{
"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-22607_0,TotalVariants=13566906,VariantsNotRead=0,HarmonisedVariants=13566906,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-22607_0/ukb-d-22607_0_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:14:41.412867",
"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-22607_0/ukb-d-22607_0.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22607_0/ukb-d-22607_0_data.vcf.gz; Date=Mon Nov 25 15:54:55 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-22607_0/ukb-d-22607_0.vcf.gz; Date=Sun May 10 09:35:39 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-22607_0/ukb-d-22607_0.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-22607_0/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 16:38:20 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22607_0/ukb-d-22607_0.vcf.gz ...
Read summary statistics for 13566906 SNPs.
Dropped 12682 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0353 (0.0056)
Lambda GC: 1.07
Mean Chi^2: 1.068
Intercept: 1.0054 (0.0065)
Ratio: 0.0789 (0.0959)
Analysis finished at Mon Nov 25 16:41:14 2019
Total time elapsed: 2.0m:53.61s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0451,
"mean_EFFECT": -0,
"n": 90145,
"n_snps": 13566906,
"n_clumped_hits": 1,
"n_p_sig": 4,
"n_mono": 0,
"n_ns": 1251222,
"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": 563168,
"n_est": 90469.2181,
"ratio_se_n": 1.0018,
"mean_diff": -0.0001,
"ratio_diff": 45.0921,
"sd_y_est1": 0.3592,
"sd_y_est2": 0.3598,
"r2_sum1": 0.0001,
"r2_sum2": 0.0004,
"r2_sum3": 0.0004,
"r2_sum4": 0.0003,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.0353,
"ldsc_observed_scale_h2_se": 0.0056,
"ldsc_intercept_beta": 1.0054,
"ldsc_intercept_se": 0.0065,
"ldsc_lambda_gc": 1.07,
"ldsc_mean_chisq": 1.068,
"ldsc_ratio": 0.0794
}
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 | 13554888 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57046 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33331 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051311e+00 | 6.184953e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902483e+07 | 5.591673e+07 | 3.0200e+02 | 3.292761e+07 | 7.013477e+07 | 1.148626e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -3.010000e-05 | 9.875900e-03 | -1.4434e-01 | -2.657700e-03 | 5.800000e-06 | 2.673600e-03 | 1.037140e-01 | ▁▁▇▂▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.079600e-03 | 6.822700e-03 | 1.3955e-03 | 2.022700e-03 | 3.720600e-03 | 1.016560e-02 | 3.431920e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.931546e-01 | 2.905908e-01 | 0.0000e+00 | 2.402050e-01 | 4.904989e-01 | 7.448898e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.931529e-01 | 2.905919e-01 | 0.0000e+00 | 2.402016e-01 | 4.904974e-01 | 7.448878e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.910656e-01 | 2.544726e-01 | 1.0000e-03 | 7.499100e-03 | 6.029750e-02 | 2.957600e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 563168 | 0.9584896 | NA | NA | NA | NA | NA | 1.965220e-01 | 2.471439e-01 | 0.0000e+00 | 5.790700e-03 | 8.446490e-02 | 3.085060e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.014500e+04 | 0.000000e+00 | 9.0145e+04 | 9.014500e+04 | 9.014500e+04 | 9.014500e+04 | 9.014500e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0013850 | 0.0029554 | 0.6393358 | 0.6393339 | 0.1113110 | 0.1894970 | 90145 |
1 | 693731 | rs12238997 | A | G | 0.0012731 | 0.0027987 | 0.6491962 | 0.6491953 | 0.1162900 | 0.1417730 | 90145 |
1 | 707522 | rs371890604 | G | C | 0.0034960 | 0.0031452 | 0.2663428 | 0.2663396 | 0.0977515 | 0.1293930 | 90145 |
1 | 717587 | rs144155419 | G | A | 0.0018692 | 0.0075063 | 0.8033459 | 0.8033462 | 0.0157464 | 0.0045926 | 90145 |
1 | 723329 | rs189787166 | A | T | -0.0153212 | 0.0220229 | 0.4866212 | 0.4866205 | 0.0017529 | 0.0003994 | 90145 |
1 | 730087 | rs148120343 | T | C | 0.0000227 | 0.0038816 | 0.9953270 | 0.9953272 | 0.0568458 | 0.0127796 | 90145 |
1 | 731718 | rs142557973 | T | C | 0.0013027 | 0.0026560 | 0.6237837 | 0.6237824 | 0.1221550 | 0.1543530 | 90145 |
1 | 732032 | rs61770163 | A | C | 0.0022122 | 0.0028323 | 0.4347674 | 0.4347648 | 0.1218610 | 0.1555510 | 90145 |
1 | 734349 | rs141242758 | T | C | 0.0013194 | 0.0026580 | 0.6196237 | 0.6196218 | 0.1213840 | 0.1525560 | 90145 |
1 | 740284 | rs61770167 | C | T | 0.0217206 | 0.0121764 | 0.0744561 | 0.0744517 | 0.0057634 | 0.0023962 | 90145 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0057808 | 0.0031049 | 0.0626297 | 0.0626267 | 0.0553120 | 0.0309934 | 90145 |
23 | 154923374 | rs111332691 | T | A | -0.0019988 | 0.0033792 | 0.5541878 | 0.5541872 | 0.0448888 | 0.0116556 | 90145 |
23 | 154925045 | rs509981 | C | T | 0.0001079 | 0.0016284 | 0.9471660 | 0.9471655 | 0.2445900 | 0.3634440 | 90145 |
23 | 154925895 | rs538470 | C | T | 0.0001962 | 0.0016647 | 0.9061780 | 0.9061775 | 0.2410980 | 0.3634440 | 90145 |
23 | 154927581 | rs644138 | G | A | 0.0013849 | 0.0015317 | 0.3658946 | 0.3658949 | 0.3003080 | 0.4635760 | 90145 |
23 | 154929412 | rs557132 | C | T | 0.0001437 | 0.0016288 | 0.9297051 | 0.9297044 | 0.2444460 | 0.3568210 | 90145 |
23 | 154929637 | rs35185538 | CT | C | 0.0012637 | 0.0017009 | 0.4575199 | 0.4575168 | 0.2288140 | 0.3011920 | 90145 |
23 | 154929952 | rs4012982 | CAA | C | -0.0000790 | 0.0017144 | 0.9632411 | 0.9632412 | 0.2383540 | 0.3165560 | 90145 |
23 | 154930230 | rs781880 | A | G | 0.0001036 | 0.0016283 | 0.9492830 | 0.9492822 | 0.2449110 | 0.3618540 | 90145 |
23 | 154930487 | rs781879 | T | A | -0.0070848 | 0.0055229 | 0.1995589 | 0.1995555 | 0.0196680 | 0.1263580 | 90145 |
1 692794 rs530212009 CA C . PASS AF=0.111311 ES:SE:LP:AF:SS:ID -0.00138499:0.0029554:0.194271:0.111311:90145:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11629 ES:SE:LP:AF:SS:ID 0.00127306:0.00279867:0.187624:0.11629:90145:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0977515 ES:SE:LP:AF:SS:ID 0.003496:0.00314521:0.574559:0.0977515:90145:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157464 ES:SE:LP:AF:SS:ID 0.00186922:0.00750634:0.0950974:0.0157464:90145:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00175286 ES:SE:LP:AF:SS:ID -0.0153212:0.0220229:0.312809:0.00175286:90145:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0568458 ES:SE:LP:AF:SS:ID 2.27325e-05:0.00388158:0.00203421:0.0568458:90145:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122155 ES:SE:LP:AF:SS:ID 0.00130274:0.00265596:0.204966:0.122155:90145:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121861 ES:SE:LP:AF:SS:ID 0.0022122:0.00283229:0.361743:0.121861:90145:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121384 ES:SE:LP:AF:SS:ID 0.00131941:0.00265803:0.207872:0.121384:90145:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00576344 ES:SE:LP:AF:SS:ID 0.0217206:0.0121764:1.1281:0.00576344:90145:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00181816 ES:SE:LP:AF:SS:ID 0.00709626:0.0233512:0.118496:0.00181816:90145:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869117 ES:SE:LP:AF:SS:ID -0.00158289:0.00261493:0.263633:0.869117:90145:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00159834 ES:SE:LP:AF:SS:ID -0.026595:0.0231118:0.602314:0.00159834:90145:rs190826124
1 751343 rs28544273 T A . PASS AF=0.123502 ES:SE:LP:AF:SS:ID 0.00194364:0.0025924:0.343509:0.123502:90145:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143012 ES:SE:LP:AF:SS:ID 0.000285206:0.0025663:0.040239:0.143012:90145:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123637 ES:SE:LP:AF:SS:ID 0.00203623:0.00258864:0.365001:0.123637:90145:rs28527770
1 753405 rs3115860 C A . PASS AF=0.870111 ES:SE:LP:AF:SS:ID -0.00178574:0.00252232:0.319698:0.870111:90145:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874755 ES:SE:LP:AF:SS:ID -0.0021925:0.00256331:0.406308:0.874755:90145:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129319 ES:SE:LP:AF:SS:ID 0.00172012:0.00253021:0.303985:0.129319:90145:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0358644 ES:SE:LP:AF:SS:ID -0.00238896:0.00461737:0.218325:0.0358644:90145:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869758 ES:SE:LP:AF:SS:ID -0.00188242:0.00252022:0.341885:0.869758:90145:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869836 ES:SE:LP:AF:SS:ID -0.0019421:0.00252133:0.35542:0.869836:90145:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869754 ES:SE:LP:AF:SS:ID -0.00188055:0.00252011:0.341475:0.869754:90145:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00532358 ES:SE:LP:AF:SS:ID 0.00434655:0.0125691:0.136984:0.00532358:90145:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00528889 ES:SE:LP:AF:SS:ID 0.00431506:0.0126003:0.135484:0.00528889:90145:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00566273 ES:SE:LP:AF:SS:ID -0.0113438:0.0123992:0.443389:0.00566273:90145:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869737 ES:SE:LP:AF:SS:ID -0.00182515:0.00251493:0.329747:0.869737:90145:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126726 ES:SE:LP:AF:SS:ID 0.00154046:0.00256716:0.260852:0.126726:90145:rs61768170
1 756604 rs3131962 A G . PASS AF=0.869261 ES:SE:LP:AF:SS:ID -0.00165396:0.00250837:0.292722:0.869261:90145:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86865 ES:SE:LP:AF:SS:ID -0.00193701:0.00250676:0.356849:0.86865:90145:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869414 ES:SE:LP:AF:SS:ID -0.0016635:0.00251067:0.294474:0.869414:90145:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869419 ES:SE:LP:AF:SS:ID -0.00166508:0.00251083:0.294793:0.869419:90145:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869421 ES:SE:LP:AF:SS:ID -0.00166484:0.00251085:0.294739:0.869421:90145:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869904 ES:SE:LP:AF:SS:ID -0.00190773:0.0025176:0.348142:0.869904:90145:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0990489 ES:SE:LP:AF:SS:ID 0.00313626:0.00292936:0.546165:0.0990489:90145:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00650816 ES:SE:LP:AF:SS:ID -0.0113667:0.0112884:0.503116:0.00650816:90145:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873894 ES:SE:LP:AF:SS:ID -0.00212005:0.00255493:0.390769:0.873894:90145:rs3115851
1 761732 rs2286139 C T . PASS AF=0.863267 ES:SE:LP:AF:SS:ID -0.0018724:0.00250611:0.342002:0.863267:90145:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868697 ES:SE:LP:AF:SS:ID -0.0016351:0.00253097:0.285455:0.868697:90145:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865579 ES:SE:LP:AF:SS:ID -0.00107676:0.0025314:0.173553:0.865579:90145:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0993705 ES:SE:LP:AF:SS:ID 0.0024708:0.00302976:0.38218:0.0993705:90145:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870867 ES:SE:LP:AF:SS:ID -0.0013055:0.00256033:0.214579:0.870867:90145:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870867 ES:SE:LP:AF:SS:ID -0.00130538:0.00256033:0.214556:0.870867:90145:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870864 ES:SE:LP:AF:SS:ID -0.00130635:0.00256034:0.214744:0.870864:90145:rs3131949
1 762632 rs3131948 T A . PASS AF=0.87123 ES:SE:LP:AF:SS:ID -0.00136503:0.00256156:0.226132:0.87123:90145:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126315 ES:SE:LP:AF:SS:ID 0.00185968:0.00256433:0.329455:0.126315:90145:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105889 ES:SE:LP:AF:SS:ID 0.00124989:0.00278719:0.184531:0.105889:90145:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854607 ES:SE:LP:AF:SS:ID -0.00238261:0.00250523:0.46651:0.854607:90145:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00166577 ES:SE:LP:AF:SS:ID -0.00903625:0.0220903:0.165899:0.00166577:90145:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839373 ES:SE:LP:AF:SS:ID 0.00681308:0.00247497:2.22841:0.839373:90145:rs376645387