{
"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:18389,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=306379,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_3082.vcf.gz --id UKB-b:18389 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_3082.txt.gz --cohort_controls 306379 --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": "2019-09-12T19:38:37.382244",
"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-18389/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18389/UKB-b-18389_raw.vcf.gz; Date=Thu Oct 17 12:36:22 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-18389/ukb-b-18389.vcf.gz; Date=Sun May 10 12:38:02 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-18389/UKB-b-18389_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18389/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18389/UKB-b-18389_data.vcf.gz ...
Read summary statistics for 9762976 SNPs.
Dropped 13904 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, 1288935 SNPs remain.
After merging with regression SNP LD, 1288935 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0011 (0.0015)
Lambda GC: 1.0016
Mean Chi^2: 1.0048
Intercept: 1.0115 (0.006)
Ratio: 2.3958 (1.252)
Analysis finished at Thu Oct 17 14:42:05 2019
Total time elapsed: 1.0m:47.09s
{
"af_correlation": 0.9496,
"inflation_factor": 1,
"mean_EFFECT": 6.6526e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 147,
"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": 174035,
"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": 1288935,
"ldsc_nsnp_merge_regression_ld": 1288935,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0115,
"ldsc_intercept_se": 0.006,
"ldsc_lambda_gc": 1.0016,
"ldsc_mean_chisq": 1.0048,
"ldsc_ratio": 2.3958
}
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 | 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 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 | 1.000000 | 3 | 58 | 0 | 9749137 | 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 | 9762976 | 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 | 8.623161e+00 | 5.748991e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.886049e+07 | 5.629120e+07 | 828.0000000 | 3.258219e+07 | 6.948158e+07 | 1.145965e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 6.700000e-06 | 6.834000e-04 | -0.0135718 | -2.174000e-04 | -7.500000e-06 | 1.970000e-04 | 1.776490e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.941000e-04 | 4.538000e-04 | 0.0001427 | 1.742000e-04 | 2.892000e-04 | 6.601000e-04 | 7.437500e-03 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.983082e-01 | 2.883279e-01 | 0.0000000 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.983077e-01 | 2.883027e-01 | 0.0000000 | 2.490303e-01 | 4.967301e-01 | 7.481675e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 2.049607e-01 | 2.568895e-01 | 0.0011430 | 1.377600e-02 | 8.008000e-02 | 3.192550e-01 | 9.988570e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 174035 | 0.982174 | NA | NA | NA | NA | NA | NA | NA | 2.078656e-01 | 2.484510e-01 | 0.0000000 | 1.218050e-02 | 1.014380e-01 | 3.224840e-01 | 1.000000e+00 | ▇▂▁▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | 0.0000691 | 0.0002623 | 0.7899998 | 0.7923303 | 0.623780 | 0.7821490 | NA |
1 | 54676 | rs2462492 | C | T | 0.0003005 | 0.0002596 | 0.2500000 | 0.2469307 | 0.400989 | NA | NA |
1 | 86028 | rs114608975 | T | C | -0.0001430 | 0.0004157 | 0.7300002 | 0.7307955 | 0.103433 | 0.0277556 | NA |
1 | 91536 | rs6702460 | G | T | 0.0004535 | 0.0002555 | 0.0759994 | 0.0759292 | 0.457148 | 0.4207270 | NA |
1 | 234313 | rs8179466 | C | T | 0.0006361 | 0.0005037 | 0.2099999 | 0.2065937 | 0.074491 | NA | NA |
1 | 534192 | rs6680723 | C | T | 0.0002804 | 0.0002917 | 0.3400001 | 0.3365458 | 0.240867 | NA | NA |
1 | 546697 | rs12025928 | A | G | -0.0000787 | 0.0003650 | 0.8300000 | 0.8292208 | 0.913709 | NA | NA |
1 | 693731 | rs12238997 | A | G | -0.0000686 | 0.0002451 | 0.7800007 | 0.7796520 | 0.115979 | 0.1417730 | NA |
1 | 705882 | rs72631875 | G | A | 0.0000888 | 0.0003597 | 0.8000000 | 0.8049447 | 0.067096 | 0.0315495 | NA |
1 | 706368 | rs55727773 | A | G | -0.0001100 | 0.0001816 | 0.5400003 | 0.5447390 | 0.516008 | 0.2751600 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219704 | rs147475742 | G | A | 0.0004618 | 0.0003808 | 0.2300001 | 0.2253271 | 0.042073 | 0.0473243 | NA |
22 | 51219766 | rs182321900 | C | T | 0.0014496 | 0.0017720 | 0.4100001 | 0.4133360 | 0.001942 | NA | NA |
22 | 51220146 | rs868950473 | C | T | 0.0013239 | 0.0017616 | 0.4500005 | 0.4523330 | 0.001979 | NA | NA |
22 | 51221190 | rs369304721 | G | A | 0.0004073 | 0.0003795 | 0.2800000 | 0.2831657 | 0.049993 | NA | NA |
22 | 51221731 | rs115055839 | T | C | 0.0000834 | 0.0002838 | 0.7700005 | 0.7687550 | 0.073701 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | 0.0000814 | 0.0003349 | 0.8100000 | 0.8079754 | 0.054491 | 0.0880591 | NA |
22 | 51223637 | rs375798137 | G | A | 0.0000925 | 0.0003365 | 0.7800007 | 0.7833979 | 0.054130 | 0.0788738 | NA |
22 | 51229805 | rs9616985 | T | C | 0.0000873 | 0.0002848 | 0.7600007 | 0.7591754 | 0.073526 | 0.0730831 | NA |
22 | 51232488 | rs376461333 | A | G | 0.0009274 | 0.0006727 | 0.1700000 | 0.1680045 | 0.019989 | NA | NA |
22 | 51237063 | rs3896457 | T | C | -0.0001113 | 0.0001747 | 0.5199996 | 0.5242123 | 0.298049 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.62378 ES:SE:LP:AF:ID 6.90675e-05:0.000262329:0.102373:0.62378:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400989 ES:SE:LP:AF:ID 0.000300542:0.000259572:0.60206:0.400989:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103433 ES:SE:LP:AF:ID -0.000143044:0.000415744:0.136677:0.103433:rs114608975
1 91536 rs6702460 G T . PASS AF=0.457148 ES:SE:LP:AF:ID 0.000453473:0.000255505:1.11919:0.457148:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074491 ES:SE:LP:AF:ID 0.000636115:0.000503659:0.677781:0.074491:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240867 ES:SE:LP:AF:ID 0.000280362:0.000291736:0.468521:0.240867:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913709 ES:SE:LP:AF:ID -7.8741e-05:0.000365047:0.0809219:0.913709:rs12025928
1 693731 rs12238997 A G . PASS AF=0.115979 ES:SE:LP:AF:ID -6.85826e-05:0.000245137:0.107905:0.115979:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067096 ES:SE:LP:AF:ID 8.8823e-05:0.000359676:0.09691:0.067096:rs72631875
1 706368 rs12029736 A G . PASS AF=0.516008 ES:SE:LP:AF:ID -0.000110001:0.000181621:0.267606:0.516008:rs12029736
1 714596 rs149887893 T C . PASS AF=0.032723 ES:SE:LP:AF:ID 0.000181981:0.000459965:0.161151:0.032723:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036302 ES:SE:LP:AF:ID 0.000156645:0.000417803:0.148742:0.036302:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036412 ES:SE:LP:AF:ID 4.43358e-05:0.000416245:0.0362122:0.036412:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036134 ES:SE:LP:AF:ID 0.000213295:0.000419148:0.21467:0.036134:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016397 ES:SE:LP:AF:ID -0.000866541:0.000641861:0.744727:0.016397:rs144155419
1 720381 rs116801199 G T . PASS AF=0.036652 ES:SE:LP:AF:ID 0.000201275:0.000414597:0.200659:0.036652:rs116801199
1 721290 rs12565286 G C . PASS AF=0.036746 ES:SE:LP:AF:ID 0.000198895:0.000413152:0.200659:0.036746:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101078 ES:SE:LP:AF:ID 0.000210745:0.000299866:0.318759:0.101078:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959485 ES:SE:LP:AF:ID -0.000362095:0.000398395:0.443698:0.959485:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031332 ES:SE:LP:AF:ID -0.00108151:0.000720364:0.886057:0.031332:rs12126395
1 725060 rs865924913 A T . PASS AF=0.05357 ES:SE:LP:AF:ID -9.2317e-05:0.00056902:0.0604807:0.05357:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036286 ES:SE:LP:AF:ID 0.000160275:0.000415735:0.154902:0.036286:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036598 ES:SE:LP:AF:ID 8.71203e-05:0.000411899:0.0809219:0.036598:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843889 ES:SE:LP:AF:ID -1.10085e-06:0.000212609:-0:0.843889:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055808 ES:SE:LP:AF:ID -2.44646e-05:0.000343706:0.0268721:0.055808:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121977 ES:SE:LP:AF:ID -5.86839e-05:0.000232484:0.09691:0.121977:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025679 ES:SE:LP:AF:ID -0.000286939:0.00057215:0.207608:0.025679:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121233 ES:SE:LP:AF:ID -5.08137e-05:0.000232571:0.0809219:0.121233:rs141242758
1 736289 rs79010578 T A . PASS AF=0.131792 ES:SE:LP:AF:ID 7.31038e-05:0.000229438:0.124939:0.131792:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011089 ES:SE:LP:AF:ID -0.000971411:0.000835196:0.619789:0.011089:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005633 ES:SE:LP:AF:ID 0.000491051:0.00108324:0.187087:0.005633:rs61770167
1 742813 rs112573343 C T . PASS AF=0.002275 ES:SE:LP:AF:ID -0.000697615:0.00179726:0.154902:0.002275:rs112573343
1 752478 rs146277091 G A . PASS AF=0.036492 ES:SE:LP:AF:ID 0.000171409:0.000407807:0.173925:0.036492:rs146277091
1 752566 rs3094315 G A . PASS AF=0.83964 ES:SE:LP:AF:ID 3.56379e-05:0.000205921:0.0655015:0.83964:rs3094315
1 752721 rs3131972 A G . PASS AF=0.839274 ES:SE:LP:AF:ID -2.22324e-05:0.000205702:0.0409586:0.839274:rs3131972
1 753405 rs3115860 C A . PASS AF=0.870226 ES:SE:LP:AF:ID 3.30105e-05:0.000220682:0.0555173:0.870226:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129404 ES:SE:LP:AF:ID 2.4738e-05:0.000221132:0.0409586:0.129404:rs2073813
1 754063 rs12184312 G T . PASS AF=0.03701 ES:SE:LP:AF:ID 0.000222504:0.000400787:0.236572:0.03701:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037247 ES:SE:LP:AF:ID 0.000230126:0.000398277:0.251812:0.037247:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869577 ES:SE:LP:AF:ID -2.63948e-05:0.000220254:0.0457575:0.869577:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869669 ES:SE:LP:AF:ID -2.78469e-05:0.000220335:0.0457575:0.869669:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037219 ES:SE:LP:AF:ID 0.000213199:0.00039999:0.229148:0.037219:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869583 ES:SE:LP:AF:ID -2.67443e-05:0.000220254:0.0457575:0.869583:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00512 ES:SE:LP:AF:ID -0.000572664:0.00112838:0.21467:0.00512:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005083 ES:SE:LP:AF:ID -0.000569209:0.00113157:0.21467:0.005083:rs142682604
1 754503 rs3115859 G A . PASS AF=0.838715 ES:SE:LP:AF:ID -2.90448e-05:0.000205117:0.05061:0.838715:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037234 ES:SE:LP:AF:ID 0.000209883:0.000400558:0.221849:0.037234:rs10454459
1 754964 rs3131966 C T . PASS AF=0.839343 ES:SE:LP:AF:ID -3.30916e-05:0.000205697:0.0604807:0.839343:rs3131966
1 755240 rs181660517 T G . PASS AF=0.014031 ES:SE:LP:AF:ID 0.000598355:0.000709409:0.39794:0.014031:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005588 ES:SE:LP:AF:ID 0.00256362:0.00110322:1.69897:0.005588:rs184270342