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:960,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=425516,StudyType=Continuous>",
"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_1259.vcf.gz --id UKB-b:960 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_1259.txt.gz --cohort_controls 425516 --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": "2019-09-13T15:31:42.584995",
"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-b-960/ukb-b-960.vcf.gz; Date=Sat May 9 20:30:41 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-960/UKB-b-960_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-960/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:53 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-960/UKB-b-960_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0116 (0.0015)
Lambda GC: 1.116
Mean Chi^2: 1.132
Intercept: 1.034 (0.0075)
Ratio: 0.2576 (0.0566)
Analysis finished at Thu Oct 17 14:44:52 2019
Total time elapsed: 1.0m:58.9s{
"af_correlation": 0.9499,
"inflation_factor": 1.0966,
"mean_EFFECT": 0.0001,
"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": 184849,
"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": 1289166,
"ldsc_nsnp_merge_regression_ld": 1289166,
"ldsc_observed_scale_h2_beta": 0.0116,
"ldsc_observed_scale_h2_se": 0.0015,
"ldsc_intercept_beta": 1.034,
"ldsc_intercept_se": 0.0075,
"ldsc_lambda_gc": 1.116,
"ldsc_mean_chisq": 1.132,
"ldsc_ratio": 0.2576
}
| name | value |
|---|---|
| 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 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 | 1.0000000 | 3 | 58 | 0 | 9837196 | 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 | 9851866 | 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 | 8.622825e+00 | 5.748290e+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 | 7.886027e+07 | 5.628334e+07 | 828.0000000 | 3.259061e+07 | 6.948835e+07 | 1.145912e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.910000e-05 | 3.718200e-03 | -0.0555486 | -1.109300e-03 | 5.700000e-06 | 1.142100e-03 | 7.034770e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.622700e-03 | 2.484800e-03 | 0.0007336 | 8.980000e-04 | 1.506000e-03 | 3.474800e-03 | 3.850100e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.858326e-01 | 2.927397e-01 | 0.0000004 | 2.300001e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.858321e-01 | 2.927142e-01 | 0.0000004 | 2.278572e-01 | 4.816083e-01 | 7.391686e-01 | 9.999995e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.035067e-01 | 2.568666e-01 | 0.0009510 | 1.316700e-02 | 7.790300e-02 | 3.164390e-01 | 9.990430e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 184849 | 0.9812372 | NA | NA | NA | NA | NA | NA | NA | 2.068392e-01 | 2.482924e-01 | 0.0000000 | 1.198080e-02 | 9.984030e-02 | 3.202880e-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 | -0.0006742 | 0.0013496 | 0.6200004 | 0.6173845 | 0.623849 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0013047 | 0.0013372 | 0.3300000 | 0.3292229 | 0.400472 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0019390 | 0.0021366 | 0.3599996 | 0.3641125 | 0.103581 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0006314 | 0.0013163 | 0.6300007 | 0.6314616 | 0.456899 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0052898 | 0.0025946 | 0.0409996 | 0.0414711 | 0.074555 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0004590 | 0.0015055 | 0.7600007 | 0.7604743 | 0.240703 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0026356 | 0.0018739 | 0.1600000 | 0.1595824 | 0.913364 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0004160 | 0.0012606 | 0.7400005 | 0.7413777 | 0.116322 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0041635 | 0.0018456 | 0.0239999 | 0.0240804 | 0.067356 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0004735 | 0.0009336 | 0.6100002 | 0.6120334 | 0.515843 | 0.2751600 | 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 | 51219704 | rs147475742 | G | A | 0.0046150 | 0.0019579 | 0.0179999 | 0.0184155 | 0.042026 | 0.0473243 | NA |
| 22 | 51219766 | rs182321900 | C | T | 0.0157237 | 0.0090815 | 0.0830004 | 0.0833806 | 0.001953 | NA | NA |
| 22 | 51220146 | rs868950473 | C | T | 0.0115249 | 0.0089895 | 0.2000000 | 0.1998291 | 0.002005 | NA | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0055825 | 0.0019541 | 0.0043000 | 0.0042788 | 0.049847 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0040949 | 0.0014618 | 0.0051000 | 0.0050892 | 0.073379 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0002836 | 0.0017208 | 0.8700001 | 0.8691197 | 0.054507 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0004643 | 0.0017292 | 0.7899998 | 0.7883257 | 0.054137 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0040911 | 0.0014672 | 0.0053001 | 0.0052960 | 0.073211 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0006319 | 0.0034499 | 0.8499999 | 0.8546663 | 0.020114 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0004795 | 0.0008981 | 0.5900000 | 0.5933828 | 0.298042 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.623849 ES:SE:LP:AF:ID -0.000674197:0.00134958:0.207608:0.623849:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400472 ES:SE:LP:AF:ID -0.00130467:0.00133719:0.481486:0.400472:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103581 ES:SE:LP:AF:ID 0.00193904:0.00213655:0.443698:0.103581:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456899 ES:SE:LP:AF:ID -0.000631376:0.00131627:0.200659:0.456899:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074555 ES:SE:LP:AF:ID 0.00528978:0.00259457:1.38722:0.074555:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240703 ES:SE:LP:AF:ID -0.000458976:0.00150554:0.119186:0.240703:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913364 ES:SE:LP:AF:ID 0.00263557:0.00187388:0.79588:0.913364:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116322 ES:SE:LP:AF:ID -0.000416045:0.00126063:0.130768:0.116322:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067356 ES:SE:LP:AF:ID -0.0041635:0.00184565:1.61979:0.067356:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515843 ES:SE:LP:AF:ID -0.00047351:0.000933626:0.21467:0.515843:rs12029736
1 714596 rs149887893 T C . PASS AF=0.032947 ES:SE:LP:AF:ID 0.00174445:0.00235567:0.337242:0.032947:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036556 ES:SE:LP:AF:ID 0.00184381:0.00213994:0.408935:0.036556:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036676 ES:SE:LP:AF:ID 0.00176612:0.00213166:0.387216:0.036676:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036374 ES:SE:LP:AF:ID 0.00188822:0.00214713:0.420216:0.036374:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016378 ES:SE:LP:AF:ID -0.0015256:0.00330672:0.19382:0.016378:rs144155419
1 720381 rs116801199 G T . PASS AF=0.03691 ES:SE:LP:AF:ID 0.00180604:0.00212339:0.39794:0.03691:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037005 ES:SE:LP:AF:ID 0.00198517:0.00211626:0.455932:0.037005:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101356 ES:SE:LP:AF:ID 0.0012854:0.0015393:0.39794:0.101356:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959187 ES:SE:LP:AF:ID -0.00189716:0.00204185:0.455932:0.959187:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031503 ES:SE:LP:AF:ID -0.000695065:0.00369289:0.0705811:0.031503:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053269 ES:SE:LP:AF:ID 0.000117736:0.00294219:0.0132283:0.053269:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036519 ES:SE:LP:AF:ID 0.0022148:0.00212993:0.522879:0.036519:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036842 ES:SE:LP:AF:ID 0.00200598:0.00211032:0.468521:0.036842:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843337 ES:SE:LP:AF:ID -0.000420192:0.001093:0.154902:0.843337:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055826 ES:SE:LP:AF:ID -6.72129e-05:0.00176967:0.0132283:0.055826:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122231 ES:SE:LP:AF:ID 0.000157056:0.00119625:0.0457575:0.122231:rs58276399
1 732989 rs369030935 C T . PASS AF=0.0257 ES:SE:LP:AF:ID 0.00266178:0.00294004:0.431798:0.0257:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121479 ES:SE:LP:AF:ID 3.75378e-05:0.00119673:0.0132283:0.121479:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132272 ES:SE:LP:AF:ID 0.000638551:0.00117923:0.229148:0.132272:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011091 ES:SE:LP:AF:ID -0.00180189:0.00429289:0.173925:0.011091:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005724 ES:SE:LP:AF:ID -0.00214468:0.00552129:0.154902:0.005724:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00227 ES:SE:LP:AF:ID -0.00442872:0.00928802:0.200659:0.00227:rs112573343
1 746189 rs139221807 A G . PASS AF=0.001005 ES:SE:LP:AF:ID 0.0305536:0.0155076:1.3098:0.001005:rs139221807
1 752478 rs146277091 G A . PASS AF=0.036747 ES:SE:LP:AF:ID 0.00213828:0.00208926:0.508638:0.036747:rs146277091
1 752566 rs3094315 G A . PASS AF=0.839071 ES:SE:LP:AF:ID -0.000954201:0.00105835:0.431798:0.839071:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838701 ES:SE:LP:AF:ID -0.00096535:0.00105725:0.443698:0.838701:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869863 ES:SE:LP:AF:ID -0.000603416:0.00113436:0.229148:0.869863:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129776 ES:SE:LP:AF:ID 0.000577729:0.00113674:0.21467:0.129776:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037264 ES:SE:LP:AF:ID 0.00141674:0.00205362:0.309804:0.037264:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037508 ES:SE:LP:AF:ID 0.00149362:0.00204055:0.337242:0.037508:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869201 ES:SE:LP:AF:ID -0.000542427:0.00113215:0.200659:0.869201:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869299 ES:SE:LP:AF:ID -0.000570277:0.00113261:0.21467:0.869299:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037465 ES:SE:LP:AF:ID 0.00143357:0.00204952:0.318759:0.037465:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869202 ES:SE:LP:AF:ID -0.000545055:0.00113213:0.200659:0.869202:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005144 ES:SE:LP:AF:ID 0.0112368:0.00579836:1.27572:0.005144:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005112 ES:SE:LP:AF:ID 0.0111681:0.00581292:1.25964:0.005112:rs142682604
1 754503 rs3115859 G A . PASS AF=0.838148 ES:SE:LP:AF:ID -0.000799124:0.00105424:0.346787:0.838148:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037479 ES:SE:LP:AF:ID 0.00156399:0.00205239:0.346787:0.037479:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838776 ES:SE:LP:AF:ID -0.000792843:0.0010572:0.346787:0.838776:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013766 ES:SE:LP:AF:ID -0.00448026:0.00368771:0.657577:0.013766:rs181660517