Summary
Summary {data-width=650}
Manhattan plot
manhattan_plot
QQ plot
qq_plot
AF plot
af_plot
P-Z plot
pz_plot
beta_std plot
beta_std_plot
Metadata
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"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_20002_1452.vcf.gz --id UKB-b:20141 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20002_1452.txt.gz --cohort_cases 11819 --cohort_controls 451114 --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": "2019-09-12T22:43:09.203994",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-20141/ukb-b-20141.vcf.gz; Date=Sun May 10 10:52:58 2020"
}
LDSC
*********************************************************************
* 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-20141/UKB-b-20141_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20141/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:06 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20141/UKB-b-20141_data.vcf.gz ...
Read summary statistics for 6192485 SNPs.
Dropped 3007 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, 1226824 SNPs remain.
After merging with regression SNP LD, 1226824 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.009 (0.0019)
Lambda GC: 1.0808
Mean Chi^2: 1.1135
Intercept: 1.0285 (0.008)
Ratio: 0.2514 (0.0709)
Analysis finished at Thu Oct 17 14:43:19 2019
Total time elapsed: 1.0m:13.03sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9271,
"inflation_factor": 1.0966,
"mean_EFFECT": -1.5547e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 17,
"n_p_sig": 1647,
"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": 56535,
"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": 1226824,
"ldsc_nsnp_merge_regression_ld": 1226824,
"ldsc_observed_scale_h2_beta": 0.009,
"ldsc_observed_scale_h2_se": 0.0019,
"ldsc_intercept_beta": 1.0285,
"ldsc_intercept_se": 0.008,
"ldsc_lambda_gc": 1.0808,
"ldsc_mean_chisq": 1.1135,
"ldsc_ratio": 0.2511
}
Flags
| 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 | TRUE |
| 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 |
Definitions
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(\(2 \times N \times MAF\)) 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, \(\widehat{n}\).ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). 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: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), 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.- \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
- \({z}_j = \frac{\beta_j}{{se}_j}\),
- and \(\beta_j\) is the reported effect size.
ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), 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.- \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
- \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
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.- \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
- \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
- and \({se}_j\) 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.- \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
- \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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: 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: \(-log_{10}^{5 \times 10^{-8}}\)
- Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)
Diagnostics
Details
Summary stats
| 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 | 6189497 | 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 | 6192485 | 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 | 8.668859e+00 | 5.762768e+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 | 7.859263e+07 | 5.651744e+07 | 828.0000000 | 3.200342e+07 | 6.902346e+07 | 1.145287e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.600000e-06 | 5.549000e-04 | -0.0107825 | -3.233000e-04 | -2.300000e-06 | 3.189000e-04 | 1.782790e-02 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.975000e-04 | 1.789000e-04 | 0.0003164 | 3.510000e-04 | 4.267000e-04 | 6.006000e-04 | 1.760800e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.864522e-01 | 2.925664e-01 | 0.0000000 | 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 | 4.864532e-01 | 2.925414e-01 | 0.0000000 | 2.302035e-01 | 4.827487e-01 | 7.398700e-01 | 9.999991e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.043824e-01 | 2.551066e-01 | 0.0296140 | 8.855000e-02 | 2.197340e-01 | 4.686430e-01 | 9.703840e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 56535 | 0.9908704 | NA | NA | NA | NA | NA | NA | NA | 3.013314e-01 | 2.479198e-01 | 0.0000000 | 9.784350e-02 | 2.278350e-01 | 4.596650e-01 | 1.000000e+00 | ▇▅▂▂▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | -0.0007319 | 0.0005822 | 0.2099999 | 0.2086948 | 0.623763 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0004714 | 0.0005768 | 0.4100001 | 0.4137278 | 0.400401 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0006446 | 0.0009222 | 0.4799997 | 0.4845678 | 0.103556 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0001135 | 0.0005679 | 0.8400000 | 0.8415919 | 0.456851 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0001936 | 0.0011198 | 0.8600001 | 0.8627439 | 0.074508 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0004738 | 0.0006487 | 0.4700002 | 0.4651691 | 0.240960 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0000772 | 0.0008093 | 0.9199999 | 0.9239839 | 0.913473 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0005120 | 0.0005437 | 0.3500000 | 0.3463445 | 0.116325 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0006219 | 0.0007967 | 0.4400003 | 0.4350378 | 0.067285 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0003322 | 0.0004027 | 0.4100001 | 0.4094485 | 0.515650 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51218377 | rs2519461 | G | C | 0.0001473 | 0.0006294 | 0.8100000 | 0.8149483 | 0.073625 | 0.0826677 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0002062 | 0.0004859 | 0.6700003 | 0.6712317 | 0.137953 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0002617 | 0.0006307 | 0.6800001 | 0.6781586 | 0.073747 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0000606 | 0.0008451 | 0.9400001 | 0.9428091 | 0.041955 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0003634 | 0.0008438 | 0.6700003 | 0.6667098 | 0.049731 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0002032 | 0.0006311 | 0.7499995 | 0.7475076 | 0.073238 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0002704 | 0.0007430 | 0.7199992 | 0.7159073 | 0.054459 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0003092 | 0.0007466 | 0.6800001 | 0.6787204 | 0.054088 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0001404 | 0.0006333 | 0.8200001 | 0.8245290 | 0.073073 | 0.0730831 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0007643 | 0.0003874 | 0.0479999 | 0.0484936 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID -0.00073193:0.000582208:0.677781:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000471435:0.000576784:0.387216:0.400401:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103556 ES:SE:LP:AF:ID 0.00064457:0.000922165:0.318759:0.103556:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -0.000113504:0.000567924:0.0757207:0.456851:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074508 ES:SE:LP:AF:ID -0.000193592:0.00111979:0.0655015:0.074508:rs8179466
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID 0.000473793:0.00064871:0.327902:0.24096:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913473 ES:SE:LP:AF:ID -7.72209e-05:0.000809302:0.0362122:0.913473:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116325 ES:SE:LP:AF:ID -0.000511959:0.000543652:0.455932:0.116325:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067285 ES:SE:LP:AF:ID 0.000621872:0.000796659:0.356547:0.067285:rs72631875
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID 0.000332182:0.000402711:0.387216:0.51565:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033004 ES:SE:LP:AF:ID 0.000120273:0.00101527:0.0409586:0.033004:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036621 ES:SE:LP:AF:ID 9.3107e-05:0.000922185:0.0362122:0.036621:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036737 ES:SE:LP:AF:ID 8.87281e-06:0.000918696:0.00436481:0.036737:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036437 ES:SE:LP:AF:ID 0.000113138:0.000925316:0.0457575:0.036437:rs12184279
1 720381 rs116801199 G T . PASS AF=0.036976 ES:SE:LP:AF:ID 0.000108496:0.000915067:0.0409586:0.036976:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037072 ES:SE:LP:AF:ID 3.43159e-05:0.000911932:0.0132283:0.037072:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101199 ES:SE:LP:AF:ID -9.33819e-05:0.000664448:0.05061:0.101199:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959096 ES:SE:LP:AF:ID 0.000196051:0.000879541:0.0861861:0.959096:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031451 ES:SE:LP:AF:ID -0.00308511:0.00159662:1.27572:0.031451:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053254 ES:SE:LP:AF:ID 0.000656157:0.00127018:0.21467:0.053254:rs865924913
1 726794 rs28454925 C G . PASS AF=0.03659 ES:SE:LP:AF:ID -7.48192e-05:0.000917835:0.0268721:0.03659:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036907 ES:SE:LP:AF:ID 3.87524e-05:0.00090948:0.0132283:0.036907:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843212 ES:SE:LP:AF:ID 0.000256179:0.000471144:0.229148:0.843212:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055911 ES:SE:LP:AF:ID -4.27665e-05:0.000762855:0.0177288:0.055911:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122307 ES:SE:LP:AF:ID -0.000321608:0.000515708:0.275724:0.122307:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121549 ES:SE:LP:AF:ID -0.000321808:0.000515925:0.275724:0.121549:rs141242758
1 736289 rs79010578 T A . PASS AF=0.13233 ES:SE:LP:AF:ID -0.000430264:0.000508495:0.39794:0.13233:rs79010578
1 752478 rs146277091 G A . PASS AF=0.036821 ES:SE:LP:AF:ID -0.000108095:0.000900282:0.0457575:0.036821:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838951 ES:SE:LP:AF:ID 0.000164847:0.000456269:0.142668:0.838951:rs3094315
1 752721 rs3131972 A G . PASS AF=0.83858 ES:SE:LP:AF:ID 0.000187121:0.000455779:0.167491:0.83858:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869781 ES:SE:LP:AF:ID 0.000284243:0.000489068:0.251812:0.869781:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129871 ES:SE:LP:AF:ID -0.000363091:0.000490069:0.337242:0.129871:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037332 ES:SE:LP:AF:ID 5.32475e-06:0.000885017:-0:0.037332:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037576 ES:SE:LP:AF:ID 7.74054e-06:0.000879424:0.00436481:0.037576:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869123 ES:SE:LP:AF:ID 0.000321681:0.000488111:0.29243:0.869123:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869221 ES:SE:LP:AF:ID 0.000328181:0.000488304:0.30103:0.869221:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037534 ES:SE:LP:AF:ID -1.90369e-05:0.000883229:0.00877392:0.037534:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869126 ES:SE:LP:AF:ID 0.000319194:0.000488101:0.29243:0.869126:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838033 ES:SE:LP:AF:ID 0.00019992:0.000454513:0.180456:0.838033:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037547 ES:SE:LP:AF:ID 6.377e-06:0.000884477:0.00436481:0.037547:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838664 ES:SE:LP:AF:ID 0.000214851:0.000455791:0.19382:0.838664:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839777 ES:SE:LP:AF:ID 0.000291546:0.000461955:0.275724:0.839777:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869405 ES:SE:LP:AF:ID 0.000264771:0.000487536:0.229148:0.869405:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868952 ES:SE:LP:AF:ID 0.000282386:0.00048631:0.251812:0.868952:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867905 ES:SE:LP:AF:ID 0.000263029:0.000485378:0.229148:0.867905:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869095 ES:SE:LP:AF:ID 0.000262201:0.000486708:0.229148:0.869095:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869104 ES:SE:LP:AF:ID 0.000263061:0.000486745:0.229148:0.869104:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869112 ES:SE:LP:AF:ID 0.000262148:0.000486756:0.229148:0.869112:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869589 ES:SE:LP:AF:ID 0.000287543:0.000488093:0.251812:0.869589:rs3131954
1 759036 rs114525117 G A . PASS AF=0.037596 ES:SE:LP:AF:ID -0.000102378:0.000879297:0.0409586:0.037596:rs114525117