manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/798d6fe0-2256-4139-9ff6-1440feae5e32/call-vcf/inputs/562856130/upload.txt.gz --id ieu-b-15 --json /data/cromwell-executions/qc/798d6fe0-2256-4139-9ff6-1440feae5e32/call-vcf/inputs/562856130/ieu-b-15_data.json --ref /data/cromwell-executions/qc/798d6fe0-2256-4139-9ff6-1440feae5e32/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/798d6fe0-2256-4139-9ff6-1440feae5e32/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-15/ieu-b-15.vcf.gz --rm_chr_prefix --cohort_cases 3070 --cohort_controls 29677; 1.2.1",
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}
*********************************************************************
* 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/798d6fe0-2256-4139-9ff6-1440feae5e32/call-ldsc/inputs/562856130/ieu-b-15.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-15/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Fri Jun 26 15:33:13 2020
Reading summary statistics from /data/cromwell-executions/qc/798d6fe0-2256-4139-9ff6-1440feae5e32/call-ldsc/inputs/562856130/ieu-b-15.vcf.gz ...
Read summary statistics for 4987251 SNPs.
Dropped 11902 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 950985 SNPs remain.
After merging with regression SNP LD, 950985 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0028 (0.0171)
Lambda GC: 1.0937
Mean Chi^2: 1.0912
Intercept: 1.0933 (0.0084)
Ratio: 1.0224 (0.0921)
Analysis finished at Fri Jun 26 15:33:51 2020
Total time elapsed: 37.33s{
"af_correlation": 0.9302,
"inflation_factor": 1.0966,
"mean_EFFECT": 0.0001,
"n": "-Inf",
"n_snps": 4987264,
"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": 29961,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NA",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 950985,
"ldsc_nsnp_merge_regression_ld": 950985,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0933,
"ldsc_intercept_se": 0.0084,
"ldsc_lambda_gc": 1.0937,
"ldsc_mean_chisq": 1.0912,
"ldsc_ratio": 1.023
}
| 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 | 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 | 1 | 0.9999998 | 3 | 35 | 0 | 4987260 | 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 | 4987264 | 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 | 8.645456e+00 | 5.871760e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.980134e+07 | 5.500905e+07 | 3.30120e+04 | 3.479413e+07 | 7.130747e+07 | 1.144010e+08 | 2.49219e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.293000e-04 | 4.729200e-03 | -4.84791e-02 | -2.460400e-03 | 1.020000e-04 | 2.643200e-03 | 5.32969e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.110500e-03 | 1.967900e-03 | 2.10030e-03 | 2.751000e-03 | 3.313500e-03 | 4.694600e-03 | 1.33366e-02 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.864542e-01 | 2.917252e-01 | 3.00000e-07 | 2.300001e-01 | 4.799997e-01 | 7.400005e-01 | 1.00000e+00 | ▇▇▇▇▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.864558e-01 | 2.917010e-01 | 3.00000e-07 | 2.302116e-01 | 4.821082e-01 | 7.386856e-01 | 1.00000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.075316e-01 | 2.583824e-01 | 1.00004e-02 | 8.979180e-02 | 2.269570e-01 | 4.777680e-01 | 9.89988e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 29961 | 0.9939925 | NA | NA | NA | NA | NA | NA | NA | 3.087296e-01 | 2.469743e-01 | 1.99700e-04 | 1.044330e-01 | 2.382190e-01 | 4.696490e-01 | 1.00000e+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 | 1029805 | rs6689308 | A | G | -0.0042738 | 0.0035153 | 0.2200002 | 0.2240636 | 0.1626170 | 0.3156950 | NA |
| 1 | 1030565 | rs6687776 | C | T | -0.0035776 | 0.0035100 | 0.3100002 | 0.3080854 | 0.1625690 | 0.3067090 | NA |
| 1 | 1030633 | rs6678318 | G | A | -0.0035874 | 0.0035101 | 0.3100002 | 0.3067717 | 0.1625750 | 0.3065100 | NA |
| 1 | 1031973 | rs9651270 | C | T | -0.0032478 | 0.0035669 | 0.3599996 | 0.3625369 | 0.1593910 | 0.3107030 | NA |
| 1 | 1033596 | rs6604964 | T | C | -0.0032456 | 0.0035691 | 0.3599996 | 0.3631630 | 0.1592550 | 0.3117010 | NA |
| 1 | 1033670 | rs6604966 | T | C | -0.0034105 | 0.0035712 | 0.3400001 | 0.3395647 | 0.1591780 | 0.3158950 | NA |
| 1 | 1033680 | rs6604967 | T | A | -0.0033279 | 0.0035710 | 0.3500000 | 0.3513689 | 0.1591790 | 0.3117010 | NA |
| 1 | 1033994 | rs6698368 | C | T | -0.0033114 | 0.0035702 | 0.3500000 | 0.3536638 | 0.1592430 | 0.3115020 | NA |
| 1 | 1034200 | rs77977351 | T | C | -0.0032189 | 0.0035703 | 0.3700002 | 0.3672846 | 0.1592610 | 0.3115020 | NA |
| 1 | 1036601 | rs72910156 | C | T | -0.0043245 | 0.0085908 | 0.6100002 | 0.6146957 | 0.0233091 | 0.0399361 | 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 |
| 23 | 139314056 | rs5955415 | C | G | -0.0000435 | 0.0036469 | 0.9900000 | 0.9904776 | 0.096204 | 0.125033 | NA |
| 23 | 139314798 | rs62609008 | C | A | 0.0004330 | 0.0036611 | 0.9100000 | 0.9058621 | 0.095354 | 0.106755 | NA |
| 23 | 139315107 | rs62609010 | T | A | 0.0006119 | 0.0036582 | 0.8700001 | 0.8671614 | 0.095470 | 0.107020 | NA |
| 23 | 139316769 | rs73230748 | T | C | 0.0003861 | 0.0036520 | 0.9199999 | 0.9158041 | 0.095831 | 0.121060 | NA |
| 23 | 139317055 | rs62609011 | C | A | 0.0003620 | 0.0036514 | 0.9199999 | 0.9210353 | 0.095866 | 0.116026 | NA |
| 23 | 139317165 | rs28877369 | C | G | 0.0002460 | 0.0036534 | 0.9500000 | 0.9463227 | 0.095778 | 0.116291 | NA |
| 23 | 139317337 | rs55757628 | A | G | 0.0002388 | 0.0036582 | 0.9500000 | 0.9479605 | 0.095484 | 0.107285 | NA |
| 23 | 139319949 | rs140616281 | A | G | 0.0005025 | 0.0036607 | 0.8900000 | 0.8908217 | 0.095444 | 0.116291 | NA |
| 23 | 139320136 | rs76621315 | C | G | 0.0000734 | 0.0036506 | 0.9800000 | 0.9839567 | 0.095958 | 0.114437 | NA |
| 23 | 139325995 | rs62609013 | G | A | 0.0000565 | 0.0036544 | 0.9900000 | 0.9876697 | 0.095753 | 0.101987 | NA |
1 1029805 rs891281851 A G . PASS AF=0.162617 ES:SE:LP:AF:ID -0.00427383:0.00351526:0.657577:0.162617:rs891281851
1 1030565 rs6687776 C T . PASS AF=0.162569 ES:SE:LP:AF:ID -0.00357761:0.00351005:0.508638:0.162569:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.162575 ES:SE:LP:AF:ID -0.00358737:0.00351008:0.508638:0.162575:rs6678318
1 1031973 rs9651270 C T . PASS AF=0.159391 ES:SE:LP:AF:ID -0.00324782:0.00356691:0.443698:0.159391:rs9651270
1 1033596 rs6604964 T C . PASS AF=0.159255 ES:SE:LP:AF:ID -0.00324555:0.00356907:0.443698:0.159255:rs6604964
1 1033670 rs1370950991 T C . PASS AF=0.159178 ES:SE:LP:AF:ID -0.00341054:0.00357115:0.468521:0.159178:rs1370950991
1 1033680 rs1370950991 T A . PASS AF=0.159179 ES:SE:LP:AF:ID -0.00332793:0.00357098:0.455932:0.159179:rs1370950991
1 1033994 rs6698368 C T . PASS AF=0.159243 ES:SE:LP:AF:ID -0.00331141:0.00357023:0.455932:0.159243:rs6698368
1 1034200 rs77977351 T C . PASS AF=0.159261 ES:SE:LP:AF:ID -0.00321888:0.0035703:0.431798:0.159261:rs77977351
1 1036601 rs72910156 C T . PASS AF=0.0233091 ES:SE:LP:AF:ID -0.00432448:0.00859085:0.21467:0.0233091:rs72910156
1 1036860 rs11579922 A C . PASS AF=0.126353 ES:SE:LP:AF:ID -0.00506655:0.00391469:0.69897:0.126353:rs11579922
1 1036959 rs1162868282 T C . PASS AF=0.112757 ES:SE:LP:AF:ID -0.00466166:0.00407455:0.60206:0.112757:rs1162868282
1 1037303 rs11260592 T C . PASS AF=0.139358 ES:SE:LP:AF:ID -0.00543481:0.0037146:0.853872:0.139358:rs11260592
1 1037313 rs11260593 A G . PASS AF=0.139445 ES:SE:LP:AF:ID -0.00540132:0.00371452:0.823909:0.139445:rs11260593
1 1037367 rs11260594 G A . PASS AF=0.139343 ES:SE:LP:AF:ID -0.0055408:0.00371515:0.853872:0.139343:rs11260594
1 1038088 rs66622470 G C . PASS AF=0.139422 ES:SE:LP:AF:ID -0.00549121:0.00371291:0.853872:0.139422:rs66622470
1 1039098 rs11260595 C A . PASS AF=0.023594 ES:SE:LP:AF:ID -0.00634762:0.00852627:0.337242:0.023594:rs11260595
1 1039268 rs9329410 T C . PASS AF=0.139561 ES:SE:LP:AF:ID -0.00567984:0.00370975:0.886057:0.139561:rs9329410
1 1039817 rs1205065516 A G . PASS AF=0.139483 ES:SE:LP:AF:ID -0.00552941:0.00371157:0.853872:0.139483:rs1205065516
1 1040026 rs6671356 T C . PASS AF=0.139875 ES:SE:LP:AF:ID -0.00556195:0.00370427:0.886057:0.139875:rs6671356
1 1040472 rs6664124 C T . PASS AF=0.139784 ES:SE:LP:AF:ID -0.00551536:0.00370624:0.853872:0.139784:rs6664124
1 1040794 rs6687681 G A . PASS AF=0.139762 ES:SE:LP:AF:ID -0.00549642:0.00370656:0.853872:0.139762:rs6687681
1 1040824 rs6656379 T C . PASS AF=0.139914 ES:SE:LP:AF:ID -0.00548387:0.0037048:0.853872:0.139914:rs6656379
1 1040985 rs6697379 C G . PASS AF=0.139739 ES:SE:LP:AF:ID -0.00547155:0.00370666:0.853872:0.139739:rs6697379
1 1041700 rs6604968 A G . PASS AF=0.139888 ES:SE:LP:AF:ID -0.00543827:0.00370556:0.853872:0.139888:rs6604968
1 1041786 rs6604969 T C . PASS AF=0.139899 ES:SE:LP:AF:ID -0.0054378:0.0037052:0.853872:0.139899:rs6604969
1 1042483 rs12733365 C T . PASS AF=0.139759 ES:SE:LP:AF:ID -0.0055029:0.00370618:0.853872:0.139759:rs12733365
1 1042527 rs1486993720 G C . PASS AF=0.112551 ES:SE:LP:AF:ID -0.00472912:0.00407564:0.60206:0.112551:rs1486993720
1 1042673 rs897825316 C T . PASS AF=0.140897 ES:SE:LP:AF:ID -0.00527933:0.00371717:0.79588:0.140897:rs897825316
1 1042927 rs4970354 G T . PASS AF=0.139747 ES:SE:LP:AF:ID -0.00548811:0.00370593:0.853872:0.139747:rs4970354
1 1043053 rs4970355 A G . PASS AF=0.13968 ES:SE:LP:AF:ID -0.00542878:0.00370666:0.853872:0.13968:rs4970355
1 1045473 rs11586034 G A . PASS AF=0.111729 ES:SE:LP:AF:ID -0.00501011:0.00409128:0.657577:0.111729:rs11586034
1 1046073 rs11590188 C A . PASS AF=0.138081 ES:SE:LP:AF:ID -0.00595424:0.00372863:0.958607:0.138081:rs11590188
1 1046164 rs386627439 C T . PASS AF=0.139722 ES:SE:LP:AF:ID -0.00548097:0.00370644:0.853872:0.139722:rs386627439
1 1046717 rs34820586 G C . PASS AF=0.112609 ES:SE:LP:AF:ID -0.00479603:0.00407474:0.619789:0.112609:rs34820586
1 1046861 rs12723165 G A . PASS AF=0.1126 ES:SE:LP:AF:ID -0.00478755:0.0040747:0.619789:0.1126:rs12723165
1 1047374 rs12743678 T A . PASS AF=0.139374 ES:SE:LP:AF:ID -0.00537703:0.00371028:0.823909:0.139374:rs12743678
1 1048501 rs7518814 G A . PASS AF=0.138091 ES:SE:LP:AF:ID -0.00591167:0.00372867:0.958607:0.138091:rs7518814
1 1048955 rs4970405 A G . PASS AF=0.104326 ES:SE:LP:AF:ID -0.00631321:0.00421657:0.886057:0.104326:rs4970405
1 1048989 rs4970406 A G . PASS AF=0.113394 ES:SE:LP:AF:ID -0.00414247:0.00406805:0.508638:0.113394:rs4970406
1 1049083 rs4970407 C A . PASS AF=0.11256 ES:SE:LP:AF:ID -0.00451554:0.00407685:0.568636:0.11256:rs4970407
1 1049950 rs12726255 A G . PASS AF=0.138388 ES:SE:LP:AF:ID -0.00449607:0.00373081:0.638272:0.138388:rs12726255
1 1052946 rs12755848 G T . PASS AF=0.111522 ES:SE:LP:AF:ID -0.00497422:0.00410396:0.638272:0.111522:rs12755848
1 1053452 rs4970409 G A . PASS AF=0.111524 ES:SE:LP:AF:ID -0.00499597:0.00410367:0.657577:0.111524:rs4970409
1 1053670 rs4970410 G A . PASS AF=0.137213 ES:SE:LP:AF:ID -0.00491876:0.00375077:0.721246:0.137213:rs4970410
1 1053724 rs4970411 A G . PASS AF=0.136835 ES:SE:LP:AF:ID -0.00482397:0.00375646:0.69897:0.136835:rs4970411
1 1054552 rs12567697 G A . PASS AF=0.110596 ES:SE:LP:AF:ID -0.00485723:0.00412075:0.619789:0.110596:rs12567697
1 1054893 rs4970412 T C . PASS AF=0.137102 ES:SE:LP:AF:ID -0.0046279:0.00375281:0.657577:0.137102:rs4970412
1 1055653 rs34808604 C G . PASS AF=0.110742 ES:SE:LP:AF:ID -0.00484075:0.00411745:0.619789:0.110742:rs34808604
1 1055797 rs76744376 A G . PASS AF=0.11129 ES:SE:LP:AF:ID -0.0042303:0.00411119:0.522879:0.11129:rs76744376