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:6848,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=69288,TotalCases=80611,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_4598.vcf.gz --id UKB-b:6848 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_4598.txt.gz --cohort_cases 80611 --cohort_controls 69288 --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": "2019-09-12T23:09:07.211649",
"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-6848/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6848/UKB-b-6848_raw.vcf.gz; Date=Thu Oct 17 12:17:55 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-6848/ukb-b-6848.vcf.gz; Date=Sun May 10 02:35:36 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-6848/UKB-b-6848_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6848/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6848/UKB-b-6848_data.vcf.gz ...
Read summary statistics for 8846533 SNPs.
Dropped 8082 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, 1286619 SNPs remain.
After merging with regression SNP LD, 1286619 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0609 (0.0044)
Lambda GC: 1.1657
Mean Chi^2: 1.1832
Intercept: 1.0018 (0.0066)
Ratio: 0.0097 (0.0363)
Analysis finished at Thu Oct 17 14:41:48 2019
Total time elapsed: 1.0m:30.67s
{
"af_correlation": 0.9472,
"inflation_factor": 1.1474,
"mean_EFFECT": 9.2279e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 6,
"n_p_sig": 643,
"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": 88106,
"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": 1286619,
"ldsc_nsnp_merge_regression_ld": 1286619,
"ldsc_observed_scale_h2_beta": 0.0609,
"ldsc_observed_scale_h2_se": 0.0044,
"ldsc_intercept_beta": 1.0018,
"ldsc_intercept_se": 0.0066,
"ldsc_lambda_gc": 1.1657,
"ldsc_mean_chisq": 1.1832,
"ldsc_ratio": 0.0098
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | TRUE |
is_snpid_non_unique | FALSE |
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 | 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 | 8838490 | 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 | 8846533 | 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 | 8.647793e+00 | 5.760085e+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 | 7.877558e+07 | 5.634741e+07 | 828.0000000 | 3.240817e+07 | 6.932496e+07 | 1.145515e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.200000e-06 | 5.796600e-03 | -0.0749254 | -2.406200e-03 | 3.500000e-06 | 2.424400e-03 | 6.671140e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.608500e-03 | 3.271000e-03 | 0.0017406 | 2.064100e-03 | 3.109700e-03 | 6.290900e-03 | 4.011250e-02 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.803569e-01 | 2.934539e-01 | 0.0000000 | 2.200002e-01 | 4.700002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▇▇▆▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.803564e-01 | 2.934291e-01 | 0.0000000 | 2.220894e-01 | 4.734421e-01 | 7.340734e-01 | 9.999999e-01 | ▇▇▇▇▆ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.238437e-01 | 2.589403e-01 | 0.0043420 | 2.236800e-02 | 1.066480e-01 | 3.535320e-01 | 9.956580e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 88106 | 0.9900406 | NA | NA | NA | NA | NA | NA | NA | 2.238710e-01 | 2.508909e-01 | 0.0000000 | 1.976840e-02 | 1.236020e-01 | 3.514380e-01 | 1.000000e+00 | ▇▂▂▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | -0.0053741 | 0.0032077 | 0.0940005 | 0.0938634 | 0.623658 | 0.7821490 | NA |
1 | 54676 | rs2462492 | C | T | 0.0018270 | 0.0031863 | 0.5700002 | 0.5663803 | 0.399273 | NA | NA |
1 | 86028 | rs114608975 | T | C | 0.0114177 | 0.0050749 | 0.0239999 | 0.0244601 | 0.103854 | 0.0277556 | NA |
1 | 91536 | rs6702460 | G | T | -0.0003467 | 0.0031396 | 0.9100000 | 0.9120793 | 0.456191 | 0.4207270 | NA |
1 | 234313 | rs8179466 | C | T | 0.0032416 | 0.0062014 | 0.5999997 | 0.6011624 | 0.074497 | NA | NA |
1 | 534192 | rs6680723 | C | T | 0.0003094 | 0.0035882 | 0.9299999 | 0.9312832 | 0.241144 | NA | NA |
1 | 546697 | rs12025928 | A | G | -0.0033623 | 0.0044509 | 0.4500005 | 0.4499965 | 0.913070 | NA | NA |
1 | 693731 | rs12238997 | A | G | -0.0049293 | 0.0029902 | 0.0990011 | 0.0992516 | 0.116954 | 0.1417730 | NA |
1 | 705882 | rs72631875 | G | A | 0.0012726 | 0.0043724 | 0.7700005 | 0.7710071 | 0.067636 | 0.0315495 | NA |
1 | 706368 | rs55727773 | A | G | -0.0000835 | 0.0022152 | 0.9699999 | 0.9699360 | 0.514890 | 0.2751600 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219006 | rs28729663 | G | A | 0.0012876 | 0.0026842 | 0.6300007 | 0.6314345 | 0.136970 | 0.2052720 | NA |
22 | 51219387 | rs9616832 | T | C | -0.0013534 | 0.0034916 | 0.6999999 | 0.6982952 | 0.072649 | 0.0654952 | NA |
22 | 51219704 | rs147475742 | G | A | -0.0062168 | 0.0046600 | 0.1800002 | 0.1821816 | 0.041641 | 0.0473243 | NA |
22 | 51221190 | rs369304721 | G | A | -0.0026763 | 0.0046735 | 0.5700002 | 0.5668792 | 0.049048 | NA | NA |
22 | 51221731 | rs115055839 | T | C | -0.0014031 | 0.0034942 | 0.6899999 | 0.6880182 | 0.072125 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | 0.0052179 | 0.0040890 | 0.2000000 | 0.2019197 | 0.054415 | 0.0880591 | NA |
22 | 51223637 | rs375798137 | G | A | 0.0048252 | 0.0041100 | 0.2399999 | 0.2403899 | 0.054025 | 0.0788738 | NA |
22 | 51229805 | rs9616985 | T | C | -0.0014274 | 0.0035069 | 0.6800001 | 0.6839984 | 0.071986 | 0.0730831 | NA |
22 | 51232488 | rs376461333 | A | G | 0.0078873 | 0.0082200 | 0.3400001 | 0.3372917 | 0.020135 | NA | NA |
22 | 51237063 | rs3896457 | T | C | -0.0003986 | 0.0021303 | 0.8499999 | 0.8515653 | 0.297770 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.623658 ES:SE:LP:AF:ID -0.00537409:0.00320772:1.02687:0.623658:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399273 ES:SE:LP:AF:ID 0.001827:0.00318631:0.244125:0.399273:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103854 ES:SE:LP:AF:ID 0.0114177:0.00507493:1.61979:0.103854:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456191 ES:SE:LP:AF:ID -0.000346667:0.00313964:0.0409586:0.456191:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074497 ES:SE:LP:AF:ID 0.00324165:0.00620139:0.221849:0.074497:rs8179466
1 534192 rs6680723 C T . PASS AF=0.241144 ES:SE:LP:AF:ID 0.000309414:0.00358822:0.0315171:0.241144:rs6680723
1 546697 rs12025928 A G . PASS AF=0.91307 ES:SE:LP:AF:ID -0.00336228:0.00445087:0.346787:0.91307:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116954 ES:SE:LP:AF:ID -0.00492929:0.00299018:1.00436:0.116954:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067636 ES:SE:LP:AF:ID 0.00127263:0.00437243:0.113509:0.067636:rs72631875
1 706368 rs12029736 A G . PASS AF=0.51489 ES:SE:LP:AF:ID -8.34887e-05:0.00221523:0.0132283:0.51489:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033635 ES:SE:LP:AF:ID 0.00474779:0.00552943:0.408935:0.033635:rs149887893
1 715265 rs12184267 C T . PASS AF=0.037358 ES:SE:LP:AF:ID 0.00349841:0.00502059:0.309804:0.037358:rs12184267
1 715367 rs12184277 A G . PASS AF=0.037484 ES:SE:LP:AF:ID 0.0044162:0.00500119:0.420216:0.037484:rs12184277
1 717485 rs12184279 C A . PASS AF=0.037132 ES:SE:LP:AF:ID 0.00393738:0.00503978:0.366532:0.037132:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016379 ES:SE:LP:AF:ID -0.0117212:0.00786852:0.853872:0.016379:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037724 ES:SE:LP:AF:ID 0.004361:0.0049813:0.420216:0.037724:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037814 ES:SE:LP:AF:ID 0.00411557:0.00496567:0.387216:0.037814:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101496 ES:SE:LP:AF:ID -0.00130288:0.00364864:0.142668:0.101496:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958223 ES:SE:LP:AF:ID -0.00587054:0.00479104:0.657577:0.958223:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031689 ES:SE:LP:AF:ID 0.00366893:0.0087719:0.167491:0.031689:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052682 ES:SE:LP:AF:ID -0.00644215:0.0070723:0.443698:0.052682:rs865924913
1 726794 rs28454925 C G . PASS AF=0.037284 ES:SE:LP:AF:ID 0.00466061:0.00500025:0.455932:0.037284:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037618 ES:SE:LP:AF:ID 0.00445498:0.0049554:0.431798:0.037618:rs116720794
1 729679 rs4951859 C G . PASS AF=0.841862 ES:SE:LP:AF:ID 0.00199509:0.00258782:0.356547:0.841862:rs4951859
1 730087 rs148120343 T C . PASS AF=0.056081 ES:SE:LP:AF:ID 0.00126044:0.00420472:0.119186:0.056081:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122885 ES:SE:LP:AF:ID -0.00387319:0.00283801:0.769551:0.122885:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025798 ES:SE:LP:AF:ID 0.000113936:0.00697252:0.00436481:0.025798:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122104 ES:SE:LP:AF:ID -0.00381609:0.00283938:0.744727:0.122104:rs141242758
1 736289 rs79010578 T A . PASS AF=0.133451 ES:SE:LP:AF:ID -0.00205673:0.00279278:0.337242:0.133451:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011257 ES:SE:LP:AF:ID -0.00970976:0.0101191:0.468521:0.011257:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005876 ES:SE:LP:AF:ID -0.00591912:0.0129071:0.187087:0.005876:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037552 ES:SE:LP:AF:ID 0.00385729:0.00490515:0.366532:0.037552:rs146277091
1 752566 rs3094315 G A . PASS AF=0.837647 ES:SE:LP:AF:ID 0.00166419:0.00250649:0.29243:0.837647:rs3094315
1 752721 rs3131972 A G . PASS AF=0.837256 ES:SE:LP:AF:ID 0.0018511:0.00250368:0.337242:0.837256:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869028 ES:SE:LP:AF:ID 0.00227765:0.00268797:0.39794:0.869028:rs3115860
1 753541 rs2073813 G A . PASS AF=0.130675 ES:SE:LP:AF:ID -0.00253616:0.00269334:0.455932:0.130675:rs2073813
1 754063 rs12184312 G T . PASS AF=0.038039 ES:SE:LP:AF:ID 0.004205:0.00482529:0.420216:0.038039:rs12184312
1 754105 rs12184325 C T . PASS AF=0.038293 ES:SE:LP:AF:ID 0.00473592:0.0047946:0.49485:0.038293:rs12184325
1 754182 rs3131969 A G . PASS AF=0.868348 ES:SE:LP:AF:ID 0.00232753:0.0026826:0.408935:0.868348:rs3131969
1 754192 rs3131968 A G . PASS AF=0.868456 ES:SE:LP:AF:ID 0.00226499:0.00268382:0.39794:0.868456:rs3131968
1 754211 rs12184313 G A . PASS AF=0.038227 ES:SE:LP:AF:ID 0.00469528:0.00481525:0.481486:0.038227:rs12184313
1 754334 rs3131967 T C . PASS AF=0.868345 ES:SE:LP:AF:ID 0.00232837:0.00268243:0.408935:0.868345:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005108 ES:SE:LP:AF:ID -0.0120908:0.0138515:0.420216:0.005108:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005078 ES:SE:LP:AF:ID -0.0122745:0.013882:0.420216:0.005078:rs142682604
1 754503 rs3115859 G A . PASS AF=0.836752 ES:SE:LP:AF:ID 0.00168923:0.00249748:0.30103:0.836752:rs3115859
1 754629 rs10454459 A G . PASS AF=0.038237 ES:SE:LP:AF:ID 0.00472491:0.00482202:0.481486:0.038237:rs10454459
1 754964 rs3131966 C T . PASS AF=0.837386 ES:SE:LP:AF:ID 0.00171377:0.00250445:0.309804:0.837386:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013275 ES:SE:LP:AF:ID -0.00229993:0.00895554:0.09691:0.013275:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005453 ES:SE:LP:AF:ID -0.000280741:0.0136168:0.00877392:0.005453:rs184270342
1 755775 rs3131965 A G . PASS AF=0.838633 ES:SE:LP:AF:ID 0.000877403:0.00253882:0.136677:0.838633:rs3131965