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/public/UKB-b-13092/UKB-b-13092_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13092/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13092/UKB-b-13092_data.vcf.gz ...
Read summary statistics for 7984082 SNPs.
Dropped 6104 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, 1282329 SNPs remain.
After merging with regression SNP LD, 1282329 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0576 (0.006)
Lambda GC: 1.0913
Mean Chi^2: 1.1105
Intercept: 1.0085 (0.0067)
Ratio: 0.0773 (0.061)
Analysis finished at Thu Oct 17 14:43:34 2019
Total time elapsed: 1.0m:24.14s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.943,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 5,
    "n_p_sig": 142,
    "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": 74550,
    "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": 1282329,
    "ldsc_nsnp_merge_regression_ld": 1282329,
    "ldsc_observed_scale_h2_beta": 0.0576,
    "ldsc_observed_scale_h2_se": 0.006,
    "ldsc_intercept_beta": 1.0085,
    "ldsc_intercept_se": 0.0067,
    "ldsc_lambda_gc": 1.0913,
    "ldsc_mean_chisq": 1.1105,
    "ldsc_ratio": 0.0769
}

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 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 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 7978005 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 7984082 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 8.661132e+00 5.763564e+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 7.869797e+07 5.641117e+07 828.0000000 3.226036e+07 6.916700e+07 1.145308e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.060000e-05 5.792200e-03 -0.0633072 -2.725600e-03 -1.240000e-05 2.713500e-03 5.545740e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.885000e-03 2.928600e-03 0.0022273 2.580600e-03 3.589700e-03 6.420300e-03 2.740310e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.890113e-01 2.918668e-01 0.0000000 2.300001e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.890119e-01 2.918426e-01 0.0000000 2.335629e-01 4.862892e-01 7.417392e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.459923e-01 2.607117e-01 0.0083900 3.572700e-02 1.372060e-01 3.895690e-01 9.916100e-01 ▇▂▂▁▁
numeric AF_reference 74550 0.9906627 NA NA NA NA NA NA NA 2.452626e-01 2.525653e-01 0.0000000 3.773960e-02 1.525560e-01 3.847840e-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 0.0096303 0.0041087 0.0189998 0.0190860 0.623745 0.7821490 NA
1 54676 rs2462492 C T -0.0065413 0.0040709 0.1100001 0.1080897 0.401015 NA NA
1 86028 rs114608975 T C -0.0011378 0.0065563 0.8600001 0.8622243 0.102565 0.0277556 NA
1 91536 rs6702460 G T 0.0049375 0.0040031 0.2200002 0.2174203 0.456972 0.4207270 NA
1 234313 rs8179466 C T 0.0016445 0.0078798 0.8300000 0.8346876 0.074471 NA NA
1 534192 rs6680723 C T 0.0059386 0.0045747 0.1900002 0.1942443 0.241599 NA NA
1 546697 rs12025928 A G -0.0089157 0.0057411 0.1199999 0.1204339 0.913953 NA NA
1 693731 rs12238997 A G -0.0003558 0.0038186 0.9299999 0.9257598 0.117978 0.1417730 NA
1 705882 rs72631875 G A 0.0092928 0.0056180 0.0980009 0.0981065 0.067216 0.0315495 NA
1 706368 rs55727773 A G 0.0037723 0.0028350 0.1800002 0.1833173 0.513498 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A -0.0000810 0.0034200 0.9800000 0.9810999 0.138489 0.2052720 NA
22 51219387 rs9616832 T C -0.0010748 0.0044338 0.8100000 0.8084638 0.074628 0.0654952 NA
22 51219704 rs147475742 G A -0.0040564 0.0059381 0.4899999 0.4945376 0.042323 0.0473243 NA
22 51221190 rs369304721 G A -0.0064249 0.0059323 0.2800000 0.2787937 0.050425 NA NA
22 51221731 rs115055839 T C -0.0016296 0.0044358 0.7099994 0.7133394 0.074080 0.0625000 NA
22 51222100 rs114553188 G T 0.0012395 0.0052467 0.8100000 0.8132469 0.054226 0.0880591 NA
22 51223637 rs375798137 G A 0.0009780 0.0052716 0.8499999 0.8528161 0.053849 0.0788738 NA
22 51229805 rs9616985 T C -0.0014828 0.0044525 0.7400005 0.7391166 0.073911 0.0730831 NA
22 51232488 rs376461333 A G 0.0050405 0.0105075 0.6300007 0.6314399 0.020121 NA NA
22 51237063 rs3896457 T C 0.0025419 0.0027384 0.3500000 0.3532758 0.297997 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623745 ES:SE:LP:AF:ID  0.00963026:0.00410874:1.72125:0.623745:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.401015 ES:SE:LP:AF:ID  -0.00654128:0.0040709:0.958607:0.401015:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.102565 ES:SE:LP:AF:ID  -0.00113781:0.00655634:0.0655015:0.102565:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456972 ES:SE:LP:AF:ID  0.00493754:0.00400314:0.657577:0.456972:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074471 ES:SE:LP:AF:ID  0.00164446:0.00787979:0.0809219:0.074471:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.241599 ES:SE:LP:AF:ID  0.00593856:0.00457472:0.721246:0.241599:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913953 ES:SE:LP:AF:ID  -0.00891567:0.0057411:0.920819:0.913953:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.117978 ES:SE:LP:AF:ID  -0.000355817:0.00381856:0.0315171:0.117978:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067216 ES:SE:LP:AF:ID  0.00929277:0.00561801:1.00877:0.067216:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.513498 ES:SE:LP:AF:ID  0.00377228:0.002835:0.744727:0.513498:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033036 ES:SE:LP:AF:ID  -0.00324658:0.0071474:0.187087:0.033036:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036638 ES:SE:LP:AF:ID  -0.00335813:0.00649522:0.21467:0.036638:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036724 ES:SE:LP:AF:ID  -0.00286105:0.00647318:0.180456:0.036724:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036473 ES:SE:LP:AF:ID  -0.00344311:0.00651556:0.221849:0.036473:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016215 ES:SE:LP:AF:ID  -0.00794797:0.0100814:0.366532:0.016215:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037001 ES:SE:LP:AF:ID  -0.00408752:0.00644367:0.275724:0.037001:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037089 ES:SE:LP:AF:ID  -0.00363379:0.00642301:0.244125:0.037089:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101179 ES:SE:LP:AF:ID  -0.00319808:0.00468526:0.309804:0.101179:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959027 ES:SE:LP:AF:ID  0.00338235:0.00619016:0.236572:0.959027:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031117 ES:SE:LP:AF:ID  -0.00746327:0.0113076:0.29243:0.031117:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053322 ES:SE:LP:AF:ID  0.0137274:0.00890688:0.920819:0.053322:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036613 ES:SE:LP:AF:ID  -0.00303592:0.00646256:0.19382:0.036613:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036867 ES:SE:LP:AF:ID  -0.00277761:0.00641134:0.180456:0.036867:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.841988 ES:SE:LP:AF:ID  0.00143715:0.00331543:0.180456:0.841988:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056958 ES:SE:LP:AF:ID  -0.000461774:0.00532613:0.0315171:0.056958:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12376  ES:SE:LP:AF:ID  0.00013432:0.00362171:0.0132283:0.12376:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025765 ES:SE:LP:AF:ID  0.0177261:0.00895255:1.31876:0.025765:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.123012 ES:SE:LP:AF:ID  -0.000161115:0.00362342:0.0177288:0.123012:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.133562 ES:SE:LP:AF:ID  -0.000985005:0.00357373:0.107905:0.133562:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.010845 ES:SE:LP:AF:ID  -0.0260639:0.0132421:1.3098:0.010845:rs181876450
1   752478  rs146277091 G   A   .   PASS    AF=0.036843 ES:SE:LP:AF:ID  -0.00358358:0.00634276:0.244125:0.036843:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.837228 ES:SE:LP:AF:ID  0.00384008:0.003204:0.638272:0.837228:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836838 ES:SE:LP:AF:ID  0.00379008:0.00320047:0.619789:0.836838:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.867934 ES:SE:LP:AF:ID  0.00285377:0.00342832:0.387216:0.867934:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131739 ES:SE:LP:AF:ID  -0.00264252:0.0034347:0.356547:0.131739:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037396 ES:SE:LP:AF:ID  -0.00327015:0.00623106:0.221849:0.037396:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037647 ES:SE:LP:AF:ID  -0.00352683:0.00619097:0.244125:0.037647:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.86728  ES:SE:LP:AF:ID  0.00280625:0.00342168:0.387216:0.86728:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.867351 ES:SE:LP:AF:ID  0.00288965:0.00342251:0.39794:0.867351:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037592 ES:SE:LP:AF:ID  -0.00316987:0.00621904:0.21467:0.037592:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.867273 ES:SE:LP:AF:ID  0.00280588:0.00342144:0.387216:0.867273:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.836301 ES:SE:LP:AF:ID  0.00381136:0.00319209:0.638272:0.836301:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.03757  ES:SE:LP:AF:ID  -0.0029529:0.00623119:0.19382:0.03757:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.836963 ES:SE:LP:AF:ID  0.00382841:0.00320136:0.638272:0.836963:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013618 ES:SE:LP:AF:ID  -0.00740437:0.0113038:0.29243:0.013618:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.837907 ES:SE:LP:AF:ID  0.00349904:0.00324162:0.552842:0.837907:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.867508 ES:SE:LP:AF:ID  0.0027529:0.00341666:0.376751:0.867508:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.867106 ES:SE:LP:AF:ID  0.00267009:0.00340847:0.366532:0.867106:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.866005 ES:SE:LP:AF:ID  0.00258121:0.00340218:0.346787:0.866005:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867199 ES:SE:LP:AF:ID  0.00266837:0.00341083:0.366532:0.867199:rs4951929