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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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 /data/cromwell-executions/qc/95ee3370-f0ac-4521-b9b7-e9abdfffbdc4/call-ldsc/inputs/562856218/ieu-b-40.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-40/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Aug 20 17:20:21 2020
Reading summary statistics from /data/cromwell-executions/qc/95ee3370-f0ac-4521-b9b7-e9abdfffbdc4/call-ldsc/inputs/562856218/ieu-b-40.vcf.gz ...
Read summary statistics for 2336255 SNPs.
Dropped 638 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, 1048422 SNPs remain.
After merging with regression SNP LD, 1048422 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.193 (0.0063)
Lambda GC: 2.727
Mean Chi^2: 3.9675
Intercept: 1.1825 (0.0209)
Ratio: 0.0615 (0.007)
Analysis finished at Thu Aug 20 17:22:39 2020
Total time elapsed: 2.0m:18.5sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9272,
"inflation_factor": 2.7889,
"mean_EFFECT": 0,
"n": 795640,
"n_snps": 2336260,
"n_clumped_hits": 507,
"n_p_sig": 41209,
"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": 12471,
"n_est": 806121.932,
"ratio_se_n": 1.0066,
"mean_diff": -2.6717e-06,
"ratio_diff": 2.5008,
"sd_y_est1": 1.0874,
"sd_y_est2": 1.0945,
"r2_sum1": 0.0524,
"r2_sum2": 0.0443,
"r2_sum3": 0.0437,
"r2_sum4": 0.0463,
"ldsc_nsnp_merge_refpanel_ld": 1048422,
"ldsc_nsnp_merge_regression_ld": 1048422,
"ldsc_observed_scale_h2_beta": 0.193,
"ldsc_observed_scale_h2_se": 0.0063,
"ldsc_intercept_beta": 1.1825,
"ldsc_intercept_se": 0.0209,
"ldsc_lambda_gc": 2.727,
"ldsc_mean_chisq": 3.9675,
"ldsc_ratio": 0.0615
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| n | FALSE |
| 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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 0 | 1.000000 | 3 | 34 | 0 | 2336259 | 0 | 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 |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 8.579708e+00 | 5.653368e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.20000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.912649e+07 | 5.559340e+07 | 1.29940e+04 | 3.317651e+07 | 7.073592e+07 | 1.145473e+08 | 2.49219e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | 1.860000e-05 | 4.911600e-03 | -1.06000e-01 | -2.700000e-03 | 0.000000e+00 | 2.700000e-03 | 7.80000e-02 | ▁▁▇▂▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 2.613400e-03 | 1.252300e-03 | 1.60000e-03 | 1.800000e-03 | 2.100000e-03 | 2.900000e-03 | 4.34000e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.431542e-01 | 3.130294e-01 | 0.00000e+00 | 4.600020e-02 | 2.599998e-01 | 5.999997e-01 | 1.00000e+00 | ▇▃▂▂▂ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.430163e-01 | 3.131608e-01 | 0.00000e+00 | 4.550030e-02 | 2.637178e-01 | 5.992887e-01 | 1.00000e+00 | ▇▃▂▂▂ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.588528e-01 | 2.716627e-01 | 9.82200e-03 | 1.249000e-01 | 2.912000e-01 | 5.610000e-01 | 9.90061e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 12471 | 0.994662 | NA | NA | NA | NA | NA | 3.619453e-01 | 2.559926e-01 | 5.99000e-04 | 1.473640e-01 | 2.977240e-01 | 5.471250e-01 | 9.99601e-01 | ▇▆▃▃▂ |
| numeric | N | 0 | 1.000000 | NA | NA | NA | NA | NA | 6.833649e+05 | 3.208988e+04 | 4.85648e+05 | 6.798850e+05 | 6.885660e+05 | 6.915470e+05 | 7.95640e+05 | ▁▁▁▇▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 753541 | rs2073813 | G | A | -0.0040 | 0.0028 | 0.1499999 | 0.1531275 | 0.14250 | 0.3019170 | 517173 |
| 1 | 754192 | rs3131968 | A | G | 0.0023 | 0.0028 | 0.4100001 | 0.4114022 | 0.85630 | 0.6785140 | 551519 |
| 1 | 777122 | rs2980319 | A | T | 0.0019 | 0.0027 | 0.4799997 | 0.4816173 | 0.86320 | 0.7472040 | 598447 |
| 1 | 779322 | rs4040617 | A | G | -0.0021 | 0.0027 | 0.4500005 | 0.4367000 | 0.13530 | 0.2264380 | 587624 |
| 1 | 780785 | rs2977612 | T | A | 0.0019 | 0.0027 | 0.4899999 | 0.4816173 | 0.85500 | 0.6693290 | 582906 |
| 1 | 785989 | rs2980300 | T | C | 0.0019 | 0.0027 | 0.4700002 | 0.4816173 | 0.85270 | 0.6269970 | 585492 |
| 1 | 798026 | rs4951864 | C | T | -0.0089 | 0.0035 | 0.0109999 | 0.0109950 | 0.91786 | 0.8941690 | 532795 |
| 1 | 798801 | rs12132517 | G | A | 0.0088 | 0.0035 | 0.0120000 | 0.0119274 | 0.08045 | 0.0740815 | 528849 |
| 1 | 798959 | rs11240777 | G | A | 0.0014 | 0.0024 | 0.5700002 | 0.5596689 | 0.21040 | 0.4099440 | 547671 |
| 1 | 990380 | rs3121561 | C | T | -0.0010 | 0.0021 | 0.6400000 | 0.6339387 | 0.28680 | 0.3434500 | 605446 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51158017 | rs6010065 | G | C | 0.0039 | 0.0018 | 0.0280001 | 0.0302603 | 0.46220 | 0.5475240 | 686976 |
| 22 | 51162059 | rs10451 | G | A | 0.0022 | 0.0019 | 0.2599998 | 0.2469070 | 0.30670 | 0.3865810 | 637122 |
| 22 | 51163138 | rs715586 | C | T | 0.0028 | 0.0023 | 0.2399999 | 0.2234554 | 0.14790 | 0.0902556 | 777640 |
| 22 | 51165664 | rs8137951 | G | A | 0.0026 | 0.0018 | 0.1499999 | 0.1486140 | 0.30430 | 0.4063500 | 789190 |
| 22 | 51171497 | rs2301584 | G | A | 0.0001 | 0.0025 | 0.9800000 | 0.9680931 | 0.17810 | 0.2533950 | 604784 |
| 22 | 51173542 | rs4824147 | T | C | 0.0030 | 0.0040 | 0.4400003 | 0.4532547 | 0.95919 | 0.9812300 | 583357 |
| 22 | 51175626 | rs3810648 | A | G | -0.0040 | 0.0037 | 0.2700001 | 0.2796610 | 0.06437 | 0.1084270 | 672619 |
| 22 | 51178090 | rs2285395 | G | A | -0.0029 | 0.0037 | 0.4299995 | 0.4331670 | 0.05548 | 0.0666933 | 773206 |
| 22 | 51196164 | rs8136603 | A | T | -0.0063 | 0.0042 | 0.1299999 | 0.1336144 | 0.05589 | 0.1427720 | 649010 |
| 22 | 51229805 | rs9616985 | T | C | 0.0049 | 0.0036 | 0.1800002 | 0.1734786 | 0.05163 | 0.0730831 | 585003 |
bcf preview
1 753541 rs1388595942 G A . PASS AF=0.1425 ES:SE:LP:AF:SS:ID -0.004:0.0028:0.823909:0.1425:517173:rs1388595942
1 754192 rs3131968 A G . PASS AF=0.8563 ES:SE:LP:AF:SS:ID 0.0023:0.0028:0.387216:0.8563:551519:rs3131968
1 777122 rs2980319 A T . PASS AF=0.8632 ES:SE:LP:AF:SS:ID 0.0019:0.0027:0.318759:0.8632:598447:rs2980319
1 779322 rs4040617 A G . PASS AF=0.1353 ES:SE:LP:AF:SS:ID -0.0021:0.0027:0.346787:0.1353:587624:rs4040617
1 780785 rs2977612 T A . PASS AF=0.855 ES:SE:LP:AF:SS:ID 0.0019:0.0027:0.309804:0.855:582906:rs2977612
1 785989 rs2980300 T C . PASS AF=0.8527 ES:SE:LP:AF:SS:ID 0.0019:0.0027:0.327902:0.8527:585492:rs2980300
1 798026 rs4951864 C T . PASS AF=0.91786 ES:SE:LP:AF:SS:ID -0.0089:0.0035:1.95861:0.91786:532795:rs4951864
1 798801 rs12132517 G A . PASS AF=0.08045 ES:SE:LP:AF:SS:ID 0.0088:0.0035:1.92082:0.08045:528849:rs12132517
1 798959 rs11240777 G A . PASS AF=0.2104 ES:SE:LP:AF:SS:ID 0.0014:0.0024:0.244125:0.2104:547671:rs11240777
1 990380 rs3121561 C T . PASS AF=0.2868 ES:SE:LP:AF:SS:ID -0.001:0.0021:0.19382:0.2868:605446:rs3121561
1 998501 rs3813193 G C . PASS AF=0.1476 ES:SE:LP:AF:SS:ID 0.0021:0.0025:0.387216:0.1476:623366:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.717 ES:SE:LP:AF:SS:ID 0.0039:0.002:1.31876:0.717:680426:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.1428 ES:SE:LP:AF:SS:ID 0.0041:0.0025:1:0.1428:635407:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.5608 ES:SE:LP:AF:SS:ID 0.0005:0.0018:0.09691:0.5608:668398:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5544 ES:SE:LP:AF:SS:ID 0.0007:0.0018:0.167491:0.5544:669144:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.1387 ES:SE:LP:AF:SS:ID 0.0058:0.0026:1.60206:0.1387:635927:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.569 ES:SE:LP:AF:SS:ID 0.0006:0.0018:0.130768:0.569:682317:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.5697 ES:SE:LP:AF:SS:ID 0.0005:0.0018:0.113509:0.5697:682866:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.1486 ES:SE:LP:AF:SS:ID 0.0059:0.0026:1.65758:0.1486:630682:rs10907177
1 1021415 rs386627436 A G . PASS AF=0.7181 ES:SE:LP:AF:SS:ID 0.0043:0.002:1.55284:0.7181:670750:rs386627436
1 1021583 rs10907178 A C . PASS AF=0.1475 ES:SE:LP:AF:SS:ID 0.0059:0.0026:1.65758:0.1475:630752:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.7204 ES:SE:LP:AF:SS:ID 0.0045:0.002:1.61979:0.7204:674336:rs9442398
1 1030565 rs6687776 C T . PASS AF=0.1579 ES:SE:LP:AF:SS:ID 0.0029:0.0024:0.638272:0.1579:642429:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.1579 ES:SE:LP:AF:SS:ID 0.0027:0.0025:0.568636:0.1579:621351:rs6678318
1 1031540 rs776599533 A G . PASS AF=0.7256 ES:SE:LP:AF:SS:ID 0.0018:0.002:0.420216:0.7256:633563:rs776599533
1 1036959 rs1162868282 T C . PASS AF=0.1136 ES:SE:LP:AF:SS:ID 0.0024:0.0028:0.420216:0.1136:662400:rs1162868282
1 1040026 rs6671356 T C . PASS AF=0.1369 ES:SE:LP:AF:SS:ID 0.0008:0.0026:0.113509:0.1369:650822:rs6671356
1 1046164 rs386627439 C T . PASS AF=0.1393 ES:SE:LP:AF:SS:ID 0.0003:0.0026:0.0457575:0.1393:657400:rs386627439
1 1048955 rs4970405 A G . PASS AF=0.1103 ES:SE:LP:AF:SS:ID 0.0014:0.0029:0.207608:0.1103:660764:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.1393 ES:SE:LP:AF:SS:ID 0.0004:0.0026:0.0655015:0.1393:657067:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.1155 ES:SE:LP:AF:SS:ID 0.002:0.0028:0.327902:0.1155:656195:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.2914 ES:SE:LP:AF:SS:ID -0.0036:0.002:1.11351:0.2914:584935:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.02228 ES:SE:LP:AF:SS:ID -0.0082:0.0058:0.79588:0.02228:622102:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.1162 ES:SE:LP:AF:SS:ID 0.0021:0.0028:0.337242:0.1162:659082:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.1161 ES:SE:LP:AF:SS:ID 0.0023:0.0028:0.387216:0.1161:659382:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.1161 ES:SE:LP:AF:SS:ID 0.0023:0.0028:0.387216:0.1161:654281:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.4058 ES:SE:LP:AF:SS:ID -0.0024:0.0019:0.721246:0.4058:616267:rs11807848
1 1062015 rs1557446446 C T . PASS AF=0.02239 ES:SE:LP:AF:SS:ID -0.0071:0.0059:0.638272:0.02239:609493:rs1557446446
1 1062638 rs9442373 C A . PASS AF=0.5558 ES:SE:LP:AF:SS:ID 0.0032:0.0018:1.10237:0.5558:625335:rs9442373
1 1064979 rs2298217 C T . PASS AF=0.1515 ES:SE:LP:AF:SS:ID -0.0013:0.0025:0.21467:0.1515:620602:rs2298217
1 1066029 rs12145826 G A . PASS AF=0.05888 ES:SE:LP:AF:SS:ID 0.0005:0.004:0.0409586:0.05888:508645:rs12145826
1 1066403 rs10907182 T C . PASS AF=0.5941 ES:SE:LP:AF:SS:ID 0.0023:0.0019:0.677781:0.5941:603771:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.5997 ES:SE:LP:AF:SS:ID 0.002:0.0019:0.552842:0.5997:607558:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.92008 ES:SE:LP:AF:SS:ID -0.0038:0.0033:0.585027:0.92008:655679:rs4970357
1 1079198 rs1310655014 T C . PASS AF=0.2335 ES:SE:LP:AF:SS:ID -0.0049:0.0022:1.56864:0.2335:531090:rs1310655014
1 1087683 rs9442380 T C . PASS AF=0.93095 ES:SE:LP:AF:SS:ID -0.0001:0.0035:0.0132283:0.93095:668827:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.97001 ES:SE:LP:AF:SS:ID 0.0003:0.005:0.0222764:0.97001:668339:rs4970358
1 1094738 rs4970362 A G . PASS AF=0.6901 ES:SE:LP:AF:SS:ID 0.005:0.0019:2.07058:0.6901:572533:rs4970362
1 1099342 rs9660710 A C . PASS AF=0.93259 ES:SE:LP:AF:SS:ID -0.0006:0.0034:0.0655015:0.93259:687168:rs9660710
1 1100217 rs1202203592 C T . PASS AF=0.9444 ES:SE:LP:AF:SS:ID -0.002:0.0039:0.207608:0.9444:685120:rs1202203592