manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
{
"fileformat": "VCFv4.2",
"FILTER": "<ID=PASS,Description=\"All filters passed\">",
"INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
"FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
"FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
"FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
"FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
"FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
"FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
"FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
"FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
"FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
"META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
"META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
"META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
"META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
"META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
"META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
"META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
"META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
"SAMPLE": "<ID=ukb-d-2877_1,TotalVariants=13566556,VariantsNotRead=0,HarmonisedVariants=13566556,VariantsNotHarmonised=0,SwitchedAlleles=229,StudyType=Continuous>",
"contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2877_1/ukb-d-2877_1_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:18:18.630753",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2877_1/ukb-d-2877_1.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2877_1/ukb-d-2877_1_data.vcf.gz; Date=Mon Nov 25 16:07:33 2019",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-2877_1/ukb-d-2877_1.vcf.gz; Date=Sun May 10 01:37:56 2020"
}
*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call:
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2877_1/ukb-d-2877_1.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2877_1/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 16:40:33 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2877_1/ukb-d-2877_1.vcf.gz ...
Read summary statistics for 13566556 SNPs.
Dropped 12681 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283499 SNPs remain.
After merging with regression SNP LD, 1283499 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0155 (0.0049)
Lambda GC: 1.0325
Mean Chi^2: 1.034
Intercept: 1.007 (0.006)
Ratio: 0.2059 (0.1772)
Analysis finished at Mon Nov 25 16:42:59 2019
Total time elapsed: 2.0m:26.2s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0293,
"mean_EFFECT": -1.9011e-06,
"n": 89224,
"n_snps": 13566556,
"n_clumped_hits": 1,
"n_p_sig": 4,
"n_mono": 0,
"n_ns": 1251062,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 564688,
"n_est": 89716.5121,
"ratio_se_n": 1.0028,
"mean_diff": -4.2714e-06,
"ratio_diff": 83.6362,
"sd_y_est1": 0.3097,
"sd_y_est2": 0.3106,
"r2_sum1": 0,
"r2_sum2": 0.0003,
"r2_sum3": 0.0003,
"r2_sum4": 0.0003,
"ldsc_nsnp_merge_refpanel_ld": 1283499,
"ldsc_nsnp_merge_regression_ld": 1283499,
"ldsc_observed_scale_h2_beta": 0.0155,
"ldsc_observed_scale_h2_se": 0.0049,
"ldsc_intercept_beta": 1.007,
"ldsc_intercept_se": 0.006,
"ldsc_lambda_gc": 1.0325,
"ldsc_mean_chisq": 1.034,
"ldsc_ratio": 0.2059
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | TRUE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | FALSE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | FALSE |
ldsc_intercept_beta | FALSE |
n_clumped_hits | FALSE |
r2_sum1 | FALSE |
r2_sum2 | FALSE |
r2_sum3 | FALSE |
r2_sum4 | FALSE |
General metrics
af_correlation
: Correlation coefficient between AF
and AF_reference
.inflation_factor
(lambda
): Genomic inflation factor.mean_EFFECT
: Mean of EFFECT
size.n
: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits
: Number of clumped hits.n_snps
: Number of SNPsn_p_sig
: Number of SNPs with pvalue below 5e-8
.n_mono
: Number of monomorphic (MAF == 1
or MAF == 0
) SNPs.n_ns
: Number of SNPs with nonsense values:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 0
or > 1
.n_mac
: Number of cases where MAC
(\(2 \times N \times MAF\)) is less than 6
.is_snpid_unique
: true
if the combination of ID
REF
ALT
is unique and therefore no duplication in snpid.n_miss_<*>
: Number of NA
observations for <*>
column.se_n metrics
n_est
: Estimated sample size value, \(\widehat{n}\).ratio_se_n
: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n
to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.mean_diff
: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
ratio_diff
: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff
and the mean of diff2
(expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
sd_y_est1
: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
sd_y_est2
: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>
: r2
statistics under various assumptions
1
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).2
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),3
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),4
: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).LDSC metrics
Metrics from LD regression
ldsc_nsnp_merge_refpanel_ld
: Number of remaining SNPs after merging with reference panel LD.ldsc_nsnp_merge_regression_ld
: Number of remaining SNPs after merging with regression SNP LD.ldsc_observed_scale_h2_{beta,se}
Coefficient value and SE for total observed scale h2.ldsc_intercept_{beta,se}
: Coefficient value and SE for intercept. Intercept is expected to be 1.ldsc_lambda_gc
: Lambda GC statistics.ldsc_mean_chisq
: Mean \(\chi^2\) statistics.ldsc_ratio
: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).Flags
When a metric needs attention, the flag should return TRUE.
af_correlation
: abs(af_correlation)
< 0.7.inflation_factor
: inflation_factor
> 1.2.n
: n
(max reported sample size) < 10000.is_snpid_non_unique
: NOT is_snpid_unique
.mean_EFFECT_nonfinite
: mean(EFFECT)
is NA
, NaN
, or Inf
.mean_EFFECT_05
: abs(mean(EFFECT))
> 0.5.mean_EFFECT_01
: abs(mean(EFFECT))
> 0.1.mean_chisq
: ldsc_mean_chisq
> 1.3 or ldsc_mean_chisq
< 0.7.n_p_sig
: n_p_sig
> 1000.miss_<*>
: n_miss_<*>
/ n_snps
> 0.01.ldsc_ratio
: ldsc_ratio
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 13554539 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57047 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33330 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051357e+00 | 6.184817e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902633e+07 | 5.591361e+07 | 3.02000e+02 | 3.292996e+07 | 7.014335e+07 | 1.148588e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.900000e-06 | 8.551500e-03 | -1.18045e-01 | -2.269300e-03 | 1.790000e-05 | 2.318700e-03 | 9.564080e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.136800e-03 | 5.916500e-03 | 1.17020e-03 | 1.753800e-03 | 3.223900e-03 | 8.805600e-03 | 3.053030e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.952060e-01 | 2.901229e-01 | 0.00000e+00 | 2.425208e-01 | 4.937885e-01 | 7.467221e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.952042e-01 | 2.901240e-01 | 0.00000e+00 | 2.425183e-01 | 4.937870e-01 | 7.467209e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.910586e-01 | 2.544574e-01 | 1.00000e-03 | 7.500600e-03 | 6.032630e-02 | 2.957970e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 564688 | 0.9583765 | NA | NA | NA | NA | NA | 1.965258e-01 | 2.471417e-01 | 0.00000e+00 | 5.790700e-03 | 8.446490e-02 | 3.085060e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.922400e+04 | 0.000000e+00 | 8.92240e+04 | 8.922400e+04 | 8.922400e+04 | 8.922400e+04 | 8.922400e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0006261 | 0.0025718 | 0.8076500 | 0.8076500 | 0.1101140 | 0.1894970 | 89224 |
1 | 693731 | rs12238997 | A | G | -0.0008191 | 0.0024345 | 0.7365394 | 0.7365373 | 0.1152820 | 0.1417730 | 89224 |
1 | 707522 | rs371890604 | G | C | -0.0021876 | 0.0027375 | 0.4242208 | 0.4242185 | 0.0969534 | 0.1293930 | 89224 |
1 | 717587 | rs144155419 | G | A | 0.0137009 | 0.0064614 | 0.0339719 | 0.0339693 | 0.0158030 | 0.0045926 | 89224 |
1 | 723329 | rs189787166 | A | T | -0.0013392 | 0.0195609 | 0.9454170 | 0.9454170 | 0.0016838 | 0.0003994 | 89224 |
1 | 730087 | rs148120343 | T | C | -0.0040140 | 0.0034119 | 0.2394131 | 0.2394110 | 0.0557130 | 0.0127796 | 89224 |
1 | 731718 | rs142557973 | T | C | 0.0001798 | 0.0023048 | 0.9378170 | 0.9378171 | 0.1214630 | 0.1543530 | 89224 |
1 | 732032 | rs61770163 | A | C | 0.0000904 | 0.0024614 | 0.9706950 | 0.9706946 | 0.1206730 | 0.1555510 | 89224 |
1 | 734349 | rs141242758 | T | C | 0.0000323 | 0.0023061 | 0.9888160 | 0.9888156 | 0.1206850 | 0.1525560 | 89224 |
1 | 740284 | rs61770167 | C | T | -0.0025269 | 0.0103751 | 0.8075801 | 0.8075798 | 0.0060019 | 0.0023962 | 89224 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0019540 | 0.0025814 | 0.4490865 | 0.4490834 | 0.0560976 | 0.0309934 | 89224 |
23 | 154923374 | rs111332691 | T | A | 0.0028749 | 0.0028437 | 0.3120233 | 0.3120199 | 0.0447525 | 0.0116556 | 89224 |
23 | 154925045 | rs509981 | C | T | 0.0012505 | 0.0013633 | 0.3590153 | 0.3590130 | 0.2467730 | 0.3634440 | 89224 |
23 | 154925895 | rs538470 | C | T | 0.0009593 | 0.0013955 | 0.4917847 | 0.4917820 | 0.2427240 | 0.3634440 | 89224 |
23 | 154927581 | rs644138 | G | A | 0.0016617 | 0.0012824 | 0.1950639 | 0.1950605 | 0.3032430 | 0.4635760 | 89224 |
23 | 154929412 | rs557132 | C | T | 0.0012373 | 0.0013636 | 0.3641816 | 0.3641808 | 0.2466620 | 0.3568210 | 89224 |
23 | 154929637 | rs35185538 | CT | C | 0.0012607 | 0.0014228 | 0.3755658 | 0.3755632 | 0.2308240 | 0.3011920 | 89224 |
23 | 154929952 | rs4012982 | CAA | C | 0.0015003 | 0.0014342 | 0.2955357 | 0.2955337 | 0.2404830 | 0.3165560 | 89224 |
23 | 154930230 | rs781880 | A | G | 0.0012977 | 0.0013636 | 0.3412848 | 0.3412814 | 0.2469950 | 0.3618540 | 89224 |
23 | 154930487 | rs781879 | T | A | -0.0041112 | 0.0046562 | 0.3772628 | 0.3772606 | 0.0195810 | 0.1263580 | 89224 |
1 692794 rs530212009 CA C . PASS AF=0.110114 ES:SE:LP:AF:SS:ID -0.000626125:0.00257179:0.0927768:0.110114:89224:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.115282 ES:SE:LP:AF:SS:ID -0.000819069:0.0024345:0.132804:0.115282:89224:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0969534 ES:SE:LP:AF:SS:ID -0.00218761:0.00273751:0.372408:0.0969534:89224:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015803 ES:SE:LP:AF:SS:ID 0.0137009:0.00646136:1.46888:0.015803:89224:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00168376 ES:SE:LP:AF:SS:ID -0.0013392:0.0195609:0.0243766:0.00168376:89224:rs189787166
1 730087 rs148120343 T C . PASS AF=0.055713 ES:SE:LP:AF:SS:ID -0.004014:0.00341193:0.620852:0.055713:89224:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121463 ES:SE:LP:AF:SS:ID 0.000179806:0.0023048:0.0278819:0.121463:89224:rs58276399
1 732032 rs61770163 A C . PASS AF=0.120673 ES:SE:LP:AF:SS:ID 9.04258e-05:0.00246143:0.0129172:0.120673:89224:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120685 ES:SE:LP:AF:SS:ID 3.23273e-05:0.00230613:0.00488451:0.120685:89224:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0060019 ES:SE:LP:AF:SS:ID -0.00252685:0.0103751:0.0928144:0.0060019:89224:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00187068 ES:SE:LP:AF:SS:ID 0.00683734:0.0199589:0.135535:0.00187068:89224:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869949 ES:SE:LP:AF:SS:ID 0.000217237:0.00227272:0.0343981:0.869949:89224:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00150826 ES:SE:LP:AF:SS:ID 0.000652095:0.0207656:0.0110185:0.00150826:89224:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12264 ES:SE:LP:AF:SS:ID -0.000547424:0.00225224:0.0926096:0.12264:89224:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142987 ES:SE:LP:AF:SS:ID -0.000187098:0.00222436:0.0301337:0.142987:89224:rs200141114
1 751756 rs28527770 T C . PASS AF=0.122753 ES:SE:LP:AF:SS:ID -0.000551001:0.00224913:0.0934123:0.122753:89224:rs28527770
1 753405 rs3115860 C A . PASS AF=0.871046 ES:SE:LP:AF:SS:ID -0.000283777:0.0021902:0.0472516:0.871046:89224:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875755 ES:SE:LP:AF:SS:ID 0.000280537:0.0022279:0.0458564:0.875755:89224:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128567 ES:SE:LP:AF:SS:ID 0.000136104:0.00219524:0.0220191:0.128567:89224:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0362739 ES:SE:LP:AF:SS:ID -0.000658695:0.00398493:0.0611247:0.0362739:89224:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870584 ES:SE:LP:AF:SS:ID -0.000240453:0.00218762:0.0397781:0.870584:89224:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870694 ES:SE:LP:AF:SS:ID -0.000219471:0.00218857:0.0361546:0.870694:89224:rs3131968
1 754334 rs3131967 T C . PASS AF=0.87059 ES:SE:LP:AF:SS:ID -0.000270569:0.00218766:0.045001:0.87059:89224:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00498758 ES:SE:LP:AF:SS:ID -0.00446191:0.0113016:0.159274:0.00498758:89224:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00495299 ES:SE:LP:AF:SS:ID -0.00452194:0.0113315:0.161245:0.00495299:89224:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00547252 ES:SE:LP:AF:SS:ID 0.0145276:0.0110293:0.726348:0.00547252:89224:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870757 ES:SE:LP:AF:SS:ID -0.000420123:0.00218394:0.0718844:0.870757:89224:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125878 ES:SE:LP:AF:SS:ID -0.000249024:0.00222742:0.0404897:0.125878:89224:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870304 ES:SE:LP:AF:SS:ID -0.000385906:0.00217776:0.0658304:0.870304:89224:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869591 ES:SE:LP:AF:SS:ID -0.000316443:0.00217657:0.0533483:0.869591:89224:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870467 ES:SE:LP:AF:SS:ID -0.00037142:0.00218021:0.0631205:0.870467:89224:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870473 ES:SE:LP:AF:SS:ID -0.000371406:0.00218037:0.0631129:0.870473:89224:rs4951862
1 758144 rs3131956 A G . PASS AF=0.87048 ES:SE:LP:AF:SS:ID -0.000394966:0.00218044:0.0673959:0.87048:89224:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870913 ES:SE:LP:AF:SS:ID -0.000362602:0.00218624:0.0613447:0.870913:89224:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988102 ES:SE:LP:AF:SS:ID -0.00246989:0.00254303:0.479607:0.0988102:89224:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00635859 ES:SE:LP:AF:SS:ID 0.00959112:0.00991349:0.477157:0.00635859:89224:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874915 ES:SE:LP:AF:SS:ID 0.0001425:0.00222036:0.0228125:0.874915:89224:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864311 ES:SE:LP:AF:SS:ID -0.000465554:0.00217708:0.0805715:0.864311:89224:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869632 ES:SE:LP:AF:SS:ID 5.29305e-05:0.00219741:0.00842707:0.869632:89224:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866681 ES:SE:LP:AF:SS:ID -0.000258589:0.00219732:0.0427194:0.866681:89224:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0985183 ES:SE:LP:AF:SS:ID -0.000247896:0.00263405:0.0338489:0.0985183:89224:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871829 ES:SE:LP:AF:SS:ID 0.000208973:0.00222289:0.0338104:0.871829:89224:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871828 ES:SE:LP:AF:SS:ID 0.000208757:0.00222289:0.0337742:0.871828:89224:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871826 ES:SE:LP:AF:SS:ID 0.00020907:0.0022229:0.0338268:0.871826:89224:rs3131949
1 762632 rs3131948 T A . PASS AF=0.872196 ES:SE:LP:AF:SS:ID 0.00025903:0.00222438:0.042251:0.872196:89224:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125335 ES:SE:LP:AF:SS:ID -0.000235555:0.00222678:0.0382207:0.125335:89224:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105208 ES:SE:LP:AF:SS:ID -0.00191245:0.00242514:0.366177:0.105208:89224:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855765 ES:SE:LP:AF:SS:ID 0.000450118:0.00217796:0.0776545:0.855765:89224:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00161047 ES:SE:LP:AF:SS:ID -0.00103823:0.0195956:0.0187497:0.00161047:89224:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.837613 ES:SE:LP:AF:SS:ID 0.0025555:0.00213558:0.635537:0.837613:89224:rs376645387