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_1498.vcf.gz --id UKB-b:5237 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_1498.txt.gz --cohort_controls 428860 --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",
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}
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-5237/UKB-b-5237_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5237/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:45:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5237/UKB-b-5237_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: 0.0478 (0.0029)
Lambda GC: 1.3517
Mean Chi^2: 1.4614
Intercept: 1.054 (0.0083)
Ratio: 0.117 (0.0179)
Analysis finished at Thu Oct 17 14:46:40 2019
Total time elapsed: 1.0m:35.28sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9499,
"inflation_factor": 1.2544,
"mean_EFFECT": -0.0001,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 40,
"n_p_sig": 3265,
"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": 0.0478,
"ldsc_observed_scale_h2_se": 0.0029,
"ldsc_intercept_beta": 1.054,
"ldsc_intercept_se": 0.0083,
"ldsc_lambda_gc": 1.3517,
"ldsc_mean_chisq": 1.4614,
"ldsc_ratio": 0.117
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| n | TRUE |
| is_snpid_non_unique | FALSE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | TRUE |
| 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 | 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 | -5.990000e-05 | 7.954500e-03 | -0.1894140 | -2.621700e-03 | -3.210000e-05 | 2.565900e-03 | 1.116580e-01 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.563000e-03 | 5.265600e-03 | 0.0015566 | 1.905600e-03 | 3.195300e-03 | 7.373300e-03 | 8.183400e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.647283e-01 | 2.982690e-01 | 0.0000000 | 2.000000e-01 | 4.500005e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.647308e-01 | 2.982448e-01 | 0.0000000 | 1.979665e-01 | 4.522216e-01 | 7.233075e-01 | 9.999999e-01 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.035078e-01 | 2.568626e-01 | 0.0009700 | 1.316800e-02 | 7.791500e-02 | 3.164540e-01 | 9.990230e-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 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | -0.0018541 | 0.0028630 | 0.5199996 | 0.5172382 | 0.623631 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0056297 | 0.0028374 | 0.0470002 | 0.0472488 | 0.400513 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0029739 | 0.0045351 | 0.5099998 | 0.5119782 | 0.103535 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0021120 | 0.0027941 | 0.4500005 | 0.4497113 | 0.456852 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0029510 | 0.0055117 | 0.5900000 | 0.5923643 | 0.074498 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0014128 | 0.0031918 | 0.6600001 | 0.6580290 | 0.240829 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0027905 | 0.0039786 | 0.4799997 | 0.4830624 | 0.913410 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0018155 | 0.0026762 | 0.5000000 | 0.4975151 | 0.116184 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0019152 | 0.0039203 | 0.6300007 | 0.6251652 | 0.067197 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0006354 | 0.0019806 | 0.7499995 | 0.7483374 | 0.515729 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219704 | rs147475742 | G | A | -0.0102834 | 0.0041607 | 0.0129999 | 0.0134525 | 0.041908 | 0.0473243 | NA |
| 22 | 51219766 | rs182321900 | C | T | -0.0096809 | 0.0193395 | 0.6200004 | 0.6166681 | 0.001942 | NA | NA |
| 22 | 51220146 | rs868950473 | C | T | -0.0118049 | 0.0191791 | 0.5400003 | 0.5382189 | 0.001987 | NA | NA |
| 22 | 51221190 | rs369304721 | G | A | -0.0101237 | 0.0041568 | 0.0150000 | 0.0148728 | 0.049629 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0078590 | 0.0031080 | 0.0109999 | 0.0114510 | 0.073083 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0017790 | 0.0036603 | 0.6300007 | 0.6269519 | 0.054335 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0019610 | 0.0036777 | 0.5900000 | 0.5938892 | 0.053969 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0074592 | 0.0031190 | 0.0170000 | 0.0167797 | 0.072931 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0041716 | 0.0073502 | 0.5700002 | 0.5703360 | 0.019998 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0001326 | 0.0019060 | 0.9400001 | 0.9445566 | 0.298090 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623631 ES:SE:LP:AF:ID -0.00185409:0.00286298:0.283997:0.623631:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400513 ES:SE:LP:AF:ID 0.00562968:0.00283745:1.3279:0.400513:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103535 ES:SE:LP:AF:ID 0.00297392:0.00453507:0.29243:0.103535:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456852 ES:SE:LP:AF:ID 0.00211202:0.00279406:0.346787:0.456852:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074498 ES:SE:LP:AF:ID 0.00295102:0.00551167:0.229148:0.074498:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240829 ES:SE:LP:AF:ID 0.00141281:0.00319181:0.180456:0.240829:rs6680723
1 546697 rs12025928 A G . PASS AF=0.91341 ES:SE:LP:AF:ID 0.00279054:0.00397861:0.318759:0.91341:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116184 ES:SE:LP:AF:ID 0.00181554:0.00267619:0.30103:0.116184:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067197 ES:SE:LP:AF:ID -0.00191525:0.00392033:0.200659:0.067197:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515729 ES:SE:LP:AF:ID -0.000635444:0.00198061:0.124939:0.515729:rs12029736
1 714596 rs149887893 T C . PASS AF=0.032884 ES:SE:LP:AF:ID -0.0094794:0.00500347:1.23657:0.032884:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036485 ES:SE:LP:AF:ID -0.00916126:0.00454498:1.35655:0.036485:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036604 ES:SE:LP:AF:ID -0.00962584:0.00452757:1.48149:0.036604:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036305 ES:SE:LP:AF:ID -0.00983745:0.00456003:1.50864:0.036305:rs12184279
1 717587 rs144155419 G A . PASS AF=0.01638 ES:SE:LP:AF:ID 0.00294176:0.0070118:0.173925:0.01638:rs144155419
1 720381 rs116801199 G T . PASS AF=0.03685 ES:SE:LP:AF:ID -0.00885778:0.00450925:1.3098:0.03685:rs116801199
1 721290 rs12565286 G C . PASS AF=0.036944 ES:SE:LP:AF:ID -0.00892039:0.00449399:1.3279:0.036944:rs12565286
1 722670 rs116030099 T C . PASS AF=0.10118 ES:SE:LP:AF:ID -0.000564941:0.00327094:0.0655015:0.10118:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959242 ES:SE:LP:AF:ID 0.00844573:0.00433401:1.29243:0.959242:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031458 ES:SE:LP:AF:ID 0.00328017:0.00785468:0.167491:0.031458:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053253 ES:SE:LP:AF:ID 0.00160246:0.00624756:0.09691:0.053253:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036461 ES:SE:LP:AF:ID -0.00994594:0.00452264:1.55284:0.036461:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036771 ES:SE:LP:AF:ID -0.00928722:0.00448155:1.42022:0.036771:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843483 ES:SE:LP:AF:ID 0.000928072:0.00231961:0.161151:0.843483:rs4951859
1 730087 rs148120343 T C . PASS AF=0.05584 ES:SE:LP:AF:ID 0.00206579:0.00375517:0.236572:0.05584:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122174 ES:SE:LP:AF:ID 0.00165956:0.00253868:0.29243:0.122174:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025719 ES:SE:LP:AF:ID 0.00271514:0.00623986:0.180456:0.025719:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121415 ES:SE:LP:AF:ID 0.00168681:0.00253978:0.29243:0.121415:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132141 ES:SE:LP:AF:ID -0.00200746:0.00250324:0.376751:0.132141:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011179 ES:SE:LP:AF:ID 0.00568074:0.00907139:0.275724:0.011179:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005701 ES:SE:LP:AF:ID -0.0137792:0.0117429:0.619789:0.005701:rs61770167
1 742813 rs112573343 C T . PASS AF=0.002282 ES:SE:LP:AF:ID 0.00836312:0.0196739:0.173925:0.002282:rs112573343
1 746189 rs139221807 A G . PASS AF=0.001025 ES:SE:LP:AF:ID 0.00795713:0.0324261:0.091515:0.001025:rs139221807
1 752478 rs146277091 G A . PASS AF=0.036687 ES:SE:LP:AF:ID -0.00837586:0.00443618:1.22915:0.036687:rs146277091
1 752566 rs3094315 G A . PASS AF=0.839295 ES:SE:LP:AF:ID 0.00121373:0.00224668:0.229148:0.839295:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838932 ES:SE:LP:AF:ID 0.00117522:0.00224424:0.221849:0.838932:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869978 ES:SE:LP:AF:ID -0.00136328:0.00240787:0.244125:0.869978:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129666 ES:SE:LP:AF:ID 0.00153727:0.00241277:0.283997:0.129666:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037201 ES:SE:LP:AF:ID -0.00805062:0.00436042:1.18709:0.037201:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037444 ES:SE:LP:AF:ID -0.00773614:0.00433286:1.13077:0.037444:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869328 ES:SE:LP:AF:ID -0.00135974:0.00240313:0.244125:0.869328:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869429 ES:SE:LP:AF:ID -0.00131098:0.00240411:0.229148:0.869429:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037404 ES:SE:LP:AF:ID -0.00825564:0.00435149:1.23657:0.037404:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869331 ES:SE:LP:AF:ID -0.0012472:0.00240309:0.221849:0.869331:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005078 ES:SE:LP:AF:ID 0.013867:0.0123858:0.585027:0.005078:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005044 ES:SE:LP:AF:ID 0.0137012:0.0124184:0.568636:0.005044:rs142682604
1 754503 rs3115859 G A . PASS AF=0.838381 ES:SE:LP:AF:ID 0.00130619:0.00223785:0.251812:0.838381:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037419 ES:SE:LP:AF:ID -0.00835018:0.00435747:1.25964:0.037419:rs10454459
1 754964 rs3131966 C T . PASS AF=0.839009 ES:SE:LP:AF:ID 0.00129601:0.00224413:0.251812:0.839009:rs3131966
1 755240 rs181660517 T G . PASS AF=0.01382 ES:SE:LP:AF:ID 0.00516268:0.00781079:0.29243:0.01382:rs181660517