{
"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=ieu-b-4818,TotalVariants=8029645,VariantsNotRead=0,HarmonisedVariants=8029645,VariantsNotHarmonised=0,SwitchedAlleles=3553418,NormalisedVariants=0,StudyType=Continuous>",
"contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
"Gwas2VCF_command": "--data /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-vcf/inputs/-261044535/upload.txt.gz --id ieu-b-4818 --json /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-vcf/inputs/-261044535/ieu-b-4818_data.json --ref /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4818/ieu-b-4818.vcf.gz --alias alias.txt; 1.3.0",
"file_date": "2022-01-05T05:25:18.170700",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-report/inputs/-261044535/ieu-b-4818.vcf.gz; Date=Wed Jan 5 05:48:40 2022"
}
*********************************************************************
* 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 /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-ldsc/inputs/-261044535/ieu-b-4818.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4818/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Wed Jan 5 05:39:51 2022
Reading summary statistics from /data/cromwell-executions/qc/72d745a0-c44f-468b-9f71-e386413f793a/call-ldsc/inputs/-261044535/ieu-b-4818.vcf.gz ...
Read summary statistics for 8029585 SNPs.
Dropped 39100 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1202658 SNPs remain.
After merging with regression SNP LD, 1202658 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1131 (0.0083)
Lambda GC: 1.327
Mean Chi^2: 1.3718
Intercept: 1.1559 (0.009)
Ratio: 0.4192 (0.0241)
Analysis finished at Wed Jan 5 05:41:38 2022
Total time elapsed: 1.0m:46.65s
{
"af_correlation": "NA",
"inflation_factor": 1.3027,
"mean_EFFECT": -0.0027,
"n": 97656,
"n_snps": 8029645,
"n_clumped_hits": 21,
"n_p_sig": 428,
"n_mono": 0,
"n_ns": 285806,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 8029645,
"n_miss_AF_reference": 162500,
"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": 1202658,
"ldsc_nsnp_merge_regression_ld": 1202658,
"ldsc_observed_scale_h2_beta": 0.1131,
"ldsc_observed_scale_h2_se": 0.0083,
"ldsc_intercept_beta": 1.1559,
"ldsc_intercept_se": 0.009,
"ldsc_lambda_gc": 1.327,
"ldsc_mean_chisq": 1.3718,
"ldsc_ratio": 0.4193
}
name | value |
---|---|
af_correlation | NA |
inflation_factor | TRUE |
n | FALSE |
is_snpid_non_unique | TRUE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | TRUE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | FALSE |
ldsc_intercept_beta | FALSE |
n_clumped_hits | FALSE |
r2_sum1 | FALSE |
r2_sum2 | FALSE |
r2_sum3 | FALSE |
r2_sum4 | FALSE |
General metrics
af_correlation
: Correlation coefficient between AF
and AF_reference
.inflation_factor
(lambda
): Genomic inflation factor.mean_EFFECT
: Mean of EFFECT
size.n
: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits
: Number of clumped hits.n_snps
: Number of SNPsn_p_sig
: Number of SNPs with pvalue below 5e-8
.n_mono
: Number of monomorphic (MAF == 1
or MAF == 0
) SNPs.n_ns
: Number of SNPs with nonsense values:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 0
or > 1
.n_mac
: Number of cases where MAC
(\(2 \times N \times MAF\)) is less than 6
.is_snpid_unique
: true
if the combination of ID
REF
ALT
is unique and therefore no duplication in snpid.n_miss_<*>
: Number of NA
observations for <*>
column.se_n metrics
n_est
: Estimated sample size value, \(\widehat{n}\).ratio_se_n
: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n
to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.mean_diff
: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
ratio_diff
: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff
and the mean of diff2
(expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
sd_y_est1
: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
sd_y_est2
: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>
: r2
statistics under various assumptions
1
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).2
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),3
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),4
: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).LDSC metrics
Metrics from LD regression
ldsc_nsnp_merge_refpanel_ld
: Number of remaining SNPs after merging with reference panel LD.ldsc_nsnp_merge_regression_ld
: Number of remaining SNPs after merging with regression SNP LD.ldsc_observed_scale_h2_{beta,se}
Coefficient value and SE for total observed scale h2.ldsc_intercept_{beta,se}
: Coefficient value and SE for intercept. Intercept is expected to be 1.ldsc_lambda_gc
: Lambda GC statistics.ldsc_mean_chisq
: Mean \(\chi^2\) statistics.ldsc_ratio
: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).Flags
When a metric needs attention, the flag should return TRUE.
af_correlation
: abs(af_correlation)
< 0.7.inflation_factor
: inflation_factor
> 1.2.n
: n
(max reported sample size) < 10000.is_snpid_non_unique
: NOT is_snpid_unique
.mean_EFFECT_nonfinite
: mean(EFFECT)
is NA
, NaN
, or Inf
.mean_EFFECT_05
: abs(mean(EFFECT))
> 0.5.mean_EFFECT_01
: abs(mean(EFFECT))
> 0.1.mean_chisq
: ldsc_mean_chisq
> 1.3 or ldsc_mean_chisq
< 0.7.n_p_sig
: n_p_sig
> 1000.miss_<*>
: n_miss_<*>
/ n_snps
> 0.01.ldsc_ratio
: ldsc_ratio
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 16 | 0.9999980 | 3 | 58 | 0 | 8029515 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 43 | 0 | 16662 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 44 | 0 | 6027 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
logical | AF | 8029645 | 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 | 8.642174e+00 | 5.752157e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.886231e+07 | 5.635232e+07 | 3.0200e+02 | 3.246903e+07 | 6.943490e+07 | 1.146235e+08 | 2.492223e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -2.729400e-03 | 2.021198e-01 | -2.2171e+00 | -1.012000e-01 | -1.500000e-03 | 9.750000e-02 | 2.232500e+00 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.566817e-01 | 8.969840e-02 | 7.4600e-02 | 8.840000e-02 | 1.174000e-01 | 2.011000e-01 | 5.434000e-01 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.576632e-01 | 2.994424e-01 | 0.0000e+00 | 1.876001e-01 | 4.413997e-01 | 7.169997e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.576634e-01 | 2.994426e-01 | 0.0000e+00 | 1.876387e-01 | 4.414103e-01 | 7.170173e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | AF_reference | 162500 | 0.9797625 | NA | NA | NA | NA | NA | NA | NA | 2.622305e-01 | 2.522768e-01 | 1.9970e-04 | 5.471250e-02 | 1.757190e-01 | 4.097440e-01 | 1.000000e+00 | ▇▃▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.112486e+04 | 9.872957e+03 | 5.8712e+04 | 9.170500e+04 | 9.463700e+04 | 9.725800e+04 | 9.765600e+04 | ▁▁▁▁▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 768448 | rs12562034 | G | A | 0.0542 | 0.1680 | 0.7471005 | 0.7469838 | NA | 0.1918930 | 60554 |
1 | 777232 | rs112618790 | C | T | 0.0256 | 0.1788 | 0.8863001 | 0.8861506 | NA | 0.0668930 | 60554 |
1 | 791853 | rs6684487 | G | A | -0.0627 | 0.1776 | 0.7240007 | 0.7240580 | NA | 0.0762780 | 60554 |
1 | 794332 | rs12127425 | G | A | -0.0618 | 0.1962 | 0.7528995 | 0.7527733 | NA | 0.1162140 | 58712 |
1 | 795222 | rs12131377 | C | G | -0.0455 | 0.1930 | 0.8137000 | 0.8136257 | NA | 0.0696885 | 59452 |
1 | 796100 | rs12132398 | C | T | -0.0466 | 0.1932 | 0.8092000 | 0.8093995 | NA | 0.0856629 | 59452 |
1 | 797281 | rs76631953 | G | C | -0.0489 | 0.1940 | 0.8008001 | 0.8009933 | NA | 0.0656949 | 59452 |
1 | 797325 | rs111739932 | T | C | -0.0436 | 0.1921 | 0.8206000 | 0.8204509 | NA | 0.0680911 | 59452 |
1 | 797440 | rs58013264 | T | C | 0.0099 | 0.1371 | 0.9425001 | 0.9424347 | NA | 0.1894970 | 81447 |
1 | 798026 | rs4951864 | C | T | 0.0324 | 0.1886 | 0.8634999 | 0.8636009 | NA | 0.8941690 | 60095 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51195550 | rs148968329 | C | A | 0.0573 | 0.2085 | 0.7835000 | 0.7834544 | NA | 0.0391374 | 59452 |
22 | 51196164 | rs8136603 | A | T | -0.1164 | 0.2205 | 0.5975001 | 0.5975749 | NA | 0.1427720 | 58712 |
22 | 51196296 | rs9616961 | G | C | 0.0467 | 0.2087 | 0.8229999 | 0.8229393 | NA | 0.0395367 | 59452 |
22 | 51197576 | rs147713773 | G | C | 0.0460 | 0.2095 | 0.8262000 | 0.8262057 | NA | 0.0471246 | 59452 |
22 | 51197602 | rs187225588 | T | A | -0.0825 | 0.2236 | 0.7123001 | 0.7121557 | NA | 0.0175719 | 58712 |
22 | 51198569 | rs142671391 | G | C | -0.2514 | 0.2569 | 0.3278000 | 0.3277822 | NA | 0.1110220 | 58712 |
22 | 51198906 | rs6010079 | G | A | 0.0352 | 0.2098 | 0.8668000 | 0.8667573 | NA | 0.0421326 | 59452 |
22 | 51202748 | rs9616963 | A | G | 0.0102 | 0.2101 | 0.9612999 | 0.9612793 | NA | 0.0391374 | 59452 |
22 | 51208568 | rs148425445 | G | T | -0.2203 | 0.2233 | 0.3239000 | 0.3238559 | NA | 0.1160140 | 58712 |
22 | 51222100 | rs114553188 | G | T | -0.3142 | 0.2624 | 0.2313002 | 0.2311474 | NA | 0.0880591 | 58712 |
1 768448 rs12562034 G A . PASS . ES:SE:LP:SS:ID 0.0542:0.168:0.126621:60554:rs12562034
1 777232 rs112618790 C T . PASS . ES:SE:LP:SS:ID 0.0256:0.1788:0.0524192:60554:rs112618790
1 791853 rs6684487 G A . PASS . ES:SE:LP:SS:ID -0.0627:0.1776:0.140261:60554:rs6684487
1 794332 rs12127425 G A . PASS . ES:SE:LP:SS:ID -0.0618:0.1962:0.123263:58712:rs12127425
1 795222 rs12131377 C G . PASS . ES:SE:LP:SS:ID -0.0455:0.193:0.0895357:59452:rs12131377
1 796100 rs12132398 C T . PASS . ES:SE:LP:SS:ID -0.0466:0.1932:0.0919441:59452:rs12132398
1 797281 rs1347695410 G C . PASS . ES:SE:LP:SS:ID -0.0489:0.194:0.0964759:59452:rs1347695410
1 797325 rs1338750774 T C . PASS . ES:SE:LP:SS:ID -0.0436:0.1921:0.0858685:59452:rs1338750774
1 797440 rs58013264 T C . PASS . ES:SE:LP:SS:ID 0.0099:0.1371:0.0257186:81447:rs58013264
1 798026 rs4951864 C T . PASS . ES:SE:LP:SS:ID 0.0324:0.1886:0.0637377:60095:rs4951864
1 798400 rs10900604 A G . PASS . ES:SE:LP:SS:ID 0.0618:0.1124:0.234779:83094:rs10900604
1 798801 rs12132517 G A . PASS . ES:SE:LP:SS:ID -0.0459:0.1916:0.0910863:59452:rs12132517
1 798959 rs11240777 G A . PASS . ES:SE:LP:SS:ID 0.0768:0.1123:0.305922:83094:rs11240777
1 799499 rs147634896 T C . PASS . ES:SE:LP:SS:ID 0.0001:0.1925:0.000130308:59452:rs147634896
1 800383 rs4951931 C T . PASS . ES:SE:LP:SS:ID 0.0355:0.1883:0.0703257:59911:rs4951931
1 801467 rs61768212 G C . PASS . ES:SE:LP:SS:ID -0.0036:0.1378:0.00908425:80804:rs61768212
1 801661 rs12132974 C T . PASS . ES:SE:LP:SS:ID -0.0563:0.1978:0.110138:58712:rs12132974
1 801680 rs12134490 A C . PASS . ES:SE:LP:SS:ID -0.0594:0.1979:0.116907:58712:rs12134490
1 801858 rs17276806 C T . PASS . ES:SE:LP:SS:ID -0.0504:0.198:0.0973445:58712:rs17276806
1 801943 rs7516866 C T . PASS . ES:SE:LP:SS:ID 0.081:0.1904:0.173666:59911:rs7516866
1 802856 rs139867617 C T . PASS . ES:SE:LP:SS:ID -0.0288:0.1987:0.0532531:58712:rs139867617
1 804759 rs7526310 C T . PASS . ES:SE:LP:SS:ID -0.0232:0.1379:0.0622816:80804:rs7526310
1 808223 rs1557576983 G C . PASS . ES:SE:LP:SS:ID 0.0375:0.1226:0.119301:65615:rs1557576983
1 808631 rs11240779 G A . PASS . ES:SE:LP:SS:ID -0.0035:0.1085:0.0113965:82187:rs11240779
1 808928 rs1247187939 C T . PASS . ES:SE:LP:SS:ID 0.0002:0.1085:0.00056495:82187:rs1247187939
1 833223 rs13303211 C T . PASS . ES:SE:LP:SS:ID -0.0886:0.1223:0.32892:60095:rs13303211
1 833302 rs28752186 C T . PASS . ES:SE:LP:SS:ID -0.0907:0.1223:0.33885:60095:rs28752186
1 833641 rs28594623 T C . PASS . ES:SE:LP:SS:ID -0.0807:0.122:0.293794:60095:rs28594623
1 833824 rs28484835 T C . PASS . ES:SE:LP:SS:ID -0.0913:0.1222:0.342084:60095:rs28484835
1 833927 rs28593608 T C . PASS . ES:SE:LP:SS:ID -0.1289:0.1245:0.522156:60095:rs28593608
1 834056 rs28482280 A C . PASS . ES:SE:LP:SS:ID 0.3125:0.3545:0.422508:58712:rs28482280
1 834198 rs28385272 T C . PASS . ES:SE:LP:SS:ID -0.1235:0.1245:0.49363:60095:rs28385272
1 834832 rs796468152 G C . PASS . ES:SE:LP:SS:ID -0.0907:0.122:0.339609:60095:rs796468152
1 834928 rs4422949 A G . PASS . ES:SE:LP:SS:ID -0.1217:0.1244:0.484391:60095:rs4422949
1 834956 rs7518581 G A . PASS . ES:SE:LP:SS:ID 0.3387:0.3557:0.467118:58712:rs7518581
1 834999 rs28570054 G A . PASS . ES:SE:LP:SS:ID -0.1285:0.1243:0.521289:60095:rs28570054
1 835092 rs72631887 T G . PASS . ES:SE:LP:SS:ID -0.1492:0.3499:0.17399:58712:rs72631887
1 835499 rs4422948 A G . PASS . ES:SE:LP:SS:ID -0.0281:0.1215:0.0877779:60095:rs4422948
1 836529 rs1192410597 C G . PASS . ES:SE:LP:SS:ID -0.1283:0.1232:0.526513:60554:rs1192410597
1 836684 rs74460547 G A . PASS . ES:SE:LP:SS:ID -0.5731:0.3916:0.843754:58712:rs74460547
1 836896 rs28705752 T C . PASS . ES:SE:LP:SS:ID -0.0885:0.1143:0.357832:60095:rs28705752
1 836924 rs72890788 G A . PASS . ES:SE:LP:SS:ID -0.1295:0.1232:0.532984:60554:rs72890788
1 837192 rs57494724 A G . PASS . ES:SE:LP:SS:ID 0.1034:0.2291:0.185819:58712:rs57494724
1 837657 rs149737509 G C . PASS . ES:SE:LP:SS:ID -0.0664:0.3771:0.0654006:58712:rs149737509
1 838387 rs4970384 T C . PASS . ES:SE:LP:SS:ID -0.1375:0.1227:0.58054:60554:rs4970384
1 838555 rs4970383 C A . PASS . ES:SE:LP:SS:ID -0.1085:0.1151:0.461175:60095:rs4970383
1 838665 rs28678693 T C . PASS . ES:SE:LP:SS:ID 0.3225:0.3576:0.435216:58712:rs28678693
1 838732 rs952157075 G A . PASS . ES:SE:LP:SS:ID 0.3256:0.3585:0.439257:58712:rs952157075
1 838890 rs28437697 A G . PASS . ES:SE:LP:SS:ID 0.3261:0.3577:0.441411:58712:rs28437697
1 838916 rs28539852 A T . PASS . ES:SE:LP:SS:ID 0.3434:0.3582:0.471469:58712:rs28539852