Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1101/ieu-a-1101.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1101/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 21:02:38 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1101/ieu-a-1101.vcf.gz ...
Read summary statistics for 2186119 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1068345 SNPs remain.
After merging with regression SNP LD, 1068345 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0516 (0.0104)
Lambda GC: 1.0494
Mean Chi^2: 1.0441
Intercept: 0.9968 (0.0069)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 21:03:07 2020
Total time elapsed: 29.4s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.901,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0,
    "n": 46061,
    "n_snps": 2186119,
    "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": 588,
    "n_miss_AF_reference": 18344,
    "n_est": 43487.5887,
    "ratio_se_n": 0.9717,
    "mean_diff": -4.7141e-06,
    "ratio_diff": 1.3384,
    "sd_y_est1": 0.988,
    "sd_y_est2": 0.96,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1068345,
    "ldsc_nsnp_merge_regression_ld": 1068345,
    "ldsc_observed_scale_h2_beta": 0.0516,
    "ldsc_observed_scale_h2_se": 0.0104,
    "ldsc_intercept_beta": 0.9968,
    "ldsc_intercept_se": 0.0069,
    "ldsc_lambda_gc": 1.0494,
    "ldsc_mean_chisq": 1.0441,
    "ldsc_ratio": -0.0726
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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 between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations 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 expect ratio_se_n to 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 of diff and the mean of diff2 (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<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 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: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_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 1.0000000 3 42 0 2186119 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.599856e+00 5.664394e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.874680e+07 5.575244e+07 1.1523e+04 3.244157e+07 7.010518e+07 1.143887e+08 2.491752e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.830000e-05 9.555900e-03 -1.8000e-01 -5.700000e-03 0.000000e+00 5.600000e-03 2.100000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.788700e-03 3.258400e-03 5.9000e-03 6.600000e-03 7.600000e-03 9.900000e-03 1.200000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.917959e-01 2.901836e-01 1.7000e-06 2.399999e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.918282e-01 2.901599e-01 9.0000e-07 2.378698e-01 4.887441e-01 7.428172e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 588 0.9997310 NA NA NA NA NA 3.810305e-01 2.560791e-01 4.0000e-03 1.590000e-01 3.260000e-01 5.730000e-01 9.960000e-01 ▇▆▅▃▂
numeric AF_reference 18344 0.9916089 NA NA NA NA NA 3.806551e-01 2.425823e-01 1.9970e-04 1.775160e-01 3.294730e-01 5.593050e-01 1.000000e+00 ▇▇▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 4.507412e+04 2.946968e+03 1.2823e+04 4.599300e+04 4.606100e+04 4.606100e+04 4.606100e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0110 0.0250 0.6499995 0.6599371 0.032 0.0371406 28632
1 723819 rs11804171 T A -0.0060 0.0250 0.8100000 0.8103303 0.034 0.1345850 28632
1 723891 rs2977670 G C 0.0060 0.0210 0.7800007 0.7750970 0.934 0.7799520 27213
1 752566 rs3094315 G A 0.0013 0.0110 0.9000000 0.9059236 0.835 0.7182510 38242
1 754192 rs3131968 A G 0.0024 0.0096 0.8000000 0.8025873 0.885 0.6785140 38871
1 768448 rs12562034 G A -0.0075 0.0320 0.8200001 0.8146939 0.102 0.1918930 27247
1 775659 rs2905035 A G 0.0014 0.0090 0.8800001 0.8763834 0.885 0.7450080 46061
1 776546 rs12124819 A G 0.0075 0.0170 0.6600001 0.6590852 0.288 0.0756789 42067
1 777122 rs2980319 A T 0.0009 0.0090 0.9199999 0.9203443 0.866 0.7472040 46061
1 779322 rs4040617 A G -0.0009 0.0120 0.9400001 0.9402147 0.133 0.2264380 36313
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C -0.0012 0.0110 0.9100000 0.9131304 0.385 0.3724040 33478
22 51216564 rs9616970 T C 0.0280 0.0160 0.0710003 0.0801183 0.146 0.1563500 32009
22 51217134 rs117417021 A G 0.0094 0.0110 0.4000000 0.3928028 0.415 0.2671730 30648
22 51222100 rs114553188 G T 0.0120 0.0220 0.5800000 0.5854409 0.062 0.0880591 28717
22 51223637 rs375798137 G A 0.0130 0.0210 0.5400003 0.5358850 0.062 0.0788738 29684
22 51229805 rs9616985 T C 0.0160 0.0210 0.4500005 0.4461168 0.092 0.0730831 31466
23 35921591 rs2204667 C G 0.0014 0.0087 0.8700001 0.8721568 0.162 NA 46052
23 51666786 rs14115 A G -0.0110 0.0170 0.5000000 0.5175939 0.027 NA 34776
23 70163799 rs1626496 A C 0.0069 0.0130 0.5900000 0.5955787 0.069 NA 46061
23 118495837 rs12882977 G A 0.0038 0.0061 0.5300002 0.5333168 0.508 0.2307280 46061

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.032    ES:SE:LP:AF:SS:ID   -0.011:0.025:0.187087:0.032:28632:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:ID   -0.006:0.025:0.091515:0.034:28632:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.934    ES:SE:LP:AF:SS:ID   0.006:0.021:0.107905:0.934:27213:rs2977670
1   752566  rs3094315   G   A   .   PASS    AF=0.835    ES:SE:LP:AF:SS:ID   0.0013:0.011:0.0457575:0.835:38242:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   0.0024:0.0096:0.09691:0.885:38871:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   -0.0075:0.032:0.0861861:0.102:27247:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   0.0014:0.009:0.0555173:0.885:46061:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.288    ES:SE:LP:AF:SS:ID   0.0075:0.017:0.180456:0.288:42067:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.866    ES:SE:LP:AF:SS:ID   0.0009:0.009:0.0362122:0.866:46061:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   -0.0009:0.012:0.0268721:0.133:36313:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.877    ES:SE:LP:AF:SS:ID   0.0024:0.012:0.0757207:0.877:38314:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.002:0.012:0.0604807:0.868:38314:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.0007:0.012:0.0222764:0.868:38198:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   -0.025:0.026:0.481486:0.9:29572:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   0.023:0.026:0.431798:0.108:29572:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.219    ES:SE:LP:AF:SS:ID   0.0054:0.011:0.200659:0.219:44700:rs11240777
1   846864  rs950122    G   C   .   PASS    AF=0.138    ES:SE:LP:AF:SS:ID   -0.017:0.017:0.481486:0.138:33534:rs950122
1   882033  rs2272756   G   A   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   -0.0088:0.0098:0.431798:0.23:39771:rs2272756
1   962210  rs3128126   A   G   .   PASS    AF=0.415    ES:SE:LP:AF:SS:ID   -0.027:0.014:1.3098:0.415:42067:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.254    ES:SE:LP:AF:SS:ID   -0.016:0.014:0.638272:0.254:39112:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.146    ES:SE:LP:AF:SS:ID   -0.021:0.016:0.744727:0.146:42404:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.734    ES:SE:LP:AF:SS:ID   0.013:0.0078:1.03621:0.734:43757:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   -0.011:0.011:0.49485:0.124:42404:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.587    ES:SE:LP:AF:SS:ID   0.015:0.0069:1.56864:0.587:46061:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.571    ES:SE:LP:AF:SS:ID   0.015:0.0067:1.65758:0.571:46061:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   -0.015:0.011:0.823909:0.124:42404:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.608    ES:SE:LP:AF:SS:ID   0.015:0.0066:1.69897:0.608:46061:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.588    ES:SE:LP:AF:SS:ID   0.015:0.0066:1.74473:0.588:46061:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.137    ES:SE:LP:AF:SS:ID   -0.015:0.011:0.769551:0.137:42404:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.735    ES:SE:LP:AF:SS:ID   0.013:0.0075:1.03621:0.735:43765:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.112    ES:SE:LP:AF:SS:ID   -0.014:0.011:0.744727:0.112:42404:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.726    ES:SE:LP:AF:SS:ID   0.013:0.0078:1:0.726:43765:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.585    ES:SE:LP:AF:SS:ID   0.017:0.0073:1.67778:0.585:44700:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.952    ES:SE:LP:AF:SS:ID   0.056:0.041:0.744727:0.952:22620:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.623    ES:SE:LP:AF:SS:ID   0.012:0.011:0.60206:0.623:42375:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   -0.013:0.01:0.638272:0.133:42404:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.134    ES:SE:LP:AF:SS:ID   -0.0087:0.013:0.30103:0.134:36543:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   0.011:0.0099:0.585027:0.717:41408:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.046    ES:SE:LP:AF:SS:ID   -0.011:0.012:0.455932:0.046:42404:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   -0.012:0.011:0.585027:0.115:42404:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.062    ES:SE:LP:AF:SS:ID   0.0025:0.016:0.0555173:0.062:42404:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.088    ES:SE:LP:AF:SS:ID   -0.0065:0.012:0.229148:0.088:42404:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   0.0017:0.016:0.0362122:0.115:42404:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.093    ES:SE:LP:AF:SS:ID   -0.006:0.017:0.142668:0.093:42404:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.314    ES:SE:LP:AF:SS:ID   -0.01:0.012:0.387216:0.314:34245:rs7548798
1   1060608 rs17160824  G   A   .   PASS    AF=0.097    ES:SE:LP:AF:SS:ID   -0.0038:0.017:0.0861861:0.097:42404:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.051    ES:SE:LP:AF:SS:ID   -0.005:0.017:0.113509:0.051:42404:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   -0.0066:0.018:0.148742:0.055:42404:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.389    ES:SE:LP:AF:SS:ID   -0.0047:0.01:0.19382:0.389:44700:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.575    ES:SE:LP:AF:SS:ID   0.0086:0.01:0.39794:0.575:42375:rs9442373