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:6806,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=459573,TotalCases=1183,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_41248_6004.vcf.gz --id UKB-b:6806 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41248_6004.txt.gz --cohort_cases 1183 --cohort_controls 459573 --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": "2019-09-13T13:24:09.659428",
"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-6806/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6806/UKB-b-6806_raw.vcf.gz; Date=Thu Oct 17 12:18:00 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-6806/ukb-b-6806.vcf.gz; Date=Sun May 10 03:17:28 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-6806/UKB-b-6806_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6806/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-6806/UKB-b-6806_data.vcf.gz ...
Read summary statistics for 1853086 SNPs.
Dropped 178 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, 476503 SNPs remain.
After merging with regression SNP LD, 476503 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0002 (0.0015)
Lambda GC: 1.1316
Mean Chi^2: 1.1366
Intercept: 1.1388 (0.0118)
Ratio: 1.0161 (0.0863)
Analysis finished at Thu Oct 17 14:40:41 2019
Total time elapsed: 23.18s{
"af_correlation": 0.6688,
"inflation_factor": 1.1474,
"mean_EFFECT": 6.0952e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 14669,
"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": 476503,
"ldsc_nsnp_merge_regression_ld": 476503,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.1388,
"ldsc_intercept_se": 0.0118,
"ldsc_lambda_gc": 1.1316,
"ldsc_mean_chisq": 1.1366,
"ldsc_ratio": 1.0161
}
| name | value |
|---|---|
| name | value |
| af_correlation | TRUE |
| 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 | 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 betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.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 below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(2×N×MAF) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations for<*>column.
se_n metrics
n_est: Estimated sample size value, ˆn.ratio_se_n: ratio_se_n=√ˆn√n. We expectratio_se_nto 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: mean_diff=∑j^βstdj−βjn_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.- ^βstdj=√z2j/(z2j+n−2)2×MAFj×(1−MAFj)×sign(zj),
- zj=βjsej,
- and βj is the reported effect size.
ratio_diff: ratio_diff=|mean_diffmean_diff2|, absolute ratio between the mean ofdiffand the mean ofdiff2(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.- mean_diff2=∑j^βstdj−β′jn_snps
- β′j=βj^sd2y
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.- ^sd1y=√n×median(sej)C,
- C=median(1√2×MAFj×(1−MAFj)),
- and sej is the reported standard error.
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.- ^sd2y=median(^sdj),
- ^sdj=βj^βstdj,
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: r2=∑j2×β2j×MAFj×(1−MAFj)var1, var1=1.2: r2=∑j2×β2j×MAFj×(1−MAFj)var2, var2=^sd1y2,3: r2=∑j2×β2j×MAFj×(1−MAFj)var3, var3=^sd2y2,4: r2=∑jFjFj+n−2, F=β2jse2j.
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 χ2 statistics.ldsc_ratio: ldsc_intercept_beta−1ldsc_mean_chisq−1, the proportion of the inflation in the mean χ2 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 h2 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: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_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<*>> 0.5
Plots
- Manhattan plot
- Red line: −log5×10−810
- Blue line: −log5×10−510
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between ^βstdj and βj
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.000000 | 4 | 58 | 0 | 1852910 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 1853086 | 0.000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.652252e+00 | 5.765471e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.871697e+07 | 5.664065e+07 | 1.23330e+04 | 3.185330e+07 | 6.932034e+07 | 1.148308e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 6.000000e-07 | 1.165000e-04 | -5.59600e-04 | -7.750000e-05 | 3.000000e-07 | 7.890000e-05 | 5.251000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 1.090000e-04 | 3.700000e-06 | 1.01500e-04 | 1.062000e-04 | 1.081000e-04 | 1.112000e-04 | 2.083000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.803088e-01 | 2.947397e-01 | 3.00000e-07 | 2.200002e-01 | 4.700002e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.803114e-01 | 2.947198e-01 | 3.00000e-07 | 2.197799e-01 | 4.726975e-01 | 7.363467e-01 | 9.999999e-01 | ▇▇▇▆▆ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.734964e-01 | 1.170109e-01 | 2.95858e-01 | 3.706082e-01 | 4.600930e-01 | 5.697980e-01 | 7.041420e-01 | ▇▇▆▅▅ |
| numeric | AF_reference | 14669 | 0.992084 | NA | NA | NA | NA | NA | NA | NA | 4.526888e-01 | 1.558787e-01 | 1.99700e-04 | 3.334660e-01 | 4.444890e-01 | 5.652960e-01 | 1.000000e+00 | ▁▇▇▃▁ |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
| 1 | 49298 | rs200943160 | T | C | -0.0001326 | 0.0001868 | 0.4799997 | 0.4779186 | 0.623762 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0001284 | 0.0001851 | 0.4899999 | 0.4876858 | 0.400374 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0001526 | 0.0001822 | 0.4000000 | 0.4022462 | 0.456837 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000205 | 0.0001292 | 0.8700001 | 0.8739304 | 0.515612 | 0.275160 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0002394 | 0.0001772 | 0.1800002 | 0.1766624 | 0.340372 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | 0.0000264 | 0.0001185 | 0.8200001 | 0.8235826 | 0.697211 | 0.691294 | NA |
| 1 | 840753 | rs4970382 | T | C | -0.0001030 | 0.0001073 | 0.3400001 | 0.3373749 | 0.400158 | 0.468850 | NA |
| 1 | 843405 | rs11516185 | A | G | -0.0002271 | 0.0001333 | 0.0879995 | 0.0883455 | 0.362554 | 0.375399 | NA |
| 1 | 850218 | rs6664536 | T | A | -0.0000027 | 0.0001070 | 0.9800000 | 0.9795991 | 0.590378 | 0.345248 | NA |
| 1 | 850371 | rs6679046 | G | T | -0.0000297 | 0.0001076 | 0.7800007 | 0.7827965 | 0.603772 | 0.508786 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
| 22 | 51164115 | rs5770996 | C | T | -0.0001298 | 0.0001062 | 0.2200002 | 0.2219234 | 0.456847 | 0.514776 | NA |
| 22 | 51164287 | rs6009957 | T | C | 0.0000315 | 0.0001143 | 0.7800007 | 0.7831655 | 0.306506 | 0.415535 | NA |
| 22 | 51165664 | rs8137951 | G | A | 0.0000277 | 0.0001146 | 0.8100000 | 0.8087579 | 0.301510 | 0.406350 | NA |
| 22 | 51174048 | rs9628245 | G | C | 0.0000956 | 0.0001200 | 0.4299995 | 0.4258656 | 0.380095 | 0.433107 | NA |
| 22 | 51181919 | rs9616825 | G | C | -0.0000685 | 0.0001210 | 0.5700002 | 0.5711782 | 0.695449 | 0.619409 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0002630 | 0.0001131 | 0.0200000 | 0.0200854 | 0.381787 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0001242 | 0.0001103 | 0.2599998 | 0.2600683 | 0.451012 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0000015 | 0.0001139 | 0.9900000 | 0.9896608 | 0.386300 | 0.422923 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0002119 | 0.0001214 | 0.0810009 | 0.0809948 | 0.331442 | 0.372404 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0001180 | 0.0001243 | 0.3400001 | 0.3425756 | 0.297971 | 0.205072 | NA |
1 49298 rs10399793 T C . PASS AF=0.623762 ES:SE:LP:AF:ID -0.000132562:0.000186798:0.318759:0.623762:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400374 ES:SE:LP:AF:ID 0.000128441:0.000185075:0.309804:0.400374:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456837 ES:SE:LP:AF:ID -0.000152607:0.000182192:0.39794:0.456837:rs6702460
1 706368 rs12029736 A G . PASS AF=0.515612 ES:SE:LP:AF:ID -2.04988e-05:0.000129193:0.0604807:0.515612:rs12029736
1 814495 rs74461805 C A . PASS AF=0.340372 ES:SE:LP:AF:ID -0.000239379:0.000177173:0.744727:0.340372:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697211 ES:SE:LP:AF:ID 2.6421e-05:0.000118512:0.0861861:0.697211:rs28444699
1 840753 rs4970382 T C . PASS AF=0.400158 ES:SE:LP:AF:ID -0.000102984:0.000107346:0.468521:0.400158:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362554 ES:SE:LP:AF:ID -0.000227143:0.000133285:1.05552:0.362554:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590378 ES:SE:LP:AF:ID -2.73728e-06:0.000107044:0.00877392:0.590378:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603772 ES:SE:LP:AF:ID -2.96752e-05:0.000107645:0.107905:0.603772:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603992 ES:SE:LP:AF:ID -1.94382e-05:0.00010763:0.0655015:0.603992:rs6657440
1 852037 rs4970463 G A . PASS AF=0.58974 ES:SE:LP:AF:ID -2.08133e-06:0.000107218:0.00877392:0.58974:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589718 ES:SE:LP:AF:ID -3.3877e-06:0.00010717:0.0132283:0.589718:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607721 ES:SE:LP:AF:ID -4.17597e-05:0.000107869:0.154902:0.607721:rs13303369
1 853954 rs1806509 C A . PASS AF=0.60788 ES:SE:LP:AF:ID -4.25508e-05:0.000107884:0.161151:0.60788:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610365 ES:SE:LP:AF:ID -3.83005e-05:0.000107987:0.142668:0.610365:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603334 ES:SE:LP:AF:ID -3.2385e-05:0.000107671:0.119186:0.603334:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610384 ES:SE:LP:AF:ID -3.94108e-05:0.00010799:0.142668:0.610384:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389888 ES:SE:LP:AF:ID 3.55031e-05:0.000108011:0.130768:0.389888:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389871 ES:SE:LP:AF:ID 3.55283e-05:0.000108016:0.130768:0.389871:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350338 ES:SE:LP:AF:ID 1.65609e-05:0.00011096:0.0555173:0.350338:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610538 ES:SE:LP:AF:ID 4.81965e-05:0.000108587:0.180456:0.610538:rs2880024
1 868418 rs28546443 C T . PASS AF=0.297956 ES:SE:LP:AF:ID -1.78798e-05:0.000119297:0.0555173:0.297956:rs28546443
1 875770 rs4970379 A G . PASS AF=0.60008 ES:SE:LP:AF:ID 3.99484e-05:0.000109499:0.142668:0.60008:rs4970379
1 881627 rs2272757 G A . PASS AF=0.652381 ES:SE:LP:AF:ID -5.66218e-05:0.000110613:0.21467:0.652381:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652417 ES:SE:LP:AF:ID -6.31722e-05:0.000110596:0.244125:0.652417:rs13303065
1 891945 rs13303106 A G . PASS AF=0.65248 ES:SE:LP:AF:ID -6.48218e-05:0.000110725:0.251812:0.65248:rs13303106
1 903245 rs28690976 A G . PASS AF=0.566954 ES:SE:LP:AF:ID -0.000118932:0.000109974:0.552842:0.566954:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386707 ES:SE:LP:AF:ID 1.77205e-06:0.000109673:0.00436481:0.386707:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571441 ES:SE:LP:AF:ID -8.25659e-06:0.000106224:0.0268721:0.571441:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324429 ES:SE:LP:AF:ID 9.57858e-05:0.000115127:0.387216:0.324429:rs28477686
1 912049 rs7367995 T C . PASS AF=0.585283 ES:SE:LP:AF:ID -0.000101219:0.000107289:0.455932:0.585283:rs7367995
1 913889 rs2340596 G A . PASS AF=0.599256 ES:SE:LP:AF:ID -0.000128555:0.000107465:0.638272:0.599256:rs2340596
1 914333 rs13302979 C G . PASS AF=0.60256 ES:SE:LP:AF:ID -0.000131501:0.000107791:0.657577:0.60256:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600122 ES:SE:LP:AF:ID -0.000124116:0.000107583:0.60206:0.600122:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584344 ES:SE:LP:AF:ID -0.000131678:0.000106983:0.657577:0.584344:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589154 ES:SE:LP:AF:ID -0.00014634:0.000107146:0.769551:0.589154:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584256 ES:SE:LP:AF:ID -0.000135709:0.000106933:0.69897:0.584256:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589378 ES:SE:LP:AF:ID -0.000150994:0.000107064:0.79588:0.589378:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583961 ES:SE:LP:AF:ID -0.000118464:0.000110724:0.552842:0.583961:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567942 ES:SE:LP:AF:ID -3.33604e-05:0.000106841:0.124939:0.567942:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578551 ES:SE:LP:AF:ID -3.20519e-05:0.000107146:0.119186:0.578551:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386003 ES:SE:LP:AF:ID -2.22567e-05:0.000108523:0.0757207:0.386003:rs3128110
1 930567 rs3121574 A G . PASS AF=0.386046 ES:SE:LP:AF:ID -2.26066e-05:0.000108526:0.0809219:0.386046:rs3121574
1 930751 rs3128111 C G . PASS AF=0.384998 ES:SE:LP:AF:ID -1.78933e-05:0.000108592:0.0604807:0.384998:rs3128111
1 931166 rs2710880 A G . PASS AF=0.386688 ES:SE:LP:AF:ID -2.2904e-05:0.000108544:0.0809219:0.386688:rs2710880
1 931362 rs2799060 G A . PASS AF=0.385491 ES:SE:LP:AF:ID -1.64346e-05:0.000108597:0.0555173:0.385491:rs2799060
1 933790 rs9442392 G A . PASS AF=0.578675 ES:SE:LP:AF:ID 6.7038e-06:0.000107111:0.0222764:0.578675:rs9442392
1 936111 rs1936360 C T . PASS AF=0.573616 ES:SE:LP:AF:ID 5.89063e-06:0.000107084:0.0177288:0.573616:rs1936360
1 940005 rs2799056 A G . PASS AF=0.39919 ES:SE:LP:AF:ID 4.50884e-05:0.000108145:0.167491:0.39919:rs2799056