1
10q21.3
22q12.3
12q24.12
7q22.1
6p22.1		 HBS1L, MYB
PRKCE
PRKAG2
HK1
TMPRSS6
SH2B3, ATXN2
TFR2
HFE		 rs9483788-C
rs10168349-C
rs10224002-G
rs16926246-T
rs2413450-T
rs11065987-G
rs7385804-C
rs1800562-A		 NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-15
4 x 10-15
6 x 10-15
1 x 10-13
2 x 10-13
1 x 10-12
4 x 10-10
2 x 10-9 		.22 [0.16-0.28] % increase
.19 [0.14-0.23] % increase
.2 [0.15-0.25] % increase
.33 [0.24-0.42] % increase
.17 [0.13-0.22] % decrease
.17 [0.12-0.22] % decrease
.15 [0.10-0.20] % decrease
.31 [0.21-0.41] % increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Hemoglobin 24,167 European ancestry individuals 9,456 European ancestry individuals 22q12.3
6p22.1
7q36.1
2p21
12q24.12
10q21.3
20q13.2		 TMPRSS6
HFE
PRKAG2
PRKCE
TRAFD1
HK1
TSHZ2		 rs855791-A
rs1800562-A
rs10224002-G
rs10495928-G
rs11065987-A
rs16926246-T
rs6013509-A		 NR
NR
NR
NR
NR
NR
NR		 3 x 10-25
6 x 10-19
3 x 10-15
7 x 10-13
1 x 10-11
2 x 10-11
1 x 10-10 		.09 [0.07-0.11] g/dl decrease
.16 [0.13-0.20] g/dl increase
.07 [0.05-0.09] g/dl increase
.06 [0.05-0.08] g/dl increase
.06 [0.04-0.08] g/dl increase
.11 [0.08-0.14] g/dl increase
.06 [0.05-0.08] g/dl decrease		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Mean corpuscular hemoglobin 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
6p22.2
22q12.3
6p21.1
6q24.1
9p24.1
3q29
19p13.13
16p13.3		 HBS1L, MYB
SLC17A3
TMPRSS6
CCND3, BYSL
CITED2
RCL1
TFRC
GCDH
ITFG3		 rs7776054-G
rs1408272-G
rs2413450-T
rs9349205-A
rs628751-C
rs10758658-A
rs11915082-A
rs11085824-G
rs1122794-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 7 x 10-69
4 x 10-39
9 x 10-34
8 x 10-20
1 x 10-17
2 x 10-14
8 x 10-13
1 x 10-11
3 x 10-10 		.01 [0.009-0.0111] pg decrease
.02 [0.01-0.02] pg decrease
.01 [0.0005-0.007] pg decrease
.01 [0.004-0.006] pg decrease
0 [0.003-0.005] pg decrease
0 [0.004-0.006] pg decrease
0 [0.003-0.005] pg increase
0 [0.003-0.005] pg decrease
0 [0.003-0.006] pg increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Mean corpuscular volume 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
6p22.1
22q12.3
6p21.1
6q24.1
9p24.1
22q13.33
4q12
2p16.1
3q29
7p12.2
16p13.3
19p13.13
7q22.1
10q11.21
6q21
14q23.3		 HBS1L, MYB
HFE
TMPRSS6
CCND3, BYSL
CITED2
RCL1
ECGF1
KIT
BCL11A
TFRC
IKZF1
ITFG3
RTBDN
TFR2
MARCH8
CD164
FNTB		 rs4895441-G
rs1800562-A
rs2413450-T
rs9349205-A
rs643381-A
rs10758658-A
rs131794-A
rs172629-G
rs2540917-C
rs9859260-C
rs12718597-A
rs7189020-T
rs7255045-A
rs7786877-G
rs11239550-G
rs9374080-C
rs4466998-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 7 x 10-86
1 x 10-46
3 x 10-41
1 x 10-31
5 x 10-25
3 x 10-20
1 x 10-15
1 x 10-15
1 x 10-14
8 x 10-14
5 x 10-13
2 x 10-12
2 x 10-12
3 x 10-11
1 x 10-10
4 x 10-10
5 x 10-8 		.01 [0.007-0.009] fl decrease
.01 [0.010-0.014] fl increase
.01 [0.004-0.006] fl decrease
.01 [0.004-0.006] fl decrease
0 [0.003-0.005] fl decrease
0 [0.003-0.005] fl decrease
0 [0.003-0.005] fl decrease
0 [0.003-0.006] fl decrease
0 [0.002-0.004] fl decrease
0 [0.002-0.004] fl increase
0 [0.002-0.004] fl increase
0 [0.002-0.004] fl decrease
0 [0.002-0.004] fl decrease
0 [0.002-0.004] fl increase
0 [0.002-0.003] fl decrease
0 [0.002-0.003] fl decrease
0 [0.001-0.003] fl increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Other erythrocyte phenotypes 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
6q23.3
1q23.1
7q22.1		 HBS1L, MYB
HBS1L, MYB
SPTA1
EPO		 rs9483788-G
rs9373124-C
rs857721-A
rs2075671-A		 NR
NR
NR
NR		 1 x 10-47 (RBC)
7 x 10-14 (MCHC)
1 x 10-10 (MCHC)
1 x 10-9 (RBC)		 0 [0.012-0.016] 1 M cells/mm^3 increase
0 [0.002-0.003] g/dl decrease
0 [0.001-0.002] g/dl decrease
0 [0.005-0.009] 1 M cell/mm^3 increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
10/30/09 Soranzo
October 11, 2009
Nat Genet
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium 		Hematological parameters 4,627 European individuals 9,316 European individuals 6q23.3
6p22.1
6p21.1
9p24.1
12q24.13
22q12.3
6p21.31
7q22.1
22q12.3
17q12
6p21.32
6q21		 HBS1L, MYB
HFE
BYSL, CCND3
AK3
PTPN11
FBX07
BAK1
TFR2
TMPRSS6
GSDMA, ORMDL3
Intergenic
Intergenic		 rs9402686-A
rs1800562-A
rs11970772-T
rs385893-C
rs11066301-G
rs9609565-G
rs210135-A
rs7385804-C
rs5756506-C
rs17609240-G
rs2227139-G
rs4947019-G		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 7 x 10-42 (MCV)
1 x 10-23 (MCV)
7 x 10-19 (MCV)
9 x 10-17 (PLT)
8 x 10-12 (PLT)
4 x 10-10 (MCV)
4 x 10-10 (PLT)
5 x 10-10 (RBC)
1 x 10-9 (MCH)
9 x 10-9 (WBC)
1 x 10-7 (WBC)
8 x 10-6 (MCV)		 .82 [0.70-0.94] fl increase
1.41 [1.13-1.69] fl increase
.58 [0.44-0.70] fl increase
6.26 [4.78-7.74] 10^9/l increase
4.65 [3.32-5.98] 10^9/l increase
.37 [0.25-0.49] fl increase
5.44 [3.74-7.14] 10^9/l increase
.01 [0.004-0.008] 10^12/l increase
.14 [0.10-0.18] pg increase
.02 [0.01-0.03] 10^9/l increase
.02 [0.01-0.03] 10^9/l increase
.01 [0.003-0.011] fl decrease		 Affymetrix and Illumina
[~2.11 million] (imputed)		 N
10/30/09 " Mean platelet volume 4,627 European individuals 9,316 European individuals 12q24.31
7q22.3
3p14.3
17q11.2
10q21.3
1q32.1
11p15.5
1q24.3
2p23.1
20p13
18q22.2
15q22.2
5q33.3
20p12.1
12q13.13		 WDR66
PIK3CG
ARHGEF3
TAOK1
JMJD1C
TMCC2
BET1L
DNM3
EHD3
SIRPA
CD226
TPM1
NR
NR
NR		 rs7961894-T
rs342293-G
rs12485738-A
rs2138852-T
rs2393967-A
rs1668873-G
rs11602954-G
rs10914144-C
rs647316-A
rs6136489-T
rs893001-C
rs11071720-T
rs1473247-C
rs6110278-T
rs10506328-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-44
2 x 10-33
6 x 10-31
1 x 10-22
3 x 10-21
1 x 10-20
1 x 10-14
2 x 10-14
3 x 10-11
8 x 10-11
1 x 10-10
2 x 10-8
3 x 10-7
4 x 10-7
5 x 10-7 		.03 [0.027-0.035] fl increase
.02 [0.013-0.017] fl increase
.02 [0.013-0.017] fl increase
.02 [0.012-0.020] fl increase
.01 [0.01-0.018] fl increase
.01 [0.01-0.014] fl increase
.01 [0.009-0.017] fl increase
.01 [0.009-0.017] fl increase
.01 [0.006-0.014] fl increase
.01 [0.006-0.014] fl increase
.01 [0.007-0.015] fl increase
.01 [0.007-0.015] fl increase
.01 [0.004-0.012] fl decrease
.01 [0.005-0.013] fl increase
.01 [0.004-0.012] fl increase		 Affymetrix and Illumina
[~2.11 million] (imputed)		 N
10/23/09 Weiss
October 08, 2009
Nature
A genome-wide linkage and association scan reveals novel loci for autism 		Autism 1,031 families with 1,553 affected offspring (multiple races/ethnicities) 2,073 trios (multiple races/ethnicities) 5p15.2 SEMA5A, TAS2R1 rs10513025-? NR 3 x 10-7 1.81 [NR] Affymetrix
[~365,000]		 N
10/16/09 Rivadeneira
October 04, 2009
Nat Genet
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies 		Bone mineral density (hip) 19,195 European individuals NR 5q14.3
1p31.3
7q21.3
6q25.1
11p15.2
3p22.1
11p11.2
8q24.12
17q21.31
1p36.12
16q24.1
4q22.1
17q21.31		 MEF2C
GPR177
FLJ42280
ESR1
SOX6
CTNNB1
ARHGAP1
TNFRSF11B
HDAC5
ZBTB40
FOXL1
MEPE
CRHR1		 rs1366594-C
rs2566755-C
rs7781370-T
rs2941740-G
rs7117858-G
rs87938-A
rs7932354-T
rs11995824-G
rs228769-G
rs6426749-C
rs10048146-G
rs1471403-T
rs9303521-T		 0.45
0.21
0.34
0.43
0.20
0.45
0.29
0.55
0.20
0.17
0.19
0.34
0.46		 1 x 10-13
2 x 10-12
5 x 10-12
2 x 10-10
6 x 10-10
8 x 10-10
4 x 10-9
7 x 10-9
2 x 10-8
9 x 10-8
2 x 10-7
8 x 10-7
4 x 10-6 		.09 [0.07-0.11] sd decrease
.1 [0.07-0.13] sd increase
.08 [0.06-0.10] sd decrease
.07 [0.05-0.09] sd increase
.09 [0.06-0.12] sd increase
.07 [0.05-0.09] sd decrease
.07 [0.05-0.09] sd increase
.07 [0.05-0.09] sd decrease
.08 [0.05-0.11] sd increase
.08 [0.05-0.11] sd increase
.09 [0.06-0.12] sd decrease
.06 [0.04-0.08] sd increase
.06 [0.04-0.07] sd decrease		 Affymetrix & Illumina
[2,543,686](imputed)		 N
10/16/09 " Bone mineral density (spine) 19,195 European individuals NR 13q14.11
8q24.12
1p31.3
6q25.1
7q21.3
1p36.12
7p14.1
11p13
18q21.33
12q13.13
17q21.31
16q24.1
2p16.2
4q22.1
11q13.2
17q21.31		 AKAP11
TNFRSF11B
GPR177
ESR1
FLJ42280
ZBTB40
STARD3NL
DCDC5
TNFRSF11A
SP7
CRHR1
FOXL1
SPTBN1
MEPE
LRP5
HDAC5		 rs9533090-T
rs2062377-T
rs1430742-C
rs2504063-A
rs4729260-G
rs7524102-G
rs1524058-T
rs16921914-A
rs884205-A
rs2016266-G
rs9303521-T
rs10048146-G
rs11898505-A
rs1471403-T
rs599083-G
rs228769-G		 0.50
0.44
0.21
0.40
0.32
0.17
0.40
0.27
0.27
0.32
0.46
0.19
0.34
0.34
0.31
0.20		 5 x 10-25
4 x 10-16
3 x 10-13
6 x 10-11
2 x10-10
3 x 10-10
1 x 10-9
2 x 10-9
9 x 10-9
1 x 10-8
1 x 10-8
2 x 10-8
2 x 10-8
2 x 10-8
5 x 10-8
4 x 10-6 		.12 [0.10-0.14] sd decrease
.09 [0.07-0.11] sd increase
.11 [0.07-0.14] sd increase
.08 [0.06-0.10] sd decrease
.08 [0.05-0.11] sd decrease
.09 [0.06-0.12] sd increase
.07 [0.05-0.09] sd decrease
.08 [0.05-0.11] sd increase
.08 [0.05-0.11] sd decrease
.07 [0.05-0.09] sd increase
.07 [0.05-0.09] sd decrease
.09 [0.06-0.12] sd decrease
.07 [0.05-0.09] sd increase
.07 [0.05-0.09] sd increase
.07 [0.05-0.09] sd decrease
.07 [0.04-0.10] sd increase		 Affymetrix & Illumina
[2,543,686](imputed)		 N
11/04/09 Hicks
October 02, 2009
PLoS Genet
Genetic determinants of circulating sphingolipid concentrations in European populations 		Sphingolipid Concentrations 4,110 European individuals NR 14q23.2
19p13.2
4p12
20p12.1
11q12.3		 SGPP1
LASS4
ATP10D
SPTLC3
FADS		 rs7157785-A
rs7258249-G
rs10938494-A
rs680379-A
rs1000778-A		 0.19
0.48
0.23
0.34
0.32		 9 x 10-66 (SM 14:0Mol%)
2 x 10-27 (SM 18:1Mol%)
8 x 10-19 (GluCer)
8 x 10-15 (Cer24:0)
7 x 10-13 (SM 16:1)		 0 [0.001-0.002] mol % increase
0 [0.0007-0.001] mol % increase
.06 [0.04-0.07] unit increase
.1 [0.08-0.13] mol % increase
.62 [0.45-0.78] unit decrease		 Illumina
[318,237]		 N
10/06/09 Roeske
September 29, 2009
Mol Psychiatry
First genome-wide association scan on neurophysiological endophenotypes points to trans-regulation effects on SLC2A3 in dyslexic children 		Speech perception in dyslexia 200 dyslexic German children 186 dyslexic German children 4q32.1
10q26.3		 CTSO, TDO2, PDGFC
NR		 rs4234898-T
rs4751178-G		 NR
NR		 5 x 10-8 (MMNb)
7 x 10-6 (MMNb)		 NS
NS		 Illumina
[297,086]		 N
10/06/09 Nakanishi
September 25, 2009
PLoS Genet
A genome-wide association analysis identified a novel susceptible locus for pathological myopia at 11q24.1 		Myopia (pathological) 297 Japanese cases, 934 Japanese controls 533 Japanese cases, 977 Japanese controls 11q24.1 BLID, LOC399959 rs577948-G 0.52 2 x 10-7 1.37 [1.21-1.54] Illumina
[411,777]		 N
10/05/09 Latourelle
September 22, 2009
BMC Med Genet
Genomewide Association Study for Onset Age in Parkinson Disease 		Parkinson disease (age of onset) 857 white familial cases, 440 white idiopathic cases 747 Italian idiopathic cases 11p13
15q12
18q12.1
1q23.3
2p14		 QSER1, PRRG4
OCA2
DSG3
ATF6
AAK1		 rs10767971-T
rs17565841-A
rs1941184-C
rs10918270-A
rs7577851-T		 NR
NR
NR
NR
NR		 5 x 10-7
3 x 10-6
4 x 10-6
8 x 10-6
9 x 10-6 		3.24 [NR] years older
2.84 [NR] years younger
2.28 [NR] years younger
2.26 [NR] years younger
6.85 [NR] years younger		 Illumina and Perlegen
[1,861,750] (imputed)		 N
10/05/09 Gudmundsson
September 20, 2009
Nat Genet
Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility 		Prostate cancer Up to 1,968 Icelandic cases, 35,382 Icelandic controls Up to 11,806 European descent cases, 12,387 European descent controls 8q24.21
8q24.21
8q24.21
11q13.2
19q13.2
3q21.3
8q24.21
17q12		 Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic		 rs1447295-A
rs16902094-G
rs16901979-A
rs11228565-A
rs8102476-C
rs10934853-A
rs445114-T
rs4430796-A		 0.11
0.15
0.04
0.20
0.54
0.28
0.64
0.52		 2 x 10-19
6 x 10-15
3 x 10-14
7 x 10-12
2 x 10-11
3 x 10-10
5 x 10-10
8 x 10-6 		1.58 [1.43-1.74]
1.21 [1.15-1.26]
1.8 [1.55-2.09]
1.23 [1.16-1.31]
1.12 [1.08-1.15]
1.12 [1.08-1.16]
1.14 [1.10-1.19]
1.19 [1.10-1.28]		 Illumina
[310,520]		 N
09/30/09 Le Clerc
September 15, 2009
J Infect Dis
Genomewide Association Study of a Rapid Progression Cohort Identifies New Susceptibility Alleles for AIDS (ANRS Genomewide Association Study 03). 		AIDS 85 French cases, 2,049 French controls NR 1p13.3
12p12.1
9p23
1q23.3
8q22.3
2q12.1
9p22.3		 Intergenic
SOX5
Intergenic
RXRG
Intergenic
TGFBRAP1
NR		 rs4118325-G
rs1522232-C
rs1360517-A
rs10800098-A
rs3108919-C
rs1020064-G
rs1556032-C		 0.81
0.52
0.06
0.05
0.27
0.23
0.49		 6 x 10-7
2 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
7 x 10-6
9 x 10-6 		4.17 [2.17-8.33]
2.22 [1.59-3.13]
3.09 [2.00-4.78]
3.29 [2.08-5.20]
2.13 [1.56-2.91]
2.94 [1.75-5.00]
2.05 [1.48-2.84]		 Illumina
[291,119]		 N
09/30/09 Suppiah
September 13, 2009
Nat Genet
IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy 		Response to Hepatitis C treatment 131 European ancestry responders, 162 European ancestry non-responders 261 European responders, 294 European non-responders 19q13.2 IL28A, IL28B rs8099917-G NR 9 x 10-9 1.98 [1.57-2.52] Illumina
[311,159]		 N
09/30/09 Tanaka
September 13, 2009
Nat Genet
Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C 		Response to Hepatitis C treatment 72 Japanese responders, 82 Japanese non-responders 122 Japanese responders, 50 Japanese non-responders 19q13.2 IL28B rs8099917-G 0.12 3 x 10-32 27.1 [14.6-50.3] Affymetrix
[621,220]		 N
09/30/09 Heinzen
September 11, 2009
J Alzheimers Dis
Genome-Wide Scan of Copy Number Variation in Late-Onset Alzheimer's Disease 		Alzheimer's Disease 331 cases, 368 controls NR 19q13.32
13q13.2
1p31.1
10q24.31
6q24.3		 TOMM40, APOE
RFC3
TTLL7
PAX2
SASH1		 rs2075650-?
rs690705-?
rs7539409-?
rs4509693-?
rs9390537-?		 0.15
0.25
0.18
0.18
0.22		 3 x 10-11
6 x 10-7
1 x 10-6
6 x 10-6
8 x 10-6 		NS
NS
NS
NS
NS		 Illumima
[~550,000]		 N
09/30/09 Sha
September 09, 2009
BMC Med Genet
Genome-wide association reveals three SNPs associated with sporadic amyotrophic lateral sclerosis through a two-locus analysis 		Amyotrophic lateral sclerosis (interaction) 276 Caucasian cases, 271 Caucasian controls NR NS NS NS NS NS NS Illumina
[549,062]		 N
09/29/09 Harold
September 06, 2009
Nat Genet
Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease 		Alzheimer's disease 3,941 European ancestry cases, 7,848 European ancestry controls 2,023 European ancestry cases, 2,340 European ancestry controls 19q13.32
8p21.1
11q14.2		 APOE, TOMM40
CLU
PICALM		 rs2075650-?
rs11136000-?
rs3851179-?		 0.15
0.60
0.63		 2 x 10-157
9 x 10-10
1 x 10-9 		2.53 [2.37-2.71]
1.16 [1.11-1.22]
1.16 [1.11-1.22]		 Illumina
[529,205]		 N
09/29/09 Lambert
September 06, 2009
Nat Genet
Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease 		Alzheimer's disease 2,032 French cases, 5,328 French controls 3,978 European cases, 3,297 European controls 19q13.32
1q32.2
8p21.1		 APOE
CR1
CLU		 rs2075650-?
2-SNP haplotype
3-SNP haplotype		 0.90
0.18
0.26		 2 x 10-16
3 x 10-10 (AA)
6 x 10-10 (CCG)		 NS
1.22 [1.15-1.30]
1.22 [1.14-1.29]		 Illumina
[537,029]		 N
09/29/09 Rung
September 06, 2009
Nat Genet
Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia 		Type 2 diabetes and other traits 679 French cases, 697 French controls 5,579 European cases, 7,096 European controls 10q25.2
6p22.3
2q36.3
4p16.1
8q24.11
5q14.3		 TCF7L2
CDKAL1
LOC64673, IRS1
WFS1, PPP2R2C
SLC30A8
LOC72901, CETN3		 rs7903146-T
rs4712523-G
rs2943641-C
rs4689388-T
rs13266634-C
rs12518099-C		 0.27
0.32
0.63
0.57
0.68
0.23		 1 x 10-30
2 x 10-12
9 x 10-12
1 x 10-8
8 x 10-8
7 x 10-7 		1.48 [1.39-1.57]
1.2 [1.14-1.26]
1.19 [1.13-1.25]
1.16 [1.10-1.21]
1.16 [1.10-1.22]
1.16 [1.10-1.22]		 Illumina
[392,365]		 N
09/29/09 van Es
September 06, 2009
Nat Genet
Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis 		Amyotrophic lateral sclerosis 2,323 European descent cases, 9,013 European descent controls 2,532 European descent cases, 5,940 European descent controls 19p13.11
9p21.2
9p21.2
Xq13.3
12p12.3
11q22.1
9p21.2
Xp22.32		 UNC13A
MOBKL2B, IFNK, C9orf72
MOBKL2B, IFNK, C9orf72
NR
NR
NR
NR
NR		 rs12608932-?
rs2814707-?
rs3849942-?
rs5937496-?
rs9971637-?
rs2405657-?
rs774359-?
rs5916687-?		 0.34
0.23
0.23
0.13
0.05
0.66
0.25
0.27		 3 x 10-14
7 x 10-9
1 x 10-8
6 x 10-7
2 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6 		1.25 [NR]
1.22 [NR]
1.23 [NR]
1.38 [NR]
1.48 [NR]
1.19 [NR]
1.19 [NR]
1.22 [NR]		 Illumina
[292,768]		 N
10/02/09 Need
September 04, 2009
Hum Mol Genet
A Genome-wide Study of Common SNPs and CNVs in Cognitive Performance in the CANTAB battery 		Cognitive performance 1,295 individuals NR 15q23
Xp22.2
3p22.3
13q34
16p12.1
17q21.32
8q24.13
21q11.2
17q25.2
14q23.2
15q21.3
2q31.1
5p15.31
11q14.2
12p13.1
15q12
1q23.2
20p12.3
21q21.3
3q27.2
16q23.3
3p25.1
7q31.1
18q22.1
1q41
3p22.1
3q26.32
9p22.2
11p12
13q12.3
14q23.2
1p32.1
1q32.1
7p15.1
12q24.23
19q12
1p36.13
3q13.33
4q28.1
7p14.1
7q31.1
8q12.1
11q13.5
6p21.2
18q12.3
Xp22.31
13q14.11		 CORO2B
HCCS
ARPP-21
Intergenic
Intergenic
Intergenic
FAM91A1
NRIP1
SEC14L1
MTHFD1
UNC13C
GORASP2
Intergenic
C11orf73
GRIN2B
GABRB3
VANGL2
PLCB1
JAM2
EHHADH
Intergenic
GRIP2
IMMP2L
C18orf4, DSEL
FAM177B
MOBP
Intergenic
SH3GL2
API5
FLT1
MTHFD1
JUN
MDM4
CPVL
CCDC64
TSHZ3
FAM131C
FBXO40
FAT4
VPS41
IMMP2L
TOX
CAPN5
C6orf129
RIT2
VCX3B
DNAJC15		 rs11856323-?
rs5934953-?
rs6799705-?
rs767210-?
rs2203512-?
rs2326017-?
rs10481151-?
rs2229741-?
rs3744064-?
rs10498514-?
rs1897031-?
rs4668356-?
rs7729273-?
rs6592284-?
rs2160519-?
rs8043440-?
rs16832015-?
rs6056209-?
rs17001239-?
rs7374394-?
rs4082514-?
rs9036-?
rs10279573-?
rs2124349-?
rs6683071-?
rs816488-?
rs7612209-?
rs10810865-?
rs10501293-?
rs17086609-?
rs2295639-?
rs4601609-?
rs12143943-?
rs2252521-?
rs11064994-?
rs1078373-?
rs9442235-?
rs3772130-?
rs12639834-?
rs11984145-?
rs12531640-?
rs960089-?
rs3781684-?
rs904251-?
rs8085804-?
rs7892812-?
rs1324015-?		 0.08
0.02
0.05
0.11
0.14
0.30
0.14
0.47
0.03
0.02
0.18
0.06
0.20
0.21
0.06
0.17
0.01
0.43
0.12
0.20
0.03
0.19
0.14
0.05
0.20
0.04
0.40
0.13
0.25
0.35
0.02
0.05
0.41
0.34
0.06
0.37
0.42
0.23
0.36
0.05
0.13
0.07
0.11
0.38
0.37
0.47
0.42		 1 x 10-7 (PAL8)
1 x 10-7 (PAL6)
2 x 10-7 (PAL8)
3 x 10-7 (PAL6)
3 x 10-7 (PRM)
3 x 10-7 (SWM strategy)
4 x 10-7 (PRM)
6 x 10-7 (SRM)
7 x 10-7 (PAL6)
8 x 10-7 (SWM strategy)
1 x 10-6 (PRM)
1 x 10-6 (PAL8)
1 x 10-6 (SSP)
2 x 10-6 (IED)
2 x 10-6 (IED)
2 x 10-6 (SRM)
2 x 10-6 (IED)
2 x 10-6 (RVP)
2 x 10-6 (PRM)
2 x 10-6 (IED)
3 x 10-6 (PC1)
3 x 10-6 (PAL6)
3 x 10-6 (IED)
4 x 10-6 (IED)
4 x 10-6 (PC1)
4 x 10-6 (IED)
4 x 10-6 (IED)
4 x 10-6 (PAL6)
5 x 10-6 (SWM Strategy)
5 x 10-6 (IED)
5 x 10-6 (SWM Strategy)
5 x 10-6 (PRM)
5 x 10-6 (PAL8)
5 x 10-6 (PAL8)
6 x 10-6 (PAL6)
6 x 10-6 (SSP)
6 x 10-6 (PC1)
6 x 10-6 (PC1)
6 x 10-6 (SWM Strategy)
6 x 10-6 (PAL8)
6 x10-6 (IED)
6 x 10-6 (PAL6)
7 x 10-6 (VRM)
7 x 10-6 (SWM Strategy)
8 x 10-6 (VRM)
8 x 10-6 (SSP)
9 x 10-6 (PC1)		 NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS		 Illumina
[475,971]		 N
09/28/09 Paterson
September 03, 2009
Arterioscler Thromb Vasc Biol
Genome-Wide Association Identifies the ABO Blood Group as a Major Locus Associated With Serum Levels of Soluble E-Selectin 		Serum soluble E-selectin 685 individuals with type 1 diabetes 477 nondiabetic siblings 9q34.2 ABO rs579459-C 0.20 1 x 10-29 NS Illumina
[~841,000]		 N
09/28/09 Tonjes
September 03, 2009
Hum Mol Genet
Genetic Variation in GPR133 is Associated with Height - Genome Wide Association Study in the Self-contained Population of Sorbs 		Height 929 Sorbian individuals, 2,986 Caucasian individuals 2,772 German individuals 12q24.33 GPR133 rs1569019-? NR 5 x 10-8 .95 [0.61-1.29] cm increase Affymetrix
[390,619]		 N
09/28/09 De Moor
September 02, 2009
Med Sci Sports Exerc
Genome-Wide Association Study of Exercise Behavior in Dutch and American Adults 		Exercise (leisure time) 1,644 Dutch individuals, 978 European individuals NR 10q23.2
18p11.32
2q33.1		 PAPSS2
C18orf2
DNAPTP6		 rs10887741-T
rs8097348-G
rs12612420-A		 NR
NR
NR		 4 x 10-6
7 x 10-6
8 x 10-6 		1.32 [1.17-1.49]
1.36 [1.19-1.56]
1.43 [1.22-1.67]		 Affymetrix and Perlegen
[~1.6 million] (imputed)		 N
09/29/09 Ising
September 01, 2009
Arch Gen Psychiatry
A genomewide association study points to multiple loci that predict antidepressant drug treatment outcome in depression 		Response to antidepressant treatment 339 German individuals 1,193 German individuals NS NS NS NS NS NS Illumina
[389,251] (pooled)		 N
09/28/09 McClay
September 01, 2009
Mol Psychiatry
Genome-wide pharmacogenomic analysis of response to treatment with antipsychotics 		Treatment response to antipsychotics 738 cases NR 4p15.1
9q33.3
12q23.1
2q14.3
1q21.3
6p24.1
15q13.3
3q28
6p21.33		 Intergenic
Intergenic
ANKS1B
CNTNAP5
Intergenic
Intergenic
TRPM1
Intergenic
Intergenic		 rs17390445-?
rs888219-?
rs7968606-?
rs17727261-?
rs10888501-?
rs1040994-?
rs17815774-?
rs7635839-?
rs12526186-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x10-7 (ziprasidone)
2 x 10-7 (risperidone)
3 x 10-7 (olanzapine)
5 x 10-7 (risperidone)
1 x 10-6 (olanzapine)
2 x 10-6 (olanzapine)
3 X 10-6 (risperidone)
3 x 10-6 (olanzapine)
3 x 10-6 (risperidone)		 17 [NR] % of variance explained
11 [NR] % of variance explained
10 [NR] % of variance explained
10 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained		 Affymetrix & Perlegen
[492,900]		 N
09/10/09 Spain
September 01, 2009
Cancer Res
Colorectal Cancer Risk Is Not Associated with Increased Levels of Homozygosity in a Population from the United Kingdom 		Colorectal cancer 921 white cases, 929 white controls 1,214 white cases, 1,435 white controls NS NS NS NS NS NS Illumina
[486,303]		 N
09/09/09 Laje
August 31, 2009
Pharmacogenet Genomics
Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients 		Response to antidepressant treatment 90 white cases, 90 white controls 30 white cases, 1,652 white controls NS NS NS NS NS NS Illumina
[100,864]		 N
09/09/09 Hancock
August 28, 2009
PLoS Genet
Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children 		Asthma (childhood onset) 492 Mexican trios 177 Mexican trios 9q21.31 TLE4, CHCHD9 rs2378383-? 0.78 7 x 10-7 1.64 [1.32-2.04] Illumina
[520,767]		 N
09/24/09 Liu
August 28, 2009
PLoS ONE
Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males 		Obesity and osteoporosis 499 Caucasian males, 501 Caucasian females 1,370 Caucasian males, 1,985 Caucasian females 11p15.1
11p15.1		 SOX6
SOX6		 rs297325-T
rs4756846-T		 0.23
0.12		 4 x 10-7 (BMI-BMD, males)
5 x 10-7 (BMI-BMD, males)		 NS
NS		 Affymetrix
[379,319]		 N
09/09/09 Shuldiner
August 26, 2009
JAMA
Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy 		Response to clopidogrel therapy 429 Amish individuals 140 white, 83 African American, and 4 unspecified individuals NS NS NS NS NS NS Affymetrix
[400,230]		 N
09/09/09 Cui
August 18, 2009
Gastroenterology
Functional variants in ADH1B and ALDH2 coupled with alcohol and smoking synergistically enhance esophageal cancer risk 		Esophageal cancer 188 Japanese cases, 938 Japanese controls 699 Japanese cases, 1,482 Japanese controls 12q24.12
4q23		 BRAP, ALDH2
ADH6, ADH1B		 rs671-A
rs1229984-G		 0.36
0.35		 3 x 10-24
8 x 10-24 		1.67 [1.58-1.76]
1.79 [1.69-1.88]		 Illumina
[359,195]		 N
09/09/09 Ge
August 16, 2009
Nature
Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance 		Response to Hepatitis C treatment 871 Caucasian, 191 African American, and 75 Hispanic participants NR 19q13.2
6q21
4q34.3		 IL28B
AKD2
Intergenic		 rs12979860-C
rs9400317-?
rs17067123-?		 0.72
NR
NR		 1 x 10-28 (combined)
7 x 10-6 (combined)
8 x 10-6 (combined)		 2 [1.8-2.3] (European-Americans)
NS
NS		 Illumina
[565,759]		 N
09/04/09 Papaemmanuil
August 16, 2009
Nat Genet
Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia 		Acute lymphoblastic leukemia (childhood) 503 European pediatric cases, 1,438 European pediatric controls 404 European pediatric cases, 960 European pediatric controls 7p12.2
10q21.2
14q11.2		 IKZF1
ARID5B
CEBPE		 rs4132601-C
rs7089424-C
rs2239633-G		 0.28
0.34
0.52		 1 x 10-19
7 x 10-19
3 x 10-7 		1.69 [1.58-1.81]
1.65 [1.54-1.76]
1.34 [1.22-1.45]		 Illumina
[291,473]		 N
09/11/09 Trevino
August 16, 2009
Nat Genet
Germline genomic variants associated with childhood acute lymphoblastic leukemia 		Acute lymphoblastic leukemia (childhood) 317 European descent cases, 17,958 European descent controls NR 10q21.2
7p12.2
12q24.22
6q24.1
19q13.31
1q43
2q36.1
1p31.1
3q26.32
1q31.3
1q44
10p11.21
12p13.32
18p11.32		 ARID5B
IKZF1, DDC
KRTHB5
Intergenic
ZNF230
RYR2
KCNE4
SIAT7C
KCNMB2
Intergenic
OR2C3
PARD3
C12orf5
Intergenic		 rs10821936-C
rs11978267-G
rs2089222-A
rs11155133-G
rs2191566-G
rs7554607-A
rs12621643-T
rs10873876-T
rs9290663-T
rs6428370-G
rs1881797-C
rs563507-A
rs10849033-G
rs1879352-C		 0.34
0.27
0.03
0.01
0.28
0.56
0.28
0.15
0.13
0.32
0.18
0.04
0.02
0.16		 1 x 10-15
8 x 10-11
8 x 10-8
3 x 10-7
4 x 10-7
2 x 10-6
3 x 10-6
4 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6 		1.91 [1.60-2.20]
1.69 [1.40-1.90]
2.26 [1.60-3.0]
3.62 [2.10-6.00]
1.52 [1.20-1.70]
1.49 [1.20-1.70]
1.48 [1.20-1.70]
1.55 [1.20-1.80]
1.58 [1.20-1.90]
1.43 [1.20-1.60]
1.52 [1.20-1.80]
2 [1.40-2.70]
2.55 [1.60-3.80]
1.53 [1.20-1.80]		 Affymetrix
[307,944]		 N
09/04/09 Alkelai
August 13, 2009
Psychopharmacology
Genome-wide association study of antipsychotic-induced parkinsonism severity among schizophrenia patients 		Response to antipsychotic treatment 199 cases, 198 controls NR 2q24.3 FIGN rs12476047-C NR 3 x 10-6 3.21 [1.97-5.25] Affymetrix & Perlegen
[495,172]		 N
09/09/09 Potkin
August 07, 2009
PLoS ONE
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease 		Hippocampal atrophy 172 cases, 209 controls NR 21q21.1
5q21.3
9q21.13
14q22.1
13q31.1
20q11.23
20q13.31
5q14.1
7p12.2
7q21.11
9q21.31
12q14.3
1q21.3
20q11.23
5q14.1
12q13.11
5p14.1
5p15.1
7p21.3
11q24.3
8q24.12		 FDPSP
EFNA5
PRUNE2
FRMD6, AL079307.7
Intergenic
C20orf132
ZBP1
AC104108.3, SCAMP1, LHFPL2
IKZF1, AC020743.7
MAGI2
RP11, 232A1.1
CAND1
AL157404.18, S100A5
RPN2
ARSB
ARID2, SFRS2IP
Intergenic
AC026790.5
Intergenic
Intergenic
MAL2		 rs1888414-?
rs10074258-?
rs10781380-?
rs11626056-?
rs4773460-?
rs8115854-?
rs2073145-?
rs6881634-?
rs10276619-?
rs11525066-?
rs10867752-?
rs1082714-?
rs4845552-?
rs6031882-?
rs337847-?
rs1373549-?
rs7727656-?
rs682748-?
rs9918508-?
rs6590322-?
rs1364705-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7
2 x 10-7
7 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6 		NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS		 Illumina
[516,645]		 N
09/04/09 Tse
August 05, 2009
Am J Hum Genet
Genome-wide Association Study Reveals Multiple Nasopharyngeal Carcinoma-Associated Loci within the HLA Region at Chromosome 6p21. 		Nasopharyngeal carcinoma 277 Han Chinese cases, 285 Han Chinese controls 635 Han Chinese cases, 1,640 Han Chinese controls 6p21.33
6p22.1
6p22.1		 HLA-A
GABBR1
HLA-F		 rs2517713-A
rs29232-A
rs3129055-G		 0.62
0.46
0.31		 4 x 10-20
9 x 10-17
7 x 10-11 		1.88 [1.65-2.15]
1.67 [1.48-1.88]
1.51 [1.34-1.71]		 Illumina
[480,365]		 N
09/14/09 Broderick
August 04, 2009
Cancer Res
Deciphering the Impact of Common Genetic Variation on Lung Cancer Risk: A Genome-Wide Association Study 		Lung cancer 1,952 European cases, 1,438 European controls 5,608 European cases, 6,767 European controls 15q25.1
6p21.33
5p15.33
10q23.31
15q15.2
3p24.1
2p14		 CHRNA3
BAT3
CLPTM1L
NR
TGM5
NR
NR		 rs8034191-?
rs3117582-?
rs4975616-?
rs1926203-?
rs748404-?
rs1530057-?
rs4254535-?		 NR
NR
NR
NR
NR
NR
NR		 3 x 10-26
4 x 10-10
3 x 10-9
1 x 10-6
1 x 10-6
3 x 10-6
5 x 10-6 		1.29 [1.23-1.35]
1.24 [1.16-1.33]
1.15 [1.10-1.20]
1.12 [NR]
1.15 [1.09-1.20]
1.26 [NR]
1.12 [NR]		 Illumina
[511,919]		 N
09/04/09 Chambers
August 03, 2009
Diabetes
Common genetic variation near melatonin receptor MTNR1B contributes to raised plasma glucose and increased risk of type-2 diabetes amongst Indian Asians and European whites 		Fasting plasma glucose 7,474 Indian Asian individuals 4,462 European controls 11q21 MTNR1B rs2166706-G 0.46 2 x 10-9 .07 (0.04-0.09) mmol/L increase Illumina
[up to 544,390]		 N
09/04/09 Grant
August 03, 2009
J Pediatr
A Genome-Wide Association Study Identifies a Locus for Nonsyndromic Cleft Lip with or without Cleft Palate on 8q24 		Nonsyndromic cleft lip with or without cleft palate 111 European ancestry cases, 5,951 European ancestry controls NR 18q22.3
8q24.21		 Intergenic
Intergenic		 rs17085106-?
rs987525-?		 0.018
0.22		 4 x 10-8
9 x 10-8 		4.07 [2.37-7.00]
2.09 [1.59-2.76]		 Illumina
[495,858]		 N
09/04/09 Amundadottir
August 02, 2009
Nat Genet
Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer 		Pancreatic cancer 1,771 European ancestry cases, 1,805 European ancestry controls 2,120 European ancestry cases, 2,127 European ancestry controls 9q34.2 ABO rs505922-T 0.35 5 x 10-8 1.2 [1.12-1.28] Illumina
[558,542]		 N
09/04/09 Song
August 02, 2009
Nat Genet
A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2 		Ovarian cancer 1,817 European ancestry cases, 2,353 European ancestry controls 6,944 European ancestry cases, 9,477 European ancestry controls 9p22.2 BNC2, LOC648570, CNTLN rs3814113-T 0.68 5 x 10-19 1.22 [1.16-1.27] Illumina
[up to ~2,000,000] (imputed)		 N
08/21/09 Wu
August 02, 2009
Nat Genet
Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer 		Bladder cancer 969 Caucasian cases, 957 Caucasian controls 5,698 US and European cases, 38,633 US and European controls 8q24.3 PSCA rs2294008-T 0.46 2 x 10-10 1.15 [1.10-1.20] Illumina
[556,429]		 N
09/04/09 Comabella
August 01, 2009
Arch Neurol
Genome-wide scan of 500,000 single-nucleotide polymorphisms among responders and nonresponders to interferon beta therapy in multiple sclerosis 		Response to interferon beta therapy 53 responders, 53 non-responders 49 responders, 45 non-responders NS NS NS NS NS NS Affymetrix
[428,867](pooled)		 N
08/21/09 Nakano
July 22, 2009
Proc Natl Acad Sci USA
Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population 		Glaucoma (primary open-angle) 418 Japanese cases, 300 Japanese controls 409 Japanese cases, 448 Japanese controls NS NS NS NS NS NS Affymetrix
[331,838]		 N
08/21/09 Skibola
July 20, 2009
Nat Genet
Genetics variants at 6p21.33 are associated with susceptibility to follicular lymphoma 		Follicular lymphoma 189 European ancestry cases, 592 European controls 456 European ancestry cases, 2,785 European ancestry controls 6p21.33 STG, PSORS1 rs6457327-C 0.62 5 x 10-11 1.69 [1.43-2.00] Illumina
[~500,000] (pooled)		 N
08/12/09 Adeyemo
July 17, 2009
PLoS Genet
A Genome-Wide Association Study of Hypertension and Blood Pressure in African Americans 		Hypertension 509 African American cases, 508 African American controls 366 West African cases, 614 West African controls 15q22.1
4q23		 ALDH1A2
ADH7		 rs1550576-?
rs991316-T		 0.86
0.45		 3 x 10-6
5 x 10-6 		1.92 [NR]
1.62 [NR]		 Affymetrix
[808,465]		 N
08/04/09 Benjamin
July 13, 2009
Nat Genet
Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry 		Atrial fibrillation 3,413 cases, 37,105 referents 2,145 cases, 4,073 controls 4q25
16q22.3
1p36.22		 PITX2
ZFHX3
MTHFR, NPPA		 rs17042171-A
rs2106261-T
rs17375901-T		 0.12
0.174
0.053		 4 x 10-63
2 x 10-15
6 x 10-7 		1.65
1.25
1.26 		Affymetrix & Illumina
[~2.5 million] (imputed)		 N
07/30/09 Gudbjartsson
July 13, 2009
Nat Genet
A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke 		Atrial fibrillation 2,385 European cases, 33,752 European controls up to 2,427 European cases, 3,379 European controls 4q25
16q22.3		 Intergenic
ZFHX3		 rs2200733-?
rs7193343-T		 0.12
NR		 1 x 10-14
1 x 10-10 		1.42 [NR]
1.21 [1.14-1.29]		 Illumina
[303,136]		 N
07/24/09 Nolte
July 09, 2009
PLoS ONE
Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies 		Cardiac repolarisation 3,558 Caucasian individuals 29,527 Caucasian individuals 1q23.3
6q22.31		 OLFML2B, NOS1AP
SLC35F1, C6orf204, PLN		 rs12143842-T
rs11153730-C		 0.25
0.50		 1 x 10-83
2 x 10-29 		.18 [NR] unit increase
.09 [NR] unit increase		 Affymetrix & Illumina
[~2,399,142] (imputed)		 N
07/24/09 Tonjes
July 08, 2009
Eur J Hum Genet
Association of FTO variants with BMI and fat mass in the self-contained population of Sorbs in Germany 		Body mass index and fat mass 948 Sorbian individuals NR NS NS NS NS NS NS Affymetrix
[390,619]		 N
08/07/09 Vasan
July 08, 2009
JAMA
Genetic Variants Associated with Cardiac Structure and Function: A Meta-analysis and Replication of Genome-wide Association Data 		Aortic root size 12,612 European ancestry individuals 4,094 European ancestry individuals 5q23.2
17p13.3
12q14.3
12p12.2
1p21.2
15q24.1		 CCDC100, PPIC
SMG6, SRR, TSR1, SGSM2
HMGA2
PDE3A
PALMD
LOXL1		 rs17470137-A
rs10852932-T
rs4026608-C
rs10770612-G
rs7543130-A
rs893817-G		 0.29
0.36
0.38
0.19
0.49
0.34		 1 x 10-11
2 x 10-11
2 x 10-9
2 x 10-8
1 x 10-7
3 x 10-6 		.03 [0.02-0.04] cm increase
.03 [0.02-0.04] cm increase
.03 [0.02-0.04] cm decrease
.03 [0.02-0.04] cm increase
.03 [0.02-0.04] cm increase
.02 [0.01-0.03] cm increase		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
08/07/09 " Cardiac structure and function 12,612 European ancestry individuals 4,094 European ancestry individuals 6q22.31
10q23.1
5q22.1
16q23.1		 SLC35F1, C6orf204, PLN
GRID1
SLC25A46
WWOX		 rs89107-G
rs7910620-G
rs17132261-T
rs2059238-A		 0.50
0.01
0.02
0.22		 1 x 10-9 (LV internal diastolic dimensions)
7 x 10-7 (LV wall thickness)
9 x 10-7 (LV wall thickness)
3 x 10-6 (LV wall thickness)		 .03 [0.02-0.04] cm decrease
.17 [0.11-0.23] cm increase
.06 [0.04-0.08] cm increase
.02 [0.01-0.03] cm decrease		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
07/16/09 Bishop
July 05, 2009
Nat Genet
Genome-wide association study identifies three loci associated with melanoma risk 		Melanoma 1,539 European ancestry cases, 3,917 European ancestry controls 2,312 European ancestry cases, 1,867 European ancestry controls 16q24.3
16q24.3
11q14.3
22q13.1
9p21.3		 MC1R
MC1R
TYR
Intergenic
CDKN2A		 rs258322-A
rs4785763-A
rs1393350-A
rs2284063-?
rs7023329-A		 0.09
0.32
0.27
0.37
0.50		 3 x 10-27
6 x 10-22
2 x 10-14
2 x 10-9
4 x 10-7 		1.67 [1.52-1.83]
1.36 [1.28-1.45]
1.29 [1.21-1.38]
1.2 [1.14-1.28]
1.18 [1.10-1.25]		 Illumina
[~317,000]		 N
07/13/09 Falchi
July 05, 2009
Nat Genet
Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi 		Cutaneous nevi 1,524 European twins 4,107 European individuals 9p21.3
22q13.1		 MTAP
PLA2G6		 rs4636294-A
rs2284063-G		 0.48
0.35		 3 x 10-15
3 x 10-8 		.2 [0.13-0.27] increase in log nevus count
.08 [-0.002-0.16] decrease in log nevus count		 Illumina
[297,108]		 N
07/12/09 Shete
July 05, 2009
Nat Genet
Genome-wide association study identifies five susceptibility loci for glioma 		Glioma 1,878 cases, 3,670 controls 2,545 cases, 2,953 controls 8q24.21
5p15.33
9p21.3
5p15.33
20q13.33
8q24.21
11q23.3		 CCDC26
TERT
CDKN2A, CDKN2B
TERT
RTEL1
CCDC26
PHLDB1		 rs4295627-G
rs2736100-G
rs4977756-G
rs2853676-A
rs6010620-G
rs891835-G
rs498872-T		 0.83
0.49
0.60
0.73
0.23
0.78
0.69		 2 x 10-18
2 x 10-17
7 x 10-15
4 x 10-14
3 x 10-12
8 x 10-11
1 x 10-8 		1.36 [1.29-1.43]
1.27 [1.19-1.37]
1.24 [1.19-1.30]
1.26 [1.20-1.32]
1.28 [1.21-1.35]
1.24 [1.17-1.30]
1.18 [1.13-1.24]		 Illumina
[454,576]		 N
07/12/09 Wrensch
July 05, 2009
Nat Genet
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility 		Glioma (high-grade) 692 high-grade cases, 3,992 controls 176 high-grade cases, 174 controls 9p21.3
20q13.33
20q13.33		 Intergenic
RTEL1
RTEL1		 rs1412829-C
rs4809324-C
rs6010620-G		 0.39
0.10
0.77		 2 x 10-10
2 x 10-9
3 x 10-9 		1.42 [1.27-1.58]
1.6 [1.37-1.87]
1.52 [1.32-1.75]		 Illumina
[326,506]		 N
07/24/09 Teichert
July 04, 2009
Hum Mol Genet
A genome-wide association study of acenocoumarol maintenance dosage 		Acenocoumarol maintenance dosage 1,451 Caucasian individuals 287 Caucasian individuals 10q23.33
19p13.12
10q23.33
3q22.3		 CYP2C18
CYP4F2
CYP2C19
CNTN4		 rs12772169-?
rs2108622-?
rs12767583-?
rs10935268-?		 NR
NR
NR
NR		 8 x 10-12
3 x 10-10
3 x 10-7
8 x 10-7 		NS
NS
NS
NS		 Illumina
[~550,000]		 N
07/12/09 Elliott
July 01, 2009
JAMA
Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease 		C-reactive protein 17,967 European and Indian Asian men and women 13,615 European and Indian Asian men and women 1q23.2
12q24.31
19q13.32
1q21.3
1p31.3		 CRP
HNF1A
APOE, APOCI, APOCII
IL6R
LEPR		 rs7553007-A
rs1183910-T
rs4420638-G
rs4537545-T
rs6700896-T		 NR
NR
NR
NR
NR		 8 x 10-44
1 x 10-30
5 x 10-27
2 x 10-14
3 x 10-14 		20.7 [18.9-23.4] % decrease
13.8 [10.9-16.6] % decrease
21.8 [18.1-25.3] % decrease
11.5 [8.5-14.4] % decrease
14.8 [12.0-17.6] % decrease		 Affymetrix, Illumina & Perlegen
[~1.4 million] (imputed)		 N
07/24/09 Estrada
July 01, 2009
Hum Mol Genet
A genome-wide association study of northwestern Europeans involves the CNP signaling pathway in the etiology of human height variation 		Height 10,074 European individuals 6,912 European individuals 2q37.1
22q13.1
5p13.3
11q14.1
22q13.1		 DIS3L2, ALPP, NPPC
TNRC6B, ADSL
C5orf23, NPR3
TMEM126B, TMEM126A
SGSM3, MKL1		 rs6717918-T
rs139909-T
rs10472828-C
rs10898392-T
rs5757949-T		 0.78
0.68
0.56
NR
NR		 3 x 10-9
2 x 10-7
3 x 10-7
3 x 10-6
4 x 10-6 		.44 [0.20-0.68] cm increase
.25 [0.03-0.47] cm increase
.22 [0.04-0.40] cm increase
NS
NS		 Affymetrix, Illumina & Perlegen
[2,228,850] (imputed)		 N
07/13/09 International Schizophrenia Consortium
July 01, 2009
Nature
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder 		Schizophrenia 3,322 European descent cases, 3,587 European descent controls 4,692 European descent cases, 15,493 European descent controls 6p22.1
18q21.2
3q26.33
1p21.3		 MHC
TCF4
FXR1
PTBP2		 rs13194053-T
rs17594526-T
rs6782299-T
rs7544736-G		 0.86
0.03
0.73
0.18		 1 x 10-8
1 x 10-7
1 x 10-7
6 x 10-7 		1.22
1.44
1.1
1.25 		Affymetrix
[739,995]		 N
07/10/09 Shi
July 01, 2009
Nature
Common variants on chromosome 6p22.1 are associated with schizophrenia 		Schizophrenia 2,681 European ancestry cases, 2,653 European ancestry controls, 1,286 African American cases, 973 African American controls 5,327 European ancestry cases, 16,424 European ancestry controls 6p22.1
6p21.32		 SLC17A1, SLC17A3, BTN3A2, BTN2A2, BTN3A1, HIST1H2AG, HIST1H2BJ, PRSS16, POM121L2, ZNF184
HLA-DQA1		 rs13194053-T
rs9272219-G		 0.82
0.72		 1 x 10-8 (EA)
7 x 10-8 (EA)		 1.28 [NR]
1.14 [NR]		 Affymetrix
[up to 843,798]		 N
07/10/09 Stefansson
July 01, 2009
Nature
Common variants conferring risk of schizophrenia 		Schizophrenia 2,663 European cases, 13,498 European controls 10,282 European cases, 21,093 European controls 6p22.1
6p21.32
11q24.2
18q21.2
2p16.1
5q21.1
9q33.1		 MHC, PRSS16
MHC, NOTCH4
NRGN
TCF4
VRK2
SLCO6A1
Intergenic		 rs6932590-T
rs3131296-G
rs12807809-T
rs9960767-C
rs2312147-C
rs1502844-C
rs1572299-A		 0.78
0.87
0.83
0.06
NR
NR
NR		 1 x 10-12
2 x 10-10
2 x 10-9
4 x 10-9
3 x 10-7
1 x 10-6
4 x 10-6 		1.16 [NR]
1.19 [NR]
1.15 [NR]
1.23 [NR]
1.09 [NR]
1.09 [NR]
1.08 [NR]		 Illumina
[314,868]		 N
07/24/09 Treutlein
July 01, 2009
Arch Gen Psychiatry
Genome-wide association study of alcohol dependence 		Alcohol dependence 476 German cases, 1,358 German controls 1,024 German cases, 996 German controls 2q35
5q32
Xp22.2
14q24.2
4q26
6q25.1		 PECR
PPP2R2B
Intergenic
Intergenic
CAST, ERAP1
ESR1		 rs7590720-G
rs1864982-A
rs12388359-T
rs36563-A
rs13150562-G
rs6902771-C		 0.29
0.13
0.11
0.15
0.68
0.51		 1 x 10-8
3 x 10-6
4 x 10-6
5 x 10-6
7 x 10-6
8 x 10-6 		1.35 [1.22-1.49]
1.36 [1.20-1.55]
1.61 [1.32-2.00]
1.33 [1.18-1.50]
1.27 [1.14-1.41]
1.24 [1.13-1.36]		 Illumina
[524,396]		 N
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 		NS
.65 [NR] cm increase
NS
NS
NS
NS
NS		 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
NS		 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 NS NS NS NS NS NS 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 NS NS NS NS NS NS 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 NS NS NS NS NS NS 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 		NS
1.21 [1.15-1.28]
1.17 [1.11-1.23]
1.19 [1.13-1.27]
NS		 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 NS NS NS NS NS NS 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 		Serum uric acid 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)		 NS
NS
NS
NS
NS		 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 NS NS NS NS NS NS 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]
NS
NS
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]
NS
2.05 [NR]
NS
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 		Response to lithium treatment in bipolar disorder 458 lithium-treated subjects, 719 non-lithium treated subjects 359 subjects NS NS NS NS NS NS 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 NS NS NS NS NS NS 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
0.10
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 		NS
NS
NS
1.33 [1.25-1.43]
NS
NS
NS
1.1 [1.04-1.17]
NS
1.28 [1.17-1.41]
NS
NS
1.09 [1.02-1.16]
1.17 [1.10-1.24]
NS
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]
NS
1.09 [1.02-1.16]
1.14 [1.06-1.22]
NS
1.16 [1.07-1.24]
1.3 [1.11-1.49]
NS
NS
NS
1.1 [1.03-1.17]
NS
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 NS NS NS NS NS NS 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-C 0.29 3 x 10-8 1.18 [1.08-1.30] 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 NS 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 2q37.1
12p12.2
Xq28		 UGT1A1
SLC01B3
G6PD		 rs887829-T
rs2117032-C
rs766420-G		 0.30
0.47
0.18		 1 x 10-69
3 x 10-14
9 x 10-9 		.57 [0.50-0.63] SD decrease
.13 [0.08-0.18] SD increase
.18 [0.12-0.24] SD decrease		 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
NS
.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
NS
.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 		Aging 89 cases, 227 controls NR 2q22.1 LRP1B rs12474609-? NR 6 x 10-9 NS 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 NS NS NS NS NS NS 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 vitamin levels 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 NS 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 NS NS NS NS NS NS 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]
NS		 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 NS NS NS NS NS NS 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 NS NS NS NS NS NS 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 NS NS NS NS NS NS 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 NS NS NS NS NS NS 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
NS
5 [2.84-7.16] ms decrease
NS
NS
4.54 [2.58-6.50] ms increase
NS		 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
10/15/09 Lowe
February 06, 2009
PLoS Genet
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae 		Quantitative traits Up to 2,906 Micronesian individuals NR 11q23.3
19q13.32
19q13.32
3q25.33
10p12.33
5q13.3
7p22.2
9q22.33
10p15.3
12p13.33
19q13.32
19q13.32
20q13.12
7p14.1
7q36.3
9p21.3
2q22.2
12q24.13
12q24.31
19q13.32
5q35.3
9p21.3
10p13
10p13
2p23.3
5q13.3
5q35.1
4q21.21
10p15.3
6q16.2
6p22.3
7p21.3
7q34		 Intergenic
TOMMM40, APOC2, APOE, APOC4, APOC1
MGC2650, BLOC1S3, XTP7
SCHIP1
CACNB2
COL4A3BP, HMGCR
SDK1
HEMGN, C9ORF156
ADARB2
ENSG00000118975, FKBP4
TOMM40, APOC2, APOE, APOC4, APOC1
MGC2650, BLOC1S3, XTP7
Intergenic
Intergenic
UBE3C
Intergenic
ARHGAP15
Intergenic
SPPL3
TOMM40, APOC2, APOE, APOC4, APOC1
MGAT1
Intergenic
ITGA8
CUBN
ENSG0000173957, UBXD4, FKBP1B, FLJ21945
COL4A3BP, HMGCR
Intergenic
Intergenic
ADARB2
Intergenic
Intergenic
Intergenic
TRIM24		 rs7396835-T
rs4420638-G
rs2159324-T
rs2222328-C
rs7069923-C
rs3846663-T
rs6462411-C
rs755109-C
rs6560749-T
rs10848704-C
rs4420638-G
rs2159324-T
rs6066084-A
rs10486715-A
rs2527866-C
rs2225614-C
rs10928195-C
rs11066587-G
rs1039302-T
rs4420638-G
rs655601-A
rs613391-G
rs7895372-G
rs10508517-A
rs7561273-A
rs3846663-T
rs254893-A
rs10518224-A
rs6560749-T
rs6909430-G
rs10498712-G
rs17157663-A
rs1874326-G		 0.32
0.21
0.44
0.32
0.49
0.39
0.20
0.23
0.14
0.35
0.21
0.44
0.06
0.07
0.23
0.50
0.08
0.16
0.36
0.21
0.47
0.49
0.04
0.43
0.35
0.39
0.06
0.23
0.14
0.08
0.25
0.32
0.47		 1 x 10-9 (TG)
3 x 10-7 (TC)
4 x 10-7 (LDL-C)
8 x 10-7 (WC)
1 x 10-6 (SBP)
1 X 10-6 (LDL-C)
1 x 10-6 (TSH)
1 x 10-6 (TSH)
2 x 10-6 (BMI)
2 x 10-6 (TSH)
2 x 10-6 (CRP)
2 x 10-6 (CRP)
2 x 10-6 (% body fat)
3 x 10-6 (height)
3 x 10-6 (SBP)
3 x 10-6 (weight)
4 x 10-6 (weight)
5 x 10-6 (CRP)
5 x 10-6 (CRP)
5 x 10-6 (TG)
5 x 10-6 (HDL-C)
5 x 10-6 (WC)
6 x 10-6 (TC)
6 x 10-6 (DBP)
6 x 10-6 (CRP)
6 x 10-6 (TC)
6 x 10-6 (DBP)
7 x 10-6 (TG)
8 x 10-6 (% body fat)
8 x 10-6 (TSH)
9 x 10-6 (HDL-C)
9 x 10-6 (TC)
9 x 10-6 (weight)		 .23 [NR] mg/dL increase
.28 [NR] mg/dL increase
.21 [NR] mg/dL decrease
.22 [NR] inch decrease
.19 [NR] mm Hg increase
.21 [NR] mg/dL increase
.36 [NR] mIU/L decrease
.31 [NR] mIU/L decrease
.32 [NR] kg/m2 decrease
.29 [NR] mIU/L decrease
.28 [NR] mg/L decrease
.19 [NR] mg/L decrease
.85 [NR] % increase
.44 [NR] inch decrease
.27 [NR] mm Hg decrease
.21 [NR] lb. decrease
.36 [NR] lb. decrease
.26 [NR] mg/L increase
.21 [NR] mg/L increase
.22 [NR] mg/dL increase
.23 [NR] mg/dL increase
.2 [NR] inch increase
.35 [NR] mg/dL decrease
.18 [NR] mm Hg decrease
.22 [NR] mg/L decrease]
.19 [NR] mg/dL increase
.58 [NR] mm Hg decrease
.19 [NR] mg/dL increase
.34 [NR] % decrease
.49 [NR] mIU/L decrease
.23 [NR] mg/dL increase
.18 [NR] mg/dL decrease
.22 [NR] lb. increase		 Affymetrix
[408,775]		 N
08/21/09 Need
February 06, 2009
PLoS Genet
A genome-wide investigation of SNPs and CNVs in schizophrenia 		Schizophrenia 871 European ancestry cases, 863 European ancestry controls 1,460 European ancestry cases, 12,995 European ancestry controls NS NS NS NS NS NS Illumina
[312,565] (pooled)		 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 		NS
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 NS NS NS NS NS NS 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 NS NS NS NS NS NS 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)		 NS
NS
NS		 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 NS NS NS NS NS NS 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 		NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS		 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 		NS
NS		 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 NS NS NS NS NS NS 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 NS 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 		NS
NS
NS		 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 		Arthritis (juvenile idiopathic) 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]
NS
NS		 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 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
NS
.66 [0.46-0.86] SD increase
.68 [0.48-0.88] SD decrease
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
NS
.43 [0.25-0.61] SD decrease
NS
NS
NS
NS
NS
NS
NS		 Illumina
[315,887]		 N
01/14/09 " 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
NS
NS		 Affymetrix
[100,846]		 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 NS 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
NS
NS
NS		 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 		NS
NS		 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 NS NS NS NS NS NS 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 p