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_41230_5J2.vcf.gz --id UKB-b:20405 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41230_5J2.txt.gz --cohort_cases 1614 --cohort_controls 461396 --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": "2019-09-12T22:13:51.292542",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-20405/ukb-b-20405.vcf.gz; Date=Sun May 10 14:01:32 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-20405/UKB-b-20405_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20405/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:09 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20405/UKB-b-20405_data.vcf.gz ...
Read summary statistics for 2684848 SNPs.
Dropped 323 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, 675245 SNPs remain.
After merging with regression SNP LD, 675245 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0017 (0.0013)
Lambda GC: 1.0751
Mean Chi^2: 1.0768
Intercept: 1.0954 (0.0103)
Ratio: 1.2435 (0.1345)
Analysis finished at Thu Oct 17 14:42:48 2019
Total time elapsed: 38.11sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7889,
"inflation_factor": 1.0475,
"mean_EFFECT": -1.1044e-07,
"n": "-Inf",
"n_snps": 9851866,
"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": 21288,
"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": 675245,
"ldsc_nsnp_merge_regression_ld": 675245,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0954,
"ldsc_intercept_se": 0.0103,
"ldsc_lambda_gc": 1.0751,
"ldsc_mean_chisq": 1.0768,
"ldsc_ratio": 1.2422
}
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 | 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 |
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 | 4 | 58 | 0 | 2684528 | 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 | 2684848 | 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 | 8.660296e+00 | 5.767610e+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 | 7.855818e+07 | 5.663090e+07 | 5687.0000000 | 3.173661e+07 | 6.895501e+07 | 1.147359e+08 | 2.492013e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.000000e-07 | 1.359000e-04 | -0.0008615 | -9.140000e-05 | -5.000000e-07 | 9.090000e-05 | 7.599000e-04 | ▁▁▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.314000e-04 | 8.100000e-06 | 0.0001182 | 1.244000e-04 | 1.290000e-04 | 1.371000e-04 | 2.657000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.905790e-01 | 2.919917e-01 | 0.0000016 | 2.300001e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.905761e-01 | 2.919686e-01 | 0.0000016 | 2.345812e-01 | 4.867195e-01 | 7.453416e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.465625e-01 | 1.605931e-01 | 0.2168530 | 3.053958e-01 | 4.210765e-01 | 5.743222e-01 | 7.831470e-01 | ▇▆▅▃▃ |
| numeric | AF_reference | 21288 | 0.9920711 | NA | NA | NA | NA | NA | NA | NA | 4.289371e-01 | 1.821918e-01 | 0.0001997 | 2.841450e-01 | 4.107430e-01 | 5.625000e-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 | 0.0000354 | 0.0002175 | 0.8700001 | 0.8705171 | 0.623765 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0002236 | 0.0002154 | 0.2999998 | 0.2993572 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0001875 | 0.0002121 | 0.3800004 | 0.3767412 | 0.456846 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0001163 | 0.0002423 | 0.6300007 | 0.6313482 | 0.240959 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0001282 | 0.0001504 | 0.3900004 | 0.3938759 | 0.515645 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0003600 | 0.0001763 | 0.0409996 | 0.0411754 | 0.706753 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | -0.0003250 | 0.0001439 | 0.0239999 | 0.0239322 | 0.761297 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | -0.0001159 | 0.0001608 | 0.4700002 | 0.4709178 | 0.265385 | 0.0756789 | NA |
| 1 | 808631 | rs11240779 | G | A | -0.0002441 | 0.0001461 | 0.0949992 | 0.0948139 | 0.772619 | 0.4534740 | NA |
| 1 | 808928 | rs11240780 | C | T | -0.0002516 | 0.0001464 | 0.0860003 | 0.0855931 | 0.772847 | 0.4522760 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | -0.0002051 | 0.0001416 | 0.1499999 | 0.1473957 | 0.713656 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | -0.0003168 | 0.0001408 | 0.0250000 | 0.0245106 | 0.695470 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -0.0002322 | 0.0001420 | 0.1000000 | 0.1019766 | 0.715502 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0000678 | 0.0001317 | 0.6100002 | 0.6065913 | 0.381825 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0001338 | 0.0001284 | 0.2999998 | 0.2973528 | 0.451061 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0002066 | 0.0001325 | 0.1199999 | 0.1189237 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0000409 | 0.0001500 | 0.7899998 | 0.7851548 | 0.254562 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0000343 | 0.0001487 | 0.8200001 | 0.8177274 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0000463 | 0.0001413 | 0.7400005 | 0.7433226 | 0.331457 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0001216 | 0.0001447 | 0.4000000 | 0.4005962 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID 3.54452e-05:0.000217453:0.0604807:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.000223575:0.000215429:0.522879:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID 0.000187492:0.000212115:0.420216:0.456846:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID 0.000116259:0.000242292:0.200659:0.240959:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID -0.000128241:0.00015041:0.408935:0.515645:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -0.000360048:0.000176342:1.38722:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID -0.000325016:0.000143926:1.61979:0.761297:rs2977608
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID -0.000115913:0.00016077:0.327902:0.265385:rs12124819
1 808631 rs11240779 G A . PASS AF=0.772619 ES:SE:LP:AF:ID -0.0002441:0.000146121:1.02228:0.772619:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772847 ES:SE:LP:AF:ID -0.000251622:0.000146367:1.0655:0.772847:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340396 ES:SE:LP:AF:ID -0.000290157:0.000206238:0.79588:0.340396:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697255 ES:SE:LP:AF:ID -9.48058e-05:0.000137984:0.309804:0.697255:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705397 ES:SE:LP:AF:ID -0.000147701:0.000135487:0.552842:0.705397:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705442 ES:SE:LP:AF:ID -0.000143474:0.000135482:0.537602:0.705442:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705627 ES:SE:LP:AF:ID -0.000145409:0.000135489:0.552842:0.705627:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705655 ES:SE:LP:AF:ID -0.000145871:0.000135503:0.552842:0.705655:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730129 ES:SE:LP:AF:ID -3.30637e-05:0.000139195:0.091515:0.730129:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294377 ES:SE:LP:AF:ID 0.000145228:0.000135497:0.552842:0.294377:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236703 ES:SE:LP:AF:ID 3.88934e-05:0.000144257:0.102373:0.236703:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236691 ES:SE:LP:AF:ID 3.92853e-05:0.000144259:0.102373:0.236691:rs28752186
1 833641 rs28594623 T C . PASS AF=0.23975 ES:SE:LP:AF:ID 1.78871e-05:0.000143796:0.0457575:0.23975:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236693 ES:SE:LP:AF:ID 3.91129e-05:0.000144257:0.102373:0.236693:rs28484835
1 834832 rs4411087 G C . PASS AF=0.237178 ES:SE:LP:AF:ID 4.14144e-05:0.000144147:0.113509:0.237178:rs4411087
1 835499 rs4422948 A G . PASS AF=0.241162 ES:SE:LP:AF:ID 4.91185e-05:0.000143141:0.136677:0.241162:rs4422948
1 836896 rs28705752 T C . PASS AF=0.269511 ES:SE:LP:AF:ID 0.000103421:0.00013812:0.346787:0.269511:rs28705752
1 838555 rs4970383 C A . PASS AF=0.246204 ES:SE:LP:AF:ID 3.38216e-06:0.000142156:0.00877392:0.246204:rs4970383
1 839103 rs28562941 A G . PASS AF=0.270019 ES:SE:LP:AF:ID 0.00013133:0.000138217:0.468521:0.270019:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400124 ES:SE:LP:AF:ID 4.98532e-05:0.000124975:0.161151:0.400124:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237102 ES:SE:LP:AF:ID -5.23622e-05:0.000145163:0.142668:0.237102:rs1574243
1 842362 rs28540380 C T . PASS AF=0.235323 ES:SE:LP:AF:ID -0.000158866:0.000147338:0.552842:0.235323:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362606 ES:SE:LP:AF:ID 8.78422e-05:0.000155139:0.244125:0.362606:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590331 ES:SE:LP:AF:ID -9.47005e-05:0.000124611:0.346787:0.590331:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603723 ES:SE:LP:AF:ID -6.87963e-05:0.00012531:0.236572:0.603723:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603942 ES:SE:LP:AF:ID -6.91692e-05:0.000125292:0.236572:0.603942:rs6657440
1 851204 rs28552953 G C . PASS AF=0.224621 ES:SE:LP:AF:ID -0.000166856:0.000148232:0.585027:0.224621:rs28552953
1 852037 rs4970463 G A . PASS AF=0.589686 ES:SE:LP:AF:ID -8.53784e-05:0.000124813:0.309804:0.589686:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589665 ES:SE:LP:AF:ID -8.77766e-05:0.000124757:0.318759:0.589665:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607671 ES:SE:LP:AF:ID -0.000104696:0.000125572:0.39794:0.607671:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607829 ES:SE:LP:AF:ID -0.000107282:0.000125589:0.408935:0.607829:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610316 ES:SE:LP:AF:ID -0.000111196:0.000125713:0.420216:0.610316:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603283 ES:SE:LP:AF:ID -7.61833e-05:0.000125341:0.267606:0.603283:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610337 ES:SE:LP:AF:ID -0.00011146:0.000125715:0.420216:0.610337:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389936 ES:SE:LP:AF:ID 0.000111239:0.000125739:0.420216:0.389936:rs28534711
1 856108 rs28742275 A G . PASS AF=0.38992 ES:SE:LP:AF:ID 0.00011086:0.000125746:0.420216:0.38992:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350356 ES:SE:LP:AF:ID 0.000103615:0.000129176:0.376751:0.350356:rs4040605
1 858040 rs4970460 C A . PASS AF=0.217965 ES:SE:LP:AF:ID -0.00011033:0.000148643:0.337242:0.217965:rs4970460
1 858051 rs4970459 C T . PASS AF=0.219021 ES:SE:LP:AF:ID -0.000103019:0.000148124:0.309804:0.219021:rs4970459
1 858801 rs7418179 A G . PASS AF=0.765846 ES:SE:LP:AF:ID 0.000100312:0.000145005:0.309804:0.765846:rs7418179
1 860416 rs61464428 G A . PASS AF=0.766638 ES:SE:LP:AF:ID 8.95183e-05:0.000145077:0.267606:0.766638:rs61464428
1 860688 rs60837925 G A . PASS AF=0.766104 ES:SE:LP:AF:ID 8.98457e-05:0.000144977:0.267606:0.766104:rs60837925