{
"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-22617_1234,TotalVariants=9930457,VariantsNotRead=0,HarmonisedVariants=9930457,VariantsNotHarmonised=0,SwitchedAlleles=209,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-22617_1234/ukb-d-22617_1234_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:25:49.939991",
"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-22617_1234/ukb-d-22617_1234.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_1234/ukb-d-22617_1234_data.vcf.gz; Date=Mon Nov 25 14:14:57 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-22617_1234/ukb-d-22617_1234.vcf.gz; Date=Sun May 10 14:43:47 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-22617_1234/ukb-d-22617_1234.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-22617_1234/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 14:59:42 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_1234/ukb-d-22617_1234.vcf.gz ...
Read summary statistics for 9930457 SNPs.
Dropped 7639 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, 1277585 SNPs remain.
After merging with regression SNP LD, 1277585 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0028 (0.0052)
Lambda GC: 0.9931
Mean Chi^2: 0.9956
Intercept: 0.9905 (0.0059)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 15:01:22 2019
Total time elapsed: 1.0m:40.12s
{
"af_correlation": 0.9413,
"inflation_factor": 0.9903,
"mean_EFFECT": -5.7197e-07,
"n": 91149,
"n_snps": 9930457,
"n_clumped_hits": 1,
"n_p_sig": 1,
"n_mono": 0,
"n_ns": 1078496,
"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": 196588,
"n_est": 91169.8127,
"ratio_se_n": 1.0001,
"mean_diff": -2.943e-06,
"ratio_diff": 2.899,
"sd_y_est1": 0.1262,
"sd_y_est2": 0.1263,
"r2_sum1": 5.6143e-06,
"r2_sum2": 0.0004,
"r2_sum3": 0.0004,
"r2_sum4": 0.0004,
"ldsc_nsnp_merge_refpanel_ld": 1277585,
"ldsc_nsnp_merge_regression_ld": 1277585,
"ldsc_observed_scale_h2_beta": 0.0028,
"ldsc_observed_scale_h2_se": 0.0052,
"ldsc_intercept_beta": 0.9905,
"ldsc_intercept_se": 0.0059,
"ldsc_lambda_gc": 0.9931,
"ldsc_mean_chisq": 0.9956,
"ldsc_ratio": 2.1591
}
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 | TRUE |
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 | 9923368 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 98 | 0 | 47950 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 30034 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.080678e+00 | 6.177128e+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 | 7.875373e+07 | 5.609541e+07 | 3.02000e+02 | 3.246418e+07 | 6.965241e+07 | 1.147353e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -6.000000e-07 | 1.401100e-03 | -1.25048e-02 | -6.546000e-04 | -8.900000e-06 | 6.377000e-04 | 1.592020e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.205000e-03 | 7.220000e-04 | 4.88600e-04 | 6.504000e-04 | 8.814000e-04 | 1.555800e-03 | 4.009600e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.014563e-01 | 2.886341e-01 | 0.00000e+00 | 2.517758e-01 | 5.020836e-01 | 7.516315e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.014546e-01 | 2.886352e-01 | 0.00000e+00 | 2.517726e-01 | 5.020822e-01 | 7.516312e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.561557e-01 | 2.629453e-01 | 8.52080e-03 | 3.969650e-02 | 1.516690e-01 | 4.084550e-01 | 9.914790e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 196588 | 0.9802035 | NA | NA | NA | NA | NA | 2.557756e-01 | 2.537728e-01 | 0.00000e+00 | 4.432910e-02 | 1.675320e-01 | 4.045530e-01 | 1.000000e+00 | ▇▃▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.114900e+04 | 0.000000e+00 | 9.11490e+04 | 9.114900e+04 | 9.114900e+04 | 9.114900e+04 | 9.114900e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0003241 | 0.0010335 | 0.7538362 | 0.7538350 | 0.1114870 | 0.1894970 | 91149 |
1 | 693731 | rs12238997 | A | G | 0.0001404 | 0.0009788 | 0.8859461 | 0.8859455 | 0.1164590 | 0.1417730 | 91149 |
1 | 707522 | rs371890604 | G | C | -0.0000677 | 0.0011000 | 0.9509500 | 0.9509499 | 0.0978765 | 0.1293930 | 91149 |
1 | 717587 | rs144155419 | G | A | 0.0001473 | 0.0026222 | 0.9551921 | 0.9551920 | 0.0157837 | 0.0045926 | 91149 |
1 | 730087 | rs148120343 | T | C | 0.0002385 | 0.0013568 | 0.8604630 | 0.8604624 | 0.0569973 | 0.0127796 | 91149 |
1 | 731718 | rs142557973 | T | C | -0.0000371 | 0.0009289 | 0.9681300 | 0.9681303 | 0.1223590 | 0.1543530 | 91149 |
1 | 732032 | rs61770163 | A | C | 0.0002353 | 0.0009904 | 0.8121950 | 0.8121943 | 0.1220470 | 0.1555510 | 91149 |
1 | 734349 | rs141242758 | T | C | -0.0000180 | 0.0009296 | 0.9845900 | 0.9845903 | 0.1215880 | 0.1525560 | 91149 |
1 | 749963 | rs529266287 | T | TAA | -0.0002382 | 0.0009144 | 0.7944729 | 0.7944722 | 0.8689170 | 0.7641770 | 91149 |
1 | 751343 | rs28544273 | T | A | 0.0002353 | 0.0009065 | 0.7952160 | 0.7952154 | 0.1236990 | 0.2426120 | 91149 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0002178 | 0.0010873 | 0.8412169 | 0.8412159 | 0.0552869 | 0.0309934 | 91149 |
23 | 154923374 | rs111332691 | T | A | 0.0002223 | 0.0011833 | 0.8509801 | 0.8509801 | 0.0448387 | 0.0116556 | 91149 |
23 | 154925045 | rs509981 | C | T | 0.0005204 | 0.0005703 | 0.3614964 | 0.3614940 | 0.2444670 | 0.3634440 | 91149 |
23 | 154925895 | rs538470 | C | T | 0.0005833 | 0.0005830 | 0.3171042 | 0.3171005 | 0.2409490 | 0.3634440 | 91149 |
23 | 154927581 | rs644138 | G | A | 0.0004232 | 0.0005364 | 0.4300847 | 0.4300834 | 0.3001640 | 0.4635760 | 91149 |
23 | 154929412 | rs557132 | C | T | 0.0005294 | 0.0005704 | 0.3533841 | 0.3533818 | 0.2443160 | 0.3568210 | 91149 |
23 | 154929637 | rs35185538 | CT | C | 0.0005855 | 0.0005956 | 0.3256132 | 0.3256112 | 0.2286640 | 0.3011920 | 91149 |
23 | 154929952 | rs4012982 | CAA | C | 0.0005458 | 0.0006004 | 0.3632871 | 0.3632840 | 0.2382530 | 0.3165560 | 91149 |
23 | 154930230 | rs781880 | A | G | 0.0005457 | 0.0005702 | 0.3385587 | 0.3385571 | 0.2447660 | 0.3618540 | 91149 |
23 | 154930487 | rs781879 | T | A | -0.0016257 | 0.0019340 | 0.4005853 | 0.4005823 | 0.0196632 | 0.1263580 | 91149 |
1 692794 rs530212009 CA C . PASS AF=0.111487 ES:SE:LP:AF:SS:ID 0.000324095:0.00103351:0.122723:0.111487:91149:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116459 ES:SE:LP:AF:SS:ID 0.000140402:0.000978845:0.0525927:0.116459:91149:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0978765 ES:SE:LP:AF:SS:ID -6.76653e-05:0.0011:0.0218423:0.0978765:91149:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157837 ES:SE:LP:AF:SS:ID 0.000147334:0.00262216:0.0199093:0.0157837:91149:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0569973 ES:SE:LP:AF:SS:ID 0.000238497:0.00135675:0.0652678:0.0569973:91149:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122359 ES:SE:LP:AF:SS:ID -3.71112e-05:0.000928863:0.0140663:0.122359:91149:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122047 ES:SE:LP:AF:SS:ID 0.000235312:0.000990386:0.0903397:0.122047:91149:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121588 ES:SE:LP:AF:SS:ID -1.79541e-05:0.000929568:0.00674458:0.121588:91149:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.868917 ES:SE:LP:AF:SS:ID -0.000238204:0.000914384:0.0999209:0.868917:91149:rs529266287
1 751343 rs28544273 T A . PASS AF=0.123699 ES:SE:LP:AF:SS:ID 0.000235288:0.000906543:0.0995149:0.123699:91149:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143202 ES:SE:LP:AF:SS:ID 0.000748988:0.000897482:0.393643:0.143202:91149:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123834 ES:SE:LP:AF:SS:ID 0.000230075:0.000905232:0.0972516:0.123834:91149:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869892 ES:SE:LP:AF:SS:ID -0.000297235:0.000882061:0.133043:0.869892:91149:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874553 ES:SE:LP:AF:SS:ID -0.000138675:0.000896366:0.0569747:0.874553:91149:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129529 ES:SE:LP:AF:SS:ID 0.000416022:0.000884828:0.195021:0.129529:91149:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0358205 ES:SE:LP:AF:SS:ID -0.000641788:0.00161649:0.160303:0.0358205:91149:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869539 ES:SE:LP:AF:SS:ID -0.000356297:0.000881323:0.163668:0.869539:91149:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869616 ES:SE:LP:AF:SS:ID -0.000317014:0.000881708:0.143158:0.869616:91149:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869535 ES:SE:LP:AF:SS:ID -0.000357679:0.000881287:0.164406:0.869535:91149:rs3131967
1 755890 rs3115858 A T . PASS AF=0.86952 ES:SE:LP:AF:SS:ID -0.000224726:0.000879471:0.0978235:0.86952:91149:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126911 ES:SE:LP:AF:SS:ID 0.00013496:0.000897786:0.0552667:0.126911:91149:rs61768170
1 756604 rs3131962 A G . PASS AF=0.86905 ES:SE:LP:AF:SS:ID -0.000176206:0.000877195:0.0753088:0.86905:91149:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868436 ES:SE:LP:AF:SS:ID -0.000244264:0.000876639:0.107614:0.868436:91149:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869199 ES:SE:LP:AF:SS:ID -0.00019462:0.00087799:0.0837698:0.869199:91149:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869205 ES:SE:LP:AF:SS:ID -0.000195421:0.000878047:0.0841381:0.869205:91149:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869207 ES:SE:LP:AF:SS:ID -0.000194201:0.000878055:0.0835676:0.869207:91149:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869687 ES:SE:LP:AF:SS:ID -0.000216878:0.000880404:0.0939776:0.869687:91149:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0991787 ES:SE:LP:AF:SS:ID 0.000129159:0.00102458:0.04591:0.0991787:91149:rs10157329
1 759837 rs3115851 T A . PASS AF=0.873682 ES:SE:LP:AF:SS:ID -0.000206514:0.000893443:0.0876701:0.873682:91149:rs3115851
1 761732 rs2286139 C T . PASS AF=0.863058 ES:SE:LP:AF:SS:ID -0.000125398:0.000876396:0.052456:0.863058:91149:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868472 ES:SE:LP:AF:SS:ID -0.000228431:0.000885091:0.0989015:0.868472:91149:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865369 ES:SE:LP:AF:SS:ID -0.000335372:0.000885257:0.15193:0.865369:91149:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0995228 ES:SE:LP:AF:SS:ID 6.81643e-05:0.00105949:0.0228702:0.0995228:91149:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870657 ES:SE:LP:AF:SS:ID -0.000320224:0.000895341:0.142305:0.870657:91149:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870657 ES:SE:LP:AF:SS:ID -0.00032021:0.000895341:0.142298:0.870657:91149:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870654 ES:SE:LP:AF:SS:ID -0.000319979:0.000895344:0.142181:0.870654:91149:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871019 ES:SE:LP:AF:SS:ID -0.000323007:0.00089576:0.143632:0.871019:91149:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126515 ES:SE:LP:AF:SS:ID 0.000297492:0.000896756:0.130719:0.126515:91149:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106037 ES:SE:LP:AF:SS:ID 4.41074e-05:0.000974782:0.015964:0.106037:91149:rs61768174
1 766105 rs2519015 T A . PASS AF=0.85438 ES:SE:LP:AF:SS:ID -0.000523108:0.000876059:0.259296:0.85438:91149:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.839153 ES:SE:LP:AF:SS:ID -0.000330039:0.000865586:0.153051:0.839153:91149:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763195 ES:SE:LP:AF:SS:ID -0.000385268:0.000695976:0.236663:0.763195:91149:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105092 ES:SE:LP:AF:SS:ID 0.000553009:0.000959061:0.248566:0.105092:91149:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.129904 ES:SE:LP:AF:SS:ID 0.000283742:0.000884231:0.125928:0.129904:91149:rs762168062
1 769223 rs60320384 C G . PASS AF=0.129636 ES:SE:LP:AF:SS:ID 0.000220528:0.000883068:0.0953937:0.129636:91149:rs60320384
1 769963 rs7518545 G A . PASS AF=0.104365 ES:SE:LP:AF:SS:ID 0.000508216:0.000966507:0.222567:0.104365:91149:rs7518545
1 770181 rs146076599 A G . PASS AF=0.00906976 ES:SE:LP:AF:SS:ID -0.00316751:0.00339802:0.454377:0.00906976:91149:rs146076599
1 770886 rs371458725 G A . PASS AF=0.103379 ES:SE:LP:AF:SS:ID 0.000595454:0.000974865:0.266539:0.103379:91149:rs371458725
1 771410 rs2519006 C T . PASS AF=0.829291 ES:SE:LP:AF:SS:ID -0.000698934:0.00086154:0.379637:0.829291:91149:rs2519006
1 771823 rs2977605 T C . PASS AF=0.869067 ES:SE:LP:AF:SS:ID -0.000191235:0.000878811:0.0821082:0.869067:91149:rs2977605