Two Sample Summary GWAS data published in Do et al (2014).

A dataset containing summary data GWAS data for 185 independent SNPs with respect to lipid fractions and coronary heart disease (CHD), previously published in Do et al (2013). Lipid fractions include low-density lipoprotein (LDL-C),high-density lipoprotein (HDL-C), and triglycerides, with association estimates obtained from the Global Lipids Genetics Consortium (GLGC) (Willer et al, 2013). Summary data for CHD was obtained from the CARDIoGRAM study (Schunkert et al, 2011). Association estimates were obtained by regressing each phenotype upon the genetic variant and additional adjusted covariates, with links to further information related to each study presented below.

Usage

data_radial

Format

A data frame with 185 rows and 21 variables. Specifically this includes the following information:

rsid

The identification number for each variant

a1

The reference allele for each variant

a2

The other allele for each variant

chr

The chromosome number in which each variant is located

pos

The genomic position for the genetic variant relative to chromosome number

ldlcbeta

The association estimate for the genetic variant obtained by regressing LDL-C upon the genetic variant

hdlcbeta

The association estimate obtained by regressing HDL-C upon the genetic variant

tgbeta

The association estimate obtained by regressing triglycerides upon the genetic variant

chdbeta

The association estimate for CHD obtained by regressing CHD upon the genetic variant

ldlcp2

The p-value corresponding to association estimate ldlcbeta

hdlcp2

The p-value corresponding to association estimate hdlcbeta

tgp2

The p-value corresponding to association estimate tgbeta

chdp2

The p-value corresponding to association estimate chdbeta

ldlcz

The z-score corresponding to association estimate ldlcbeta

ldlcse

The standard error corresponding to association estimate ldlcbeta

hdlcz

The z-score corresponding to association estimate hdlcbeta

hdlcse

The standard error corresponding to association estimate hdlcbeta

tgz

The z-score corresponding to association estimate tgbeta

tgse

The standard error corresponding to association estimate tgbeta

chdz

The z-score corresponding to association estimate chdbeta

chdse

The standard error corresponding to association estimate chdbeta

Source

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904346/

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838666/

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119261/

Details

data_radial

Author

Wes Spiller; Jack Bowden; Tom Palmer.

Examples

head(data_radial)
#>         rsid a1 a2 chr      pos ldlcbeta hdlcbeta  tgbeta chdbeta  ldlcp2
#> 1 rs10903129  A  G   1 25641524   -0.033  -0.0009 -0.0080 -0.0120 4.0e-19
#> 2  rs4660293  A  G   1 39800767   -0.011   0.0350 -0.0200 -0.0110 1.4e-02
#> 3  rs1998013  T  C   1 55730618   -0.380   0.0350  0.0089 -0.1500 4.0e-67
#> 4 rs10493326  A  G   1 62725961    0.021  -0.0013  0.0310 -0.0087 6.0e-07
#> 5  rs4587594  A  G   1 62906518   -0.049  -0.0150 -0.0690  0.0170 3.0e-37
#> 6  rs6603981  T  C   1 92766395    0.034   0.0039  0.0072  0.0120 2.0e-14
#>    hdlcp2    tgp2 chdp2     ldlcz      ldlcse     hdlcz      hdlcse        tgz
#> 1 7.9e-01 1.7e-02  0.38  8.936966 0.003692528 0.2663106 0.003379512  2.3867077
#> 2 7.0e-19 1.0e-07  0.48  2.457263 0.004476525 8.8748941 0.003943709  5.3267239
#> 3 7.7e-02 6.6e-01  0.12 17.309336 0.021953470 1.7683644 0.019792300  0.4399132
#> 4 7.4e-01 1.0e-15  0.65  4.991217 0.004207391 0.3318533 0.003917393  8.0268589
#> 5 5.0e-05 3.0e-87  0.26 12.752994 0.003842235 4.0556270 0.003698565 19.7996112
#> 6 3.5e-01 7.6e-02  0.48  7.650628 0.004444080 0.9345893 0.004172956  1.7743819
#>          tgse      chdz      chdse
#> 1 0.003351898 0.8778963 0.01366904
#> 2 0.003754653 0.7063026 0.01557406
#> 3 0.020231265 1.5547736 0.09647707
#> 4 0.003862034 0.4537622 0.01917304
#> 5 0.003484917 1.1263911 0.01509245
#> 6 0.004057751 0.7063026 0.01698989