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-b:17685,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=276098,TotalCases=121634,StudyType=CaseControl>",
"contig": "<ID=1,length=249250621,assembly=GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=GRCh37>",
"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_1787.vcf.gz --id UKB-b:17685 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_1787.txt.gz --cohort_cases 121634 --cohort_controls 276098 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T07:54:53.328932",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17685/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17685/UKB-b-17685_raw.vcf.gz; Date=Thu Oct 17 12:35:19 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-17685/ukb-b-17685.vcf.gz; Date=Sun May 10 13:10:58 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/public/UKB-b-17685/UKB-b-17685_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17685/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17685/UKB-b-17685_data.vcf.gz ...
Read summary statistics for 9165826 SNPs.
Dropped 9499 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1287607 SNPs remain.
After merging with regression SNP LD, 1287607 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0464 (0.0024)
Lambda GC: 1.3936
Mean Chi^2: 1.4565
Intercept: 1.1002 (0.009)
Ratio: 0.2194 (0.0197)
Analysis finished at Thu Oct 17 14:41:56 2019
Total time elapsed: 1.0m:36.87s
{
"af_correlation": 0.9482,
"inflation_factor": 1.3107,
"mean_EFFECT": 6.6585e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 16,
"n_p_sig": 601,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 102142,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NaN",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1287607,
"ldsc_nsnp_merge_regression_ld": 1287607,
"ldsc_observed_scale_h2_beta": 0.0464,
"ldsc_observed_scale_h2_se": 0.0024,
"ldsc_intercept_beta": 1.1002,
"ldsc_intercept_se": 0.009,
"ldsc_lambda_gc": 1.3936,
"ldsc_mean_chisq": 1.4565,
"ldsc_ratio": 0.2195
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | TRUE |
n | TRUE |
is_snpid_non_unique | FALSE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | TRUE |
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 | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 58 | 0 | 9156374 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
logical | N | 9165826 | 0.0000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.638849e+00 | 5.755787e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.880016e+07 | 5.632090e+07 | 828.0000000 | 3.247362e+07 | 6.937471e+07 | 1.145283e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.700000e-06 | 3.844100e-03 | -0.0443014 | -1.539100e-03 | 5.900000e-06 | 1.550600e-03 | 4.236920e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.835100e-03 | 2.158000e-03 | 0.0009883 | 1.183900e-03 | 1.842600e-03 | 3.890900e-03 | 2.410800e-02 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.570338e-01 | 2.996687e-01 | 0.0000000 | 1.900002e-01 | 4.400003e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▅▆ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.570341e-01 | 2.996452e-01 | 0.0000000 | 1.865225e-01 | 4.407602e-01 | 7.166865e-01 | 9.999997e-01 | ▇▆▆▆▅ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.167117e-01 | 2.581612e-01 | 0.0028780 | 1.883000e-02 | 9.660500e-02 | 3.412140e-01 | 9.971220e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 102142 | 0.9888562 | NA | NA | NA | NA | NA | NA | NA | 2.173288e-01 | 2.500081e-01 | 0.0000000 | 1.597440e-02 | 1.146170e-01 | 3.402560e-01 | 1.000000e+00 | ▇▂▁▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | -0.0001113 | 0.0018190 | 0.9500000 | 0.9512189 | 0.623717 | 0.7821490 | NA |
1 | 54676 | rs2462492 | C | T | 0.0010367 | 0.0018008 | 0.5600000 | 0.5648290 | 0.400557 | NA | NA |
1 | 86028 | rs114608975 | T | C | 0.0018351 | 0.0028809 | 0.5199996 | 0.5241307 | 0.103598 | 0.0277556 | NA |
1 | 91536 | rs6702460 | G | T | 0.0012818 | 0.0017751 | 0.4700002 | 0.4702344 | 0.457022 | 0.4207270 | NA |
1 | 234313 | rs8179466 | C | T | 0.0050379 | 0.0035042 | 0.1499999 | 0.1505294 | 0.074478 | NA | NA |
1 | 534192 | rs6680723 | C | T | -0.0009546 | 0.0020279 | 0.6400000 | 0.6378403 | 0.240922 | NA | NA |
1 | 546697 | rs12025928 | A | G | 0.0007572 | 0.0025232 | 0.7600007 | 0.7640955 | 0.913252 | NA | NA |
1 | 693731 | rs12238997 | A | G | 0.0020058 | 0.0016969 | 0.2399999 | 0.2371890 | 0.116373 | 0.1417730 | NA |
1 | 705882 | rs72631875 | G | A | 0.0001419 | 0.0024844 | 0.9500000 | 0.9544646 | 0.067486 | 0.0315495 | NA |
1 | 706368 | rs55727773 | A | G | -0.0011491 | 0.0012577 | 0.3599996 | 0.3609074 | 0.515509 | 0.2751600 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219006 | rs28729663 | G | A | -0.0013540 | 0.0015203 | 0.3700002 | 0.3731372 | 0.137695 | 0.2052720 | NA |
22 | 51219387 | rs9616832 | T | C | -0.0008731 | 0.0019732 | 0.6600001 | 0.6581449 | 0.073597 | 0.0654952 | NA |
22 | 51219704 | rs147475742 | G | A | -0.0024840 | 0.0026441 | 0.3500000 | 0.3475033 | 0.041867 | 0.0473243 | NA |
22 | 51221190 | rs369304721 | G | A | 0.0001830 | 0.0026374 | 0.9400001 | 0.9446737 | 0.049682 | NA | NA |
22 | 51221731 | rs115055839 | T | C | -0.0009393 | 0.0019743 | 0.6300007 | 0.6342522 | 0.073098 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | -0.0016540 | 0.0023238 | 0.4799997 | 0.4766079 | 0.054419 | 0.0880591 | NA |
22 | 51223637 | rs375798137 | G | A | -0.0017398 | 0.0023349 | 0.4600002 | 0.4562039 | 0.054055 | 0.0788738 | NA |
22 | 51229805 | rs9616985 | T | C | -0.0010387 | 0.0019814 | 0.5999997 | 0.6001183 | 0.072933 | 0.0730831 | NA |
22 | 51232488 | rs376461333 | A | G | -0.0059992 | 0.0046662 | 0.2000000 | 0.1985606 | 0.020027 | NA | NA |
22 | 51237063 | rs3896457 | T | C | 0.0000351 | 0.0012108 | 0.9800000 | 0.9769044 | 0.297982 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.623717 ES:SE:LP:AF:ID -0.00011128:0.00181901:0.0222764:0.623717:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400557 ES:SE:LP:AF:ID 0.00103672:0.00180085:0.251812:0.400557:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103598 ES:SE:LP:AF:ID 0.00183512:0.00288092:0.283997:0.103598:rs114608975
1 91536 rs6702460 G T . PASS AF=0.457022 ES:SE:LP:AF:ID 0.00128181:0.00177512:0.327902:0.457022:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074478 ES:SE:LP:AF:ID 0.00503792:0.00350424:0.823909:0.074478:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240922 ES:SE:LP:AF:ID -0.00095456:0.00202787:0.19382:0.240922:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913252 ES:SE:LP:AF:ID 0.000757242:0.00252324:0.119186:0.913252:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116373 ES:SE:LP:AF:ID 0.00200576:0.00169686:0.619789:0.116373:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067486 ES:SE:LP:AF:ID 0.000141865:0.00248445:0.0222764:0.067486:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515509 ES:SE:LP:AF:ID -0.0011491:0.00125772:0.443698:0.515509:rs12029736
1 714596 rs149887893 T C . PASS AF=0.03315 ES:SE:LP:AF:ID -0.00297108:0.00316306:0.455932:0.03315:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036761 ES:SE:LP:AF:ID -0.00284646:0.00287412:0.49485:0.036761:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036875 ES:SE:LP:AF:ID -0.00274435:0.0028634:0.468521:0.036875:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036571 ES:SE:LP:AF:ID -0.00232983:0.00288417:0.376751:0.036571:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016358 ES:SE:LP:AF:ID 0.00625711:0.00445609:0.79588:0.016358:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037121 ES:SE:LP:AF:ID -0.00225488:0.00285178:0.366532:0.037121:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037222 ES:SE:LP:AF:ID -0.00245911:0.00284177:0.408935:0.037222:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101121 ES:SE:LP:AF:ID 0.000161318:0.00207389:0.0268721:0.101121:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958949 ES:SE:LP:AF:ID 0.00234722:0.00274089:0.408935:0.958949:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031431 ES:SE:LP:AF:ID -0.00168575:0.00498824:0.130768:0.031431:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053237 ES:SE:LP:AF:ID -0.00369355:0.003966:0.455932:0.053237:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036737 ES:SE:LP:AF:ID -0.00216587:0.00286025:0.346787:0.036737:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037056 ES:SE:LP:AF:ID -0.0025874:0.00283443:0.443698:0.037056:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843016 ES:SE:LP:AF:ID -0.000586169:0.00146982:0.161151:0.843016:rs4951859
1 730087 rs148120343 T C . PASS AF=0.056073 ES:SE:LP:AF:ID 0.000195969:0.00237849:0.0315171:0.056073:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122344 ES:SE:LP:AF:ID 0.00177949:0.00160977:0.568636:0.122344:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025674 ES:SE:LP:AF:ID 0.00126973:0.00396665:0.124939:0.025674:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121582 ES:SE:LP:AF:ID 0.00191964:0.00161048:0.638272:0.121582:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132589 ES:SE:LP:AF:ID 0.00015151:0.00158606:0.0362122:0.132589:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011131 ES:SE:LP:AF:ID -0.00675887:0.00576993:0.619789:0.011131:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005696 ES:SE:LP:AF:ID 0.00578149:0.00745491:0.356547:0.005696:rs61770167
1 752478 rs146277091 G A . PASS AF=0.03697 ES:SE:LP:AF:ID -0.00245814:0.00280563:0.420216:0.03697:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838777 ES:SE:LP:AF:ID -0.000790194:0.00142377:0.236572:0.838777:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838415 ES:SE:LP:AF:ID -0.000853448:0.00142233:0.259637:0.838415:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869758 ES:SE:LP:AF:ID -0.00181171:0.00152692:0.619789:0.869758:rs3115860
1 753541 rs2073813 G A . PASS AF=0.1299 ES:SE:LP:AF:ID 0.00214186:0.00153015:0.79588:0.1299:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037467 ES:SE:LP:AF:ID -0.00197769:0.0027584:0.327902:0.037467:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037708 ES:SE:LP:AF:ID -0.00185322:0.00274125:0.30103:0.037708:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869104 ES:SE:LP:AF:ID -0.00190777:0.001524:0.677781:0.869104:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869197 ES:SE:LP:AF:ID -0.00189484:0.00152454:0.677781:0.869197:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037666 ES:SE:LP:AF:ID -0.00175219:0.00275291:0.283997:0.037666:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869104 ES:SE:LP:AF:ID -0.00189637:0.00152396:0.677781:0.869104:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005103 ES:SE:LP:AF:ID 0.00440506:0.00784219:0.244125:0.005103:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005066 ES:SE:LP:AF:ID 0.00410667:0.00786431:0.221849:0.005066:rs142682604
1 754503 rs3115859 G A . PASS AF=0.83786 ES:SE:LP:AF:ID -0.00100435:0.00141835:0.318759:0.83786:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037684 ES:SE:LP:AF:ID -0.00177991:0.00275661:0.283997:0.037684:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838487 ES:SE:LP:AF:ID -0.000994837:0.00142236:0.318759:0.838487:rs3131966
1 755240 rs181660517 T G . PASS AF=0.01371 ES:SE:LP:AF:ID 0.000990981:0.00497776:0.0757207:0.01371:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005573 ES:SE:LP:AF:ID -0.0104761:0.0076432:0.769551:0.005573:rs184270342
1 755775 rs3131965 A G . PASS AF=0.839628 ES:SE:LP:AF:ID -0.00117456:0.00144161:0.376751:0.839628:rs3131965