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_41210_Z841.vcf.gz --id UKB-b:16715 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41210_Z841.txt.gz --cohort_cases 1003 --cohort_controls 462007 --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": "2019-09-13T01:24:47.442641",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-16715/ukb-b-16715.vcf.gz; Date=Sun May 10 01:25:40 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-16715/UKB-b-16715_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16715/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:45:16 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16715/UKB-b-16715_data.vcf.gz ...
Read summary statistics for 1344553 SNPs.
Dropped 109 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, 348374 SNPs remain.
After merging with regression SNP LD, 348374 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0027 (0.0017)
Lambda GC: 1.0167
Mean Chi^2: 1.0225
Intercept: 0.9922 (0.0133)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:45:39 2019
Total time elapsed: 23.19sQC metrics
Metrics
Metrics
{
"af_correlation": 0.5515,
"inflation_factor": 1,
"mean_EFFECT": -2.3067e-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": 10735,
"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": 348374,
"ldsc_nsnp_merge_regression_ld": 348374,
"ldsc_observed_scale_h2_beta": 0.0027,
"ldsc_observed_scale_h2_se": 0.0017,
"ldsc_intercept_beta": 0.9922,
"ldsc_intercept_se": 0.0133,
"ldsc_lambda_gc": 1.0167,
"ldsc_mean_chisq": 1.0225,
"ldsc_ratio": -0.3467
}
Flags
| name | value |
|---|---|
| af_correlation | TRUE |
| 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 | 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 | 4 | 58 | 0 | 1344446 | 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 | 1344553 | 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 | 8.679110e+00 | 5.768577e+00 | 1.00000e+00 | 4.00000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.842830e+07 | 5.650863e+07 | 1.23330e+04 | 3.16052e+07 | 6.887353e+07 | 1.143183e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -2.000000e-07 | 9.980000e-05 | -5.42100e-04 | -6.73000e-05 | -6.000000e-07 | 6.690000e-05 | 5.673000e-04 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.870000e-05 | 2.500000e-06 | 9.32000e-05 | 9.72000e-05 | 9.820000e-05 | 9.970000e-05 | 1.824000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.973773e-01 | 2.900360e-01 | 1.20000e-06 | 2.50000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.973811e-01 | 2.900115e-01 | 1.20000e-06 | 2.45113e-01 | 4.961044e-01 | 7.495766e-01 | 9.999992e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.853647e-01 | 8.692540e-02 | 3.48954e-01 | 4.08753e-01 | 4.779340e-01 | 5.576970e-01 | 6.510460e-01 | ▇▇▆▆▅ |
| numeric | AF_reference | 10735 | 0.9920159 | NA | NA | NA | NA | NA | NA | NA | 4.629510e-01 | 1.409979e-01 | 1.99700e-04 | 3.58227e-01 | 4.576680e-01 | 5.634980e-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 | 0.0000939 | 0.0001716 | 0.5800000 | 0.5842906 | 0.623765 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000305 | 0.0001700 | 0.8600001 | 0.8574280 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0001400 | 0.0001674 | 0.4000000 | 0.4029051 | 0.456846 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000686 | 0.0001187 | 0.5600000 | 0.5631700 | 0.515645 | 0.275160 | NA |
| 1 | 840753 | rs4970382 | T | C | -0.0000334 | 0.0000986 | 0.7300002 | 0.7347708 | 0.400124 | 0.468850 | NA |
| 1 | 843405 | rs11516185 | A | G | -0.0001388 | 0.0001224 | 0.2599998 | 0.2567864 | 0.362606 | 0.375399 | NA |
| 1 | 850218 | rs6664536 | T | A | -0.0000694 | 0.0000983 | 0.4799997 | 0.4802186 | 0.590331 | 0.345248 | NA |
| 1 | 850371 | rs6679046 | G | T | -0.0000614 | 0.0000989 | 0.5300002 | 0.5348762 | 0.603723 | 0.508786 | NA |
| 1 | 850780 | rs6657440 | C | T | -0.0000630 | 0.0000989 | 0.5199996 | 0.5242825 | 0.603942 | 0.560304 | NA |
| 1 | 852037 | rs4970463 | G | A | -0.0000721 | 0.0000985 | 0.4600002 | 0.4638703 | 0.589686 | 0.345048 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51158017 | rs6010065 | G | C | 0.0002522 | 0.0000969 | 0.0092999 | 0.0092603 | 0.461411 | 0.547524 | NA |
| 22 | 51158499 | rs8136930 | T | G | 0.0002510 | 0.0000970 | 0.0097000 | 0.0096702 | 0.461636 | 0.544728 | NA |
| 22 | 51161019 | rs5770994 | C | T | -0.0001826 | 0.0000967 | 0.0589997 | 0.0590632 | 0.482204 | 0.425719 | NA |
| 22 | 51163039 | rs715584 | G | T | 0.0002297 | 0.0000982 | 0.0189998 | 0.0193805 | 0.426975 | 0.473642 | NA |
| 22 | 51164109 | rs5770995 | G | C | 0.0002503 | 0.0000976 | 0.0100000 | 0.0103516 | 0.452705 | 0.510982 | NA |
| 22 | 51164115 | rs5770996 | C | T | 0.0002518 | 0.0000976 | 0.0099001 | 0.0098508 | 0.456917 | 0.514776 | NA |
| 22 | 51174048 | rs9628245 | G | C | 0.0001423 | 0.0001102 | 0.2000000 | 0.1966542 | 0.380135 | 0.433107 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0001135 | 0.0001039 | 0.2700001 | 0.2746554 | 0.381825 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0002037 | 0.0001013 | 0.0439997 | 0.0442400 | 0.451061 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0002244 | 0.0001046 | 0.0320000 | 0.0318287 | 0.386333 | 0.422923 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID 9.3879e-05:0.000171585:0.236572:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 3.05382e-05:0.000169988:0.0655015:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID 0.000139999:0.000167374:0.39794:0.456846:rs6702460
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID 6.86159e-05:0.000118684:0.251812:0.515645:rs12029736
1 840753 rs4970382 T C . PASS AF=0.400124 ES:SE:LP:AF:ID -3.34091e-05:9.86141e-05:0.136677:0.400124:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362606 ES:SE:LP:AF:ID -0.000138821:0.000122415:0.585027:0.362606:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590331 ES:SE:LP:AF:ID -6.94137e-05:9.83265e-05:0.318759:0.590331:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603723 ES:SE:LP:AF:ID -6.13618e-05:9.88782e-05:0.275724:0.603723:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603942 ES:SE:LP:AF:ID -6.29527e-05:9.88644e-05:0.283997:0.603942:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589686 ES:SE:LP:AF:ID -7.21401e-05:9.84863e-05:0.337242:0.589686:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589665 ES:SE:LP:AF:ID -7.15058e-05:9.84421e-05:0.327902:0.589665:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607671 ES:SE:LP:AF:ID -9.19608e-05:9.90852e-05:0.455932:0.607671:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607829 ES:SE:LP:AF:ID -9.6174e-05:9.90987e-05:0.481486:0.607829:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610316 ES:SE:LP:AF:ID -0.000102496:9.91962e-05:0.522879:0.610316:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603283 ES:SE:LP:AF:ID -6.95537e-05:9.89024e-05:0.318759:0.603283:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610337 ES:SE:LP:AF:ID -0.000102692:9.91981e-05:0.522879:0.610337:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389936 ES:SE:LP:AF:ID 0.000101982:9.92169e-05:0.522879:0.389936:rs28534711
1 856108 rs28742275 A G . PASS AF=0.38992 ES:SE:LP:AF:ID 0.000102076:9.9222e-05:0.522879:0.38992:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350356 ES:SE:LP:AF:ID -1.08544e-05:0.000101929:0.0362122:0.350356:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610552 ES:SE:LP:AF:ID -1.0634e-06:9.97545e-05:0.00436481:0.610552:rs2880024
1 875770 rs4970379 A G . PASS AF=0.600085 ES:SE:LP:AF:ID -3.70593e-05:0.000100584:0.148742:0.600085:rs4970379
1 903245 rs28690976 A G . PASS AF=0.566938 ES:SE:LP:AF:ID 1.61945e-05:0.00010102:0.0604807:0.566938:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386681 ES:SE:LP:AF:ID 1.06344e-05:0.000100745:0.0362122:0.386681:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571408 ES:SE:LP:AF:ID 6.88273e-05:9.75691e-05:0.318759:0.571408:rs3829740
1 912049 rs7367995 T C . PASS AF=0.585249 ES:SE:LP:AF:ID -2.47273e-05:9.85582e-05:0.09691:0.585249:rs7367995
1 913889 rs2340596 G A . PASS AF=0.59921 ES:SE:LP:AF:ID -6.47466e-05:9.87183e-05:0.29243:0.59921:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602516 ES:SE:LP:AF:ID -9.86545e-05:9.90173e-05:0.49485:0.602516:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600074 ES:SE:LP:AF:ID -6.90915e-05:9.88272e-05:0.318759:0.600074:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584289 ES:SE:LP:AF:ID -8.82286e-05:9.82733e-05:0.431798:0.584289:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589102 ES:SE:LP:AF:ID -0.000110678:9.84234e-05:0.585027:0.589102:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584202 ES:SE:LP:AF:ID -7.36089e-05:9.82272e-05:0.346787:0.584202:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589327 ES:SE:LP:AF:ID -9.74904e-05:9.83478e-05:0.49485:0.589327:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583926 ES:SE:LP:AF:ID -0.000137067:0.000101708:0.744727:0.583926:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567888 ES:SE:LP:AF:ID -0.000108048:9.81449e-05:0.568636:0.567888:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578491 ES:SE:LP:AF:ID -0.000136218:9.84264e-05:0.769551:0.578491:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386082 ES:SE:LP:AF:ID 0.000135993:9.96832e-05:0.769551:0.386082:rs3128110
1 930567 rs3121574 A G . PASS AF=0.386124 ES:SE:LP:AF:ID 0.000135588:9.96857e-05:0.769551:0.386124:rs3121574
1 930751 rs3128111 C G . PASS AF=0.385079 ES:SE:LP:AF:ID 0.000145371:9.97462e-05:0.823909:0.385079:rs3128111
1 931166 rs2710880 A G . PASS AF=0.386765 ES:SE:LP:AF:ID 0.000139595:9.9702e-05:0.79588:0.386765:rs2710880
1 931362 rs2799060 G A . PASS AF=0.385571 ES:SE:LP:AF:ID 0.000150022:9.97505e-05:0.886057:0.385571:rs2799060
1 933790 rs9442392 G A . PASS AF=0.578604 ES:SE:LP:AF:ID -0.000138283:9.83929e-05:0.79588:0.578604:rs9442392
1 936111 rs1936360 C T . PASS AF=0.573545 ES:SE:LP:AF:ID -0.000113829:9.83693e-05:0.60206:0.573545:rs1936360
1 940005 rs2799056 A G . PASS AF=0.399264 ES:SE:LP:AF:ID 0.000134776:9.93379e-05:0.769551:0.399264:rs2799056
1 940096 rs4503294 C T . PASS AF=0.565308 ES:SE:LP:AF:ID -0.000128955:9.80879e-05:0.721246:0.565308:rs4503294
1 941284 rs3128116 C T . PASS AF=0.397398 ES:SE:LP:AF:ID 0.000138774:9.93593e-05:0.79588:0.397398:rs3128116
1 941334 rs57683598 G A . PASS AF=0.397402 ES:SE:LP:AF:ID 0.000138936:9.93655e-05:0.79588:0.397402:rs57683598
1 941539 rs9778087 C T . PASS AF=0.399593 ES:SE:LP:AF:ID 0.000133784:9.93691e-05:0.744727:0.399593:rs9778087
1 943687 rs2465140 G C . PASS AF=0.395214 ES:SE:LP:AF:ID 0.000128739:9.94107e-05:0.69897:0.395214:rs2465140
1 943968 rs13303313 C T . PASS AF=0.569673 ES:SE:LP:AF:ID -0.000111763:9.81381e-05:0.60206:0.569673:rs13303313
1 944564 rs3128117 T C . PASS AF=0.396446 ES:SE:LP:AF:ID 0.000132021:9.92616e-05:0.744727:0.396446:rs3128117