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"FORMAT.2": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
"FORMAT.3": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
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"META.1": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
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"META.7": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
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"file_date": "2019-10-26T21:45:53.172743",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006907/EBI-a-GCST006907_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/hg38/hg38.fa; 1.1.1",
"reference": "file:/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006907/EBI-a-GCST006907.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006907/EBI-a-GCST006907_data.vcf.gz; Date=Sat Oct 26 22:03:15 2019",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST006907/ebi-a-GCST006907.vcf.gz; Date=Sat May 9 23:25:49 2020"
}
*********************************************************************
* 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/ebi_gwas_import/processed/EBI-a-GCST006907/EBI-a-GCST006907.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/ebi_gwas_import/processed/EBI-a-GCST006907/ldsc.txt \
--snplist /data/ref/snplist.gz \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Sat Oct 26 22:27:33 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006907/EBI-a-GCST006907.vcf.gz ...
and extracting SNPs specified in /data/ref/snplist.gz ...
Traceback (most recent call last):
File "./ldsc/ldsc.py", line 647, in <module>
sumstats.estimate_h2(args, log)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
args, log, args.h2)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 246, in _read_ld_sumstats
sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 165, in _read_sumstats
sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna, slh=args.snplist)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/parse.py", line 85, in sumstats
x = read_vcf(fh, alleles, slh)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/parse.py", line 161, in read_vcf
with gzip.open(slh) as f:
File "/mnt/storage/home/gh13047/mr-eve/conda/ldsc/lib/python2.7/gzip.py", line 34, in open
return GzipFile(filename, mode, compresslevel)
File "/mnt/storage/home/gh13047/mr-eve/conda/ldsc/lib/python2.7/gzip.py", line 94, in __init__
fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: '/data/ref/snplist.gz'
Analysis finished at Sat Oct 26 22:28:28 2019
Total time elapsed: 54.22s
{
"af_correlation": 0.9433,
"inflation_factor": 1.1324,
"mean_EFFECT": 0.0163,
"n": "-Inf",
"n_snps": 8418349,
"n_clumped_hits": 4,
"n_p_sig": 49,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 177462,
"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": "NA",
"ldsc_nsnp_merge_regression_ld": "NA",
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": "NA",
"ldsc_intercept_se": "NA",
"ldsc_lambda_gc": "NA",
"ldsc_mean_chisq": "NA",
"ldsc_ratio": "NA"
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | TRUE |
is_snpid_non_unique | TRUE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | TRUE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | TRUE |
ldsc_intercept_beta | TRUE |
n_clumped_hits | FALSE |
r2_sum1 | FALSE |
r2_sum2 | FALSE |
r2_sum3 | FALSE |
r2_sum4 | FALSE |
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 SNPsn_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:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 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.
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.
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.
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.
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
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
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 | 59 | 0 | 8400450 | 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 | 8400475 | 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 | 8.647044e+00 | 5.751974e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.853467e+07 | 5.640802e+07 | 828.0000 | 3.216359e+07 | 6.894667e+07 | 1.143224e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.626040e-02 | 8.157910e-02 | -2.0652 | -2.150000e-02 | 7.500000e-03 | 4.140000e-02 | 1.595400e+00 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.049720e-02 | 4.915760e-02 | 0.0221 | 2.820000e-02 | 3.910000e-02 | 7.420000e-02 | 1.390800e+00 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.797949e-01 | 2.937775e-01 | 0.0000 | 2.202997e-01 | 4.728997e-01 | 7.345003e-01 | 9.998000e-01 | ▇▇▇▆▆ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.797948e-01 | 2.937773e-01 | 0.0000 | 2.203122e-01 | 4.729235e-01 | 7.344951e-01 | 9.998116e-01 | ▇▇▇▆▆ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.519081e-01 | 2.591870e-01 | 0.0101 | 4.140000e-02 | 1.467000e-01 | 3.970000e-01 | 9.899000e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 177462 | 0.9788748 | NA | NA | NA | NA | NA | NA | NA | 2.520587e-01 | 2.533801e-01 | 0.0000 | 4.412940e-02 | 1.607430e-01 | 3.953670e-01 | 1.000000e+00 | ▇▃▂▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 662622 | rs61769339 | G | A | 0.0760 | 0.0613 | 0.2154999 | 0.2150478 | 0.1293 | 0.1475640 | NA |
1 | 693731 | rs12238997 | A | G | 0.0321 | 0.0592 | 0.5869999 | 0.5876603 | 0.1361 | 0.1417730 | NA |
1 | 729679 | rs4951859 | C | G | -0.0237 | 0.0544 | 0.6629000 | 0.6630822 | 0.8283 | 0.6399760 | NA |
1 | 731718 | rs142557973 | T | C | 0.0617 | 0.0564 | 0.2746003 | 0.2739674 | 0.1425 | 0.1543530 | NA |
1 | 732809 | rs12131618 | T | C | 0.0479 | 0.0790 | 0.5441003 | 0.5442962 | 0.0724 | 0.0615016 | NA |
1 | 734349 | rs141242758 | T | C | 0.0636 | 0.0566 | 0.2605002 | 0.2611510 | 0.1410 | 0.1525560 | NA |
1 | 736289 | rs79010578 | T | A | 0.0402 | 0.0611 | 0.5114003 | 0.5105781 | 0.1465 | 0.1395770 | NA |
1 | 751756 | rs143225517 | T | C | 0.0539 | 0.0474 | 0.2556001 | 0.2554836 | 0.1462 | 0.2422120 | NA |
1 | 752566 | rs3094315 | G | A | -0.0224 | 0.0423 | 0.5953002 | 0.5964234 | 0.8289 | 0.7182510 | NA |
1 | 752721 | rs3131972 | A | G | -0.0218 | 0.0429 | 0.6119994 | 0.6113422 | 0.8126 | 0.6533550 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51224600 | rs187908482 | G | A | -0.0686 | 0.0630 | 0.2757998 | 0.2762029 | 0.1091 | 0.0387380 | NA |
22 | 51228910 | rs145146472 | G | A | -0.0149 | 0.0400 | 0.7096006 | 0.7095206 | 0.2888 | 0.2276360 | NA |
22 | 51229805 | rs9616985 | T | C | -0.0057 | 0.0662 | 0.9320000 | 0.9313848 | 0.0720 | 0.0730831 | NA |
22 | 51229855 | rs144549712 | G | A | 0.0580 | 0.0656 | 0.3762002 | 0.3766172 | 0.1301 | 0.1160140 | NA |
22 | 51233300 | rs9616839 | C | T | 0.0296 | 0.0455 | 0.5153995 | 0.5153374 | 0.3318 | 0.3146960 | NA |
22 | 51234799 | rs191117135 | G | A | -0.2570 | 0.4750 | 0.5884994 | 0.5884713 | 0.0129 | 0.0059904 | NA |
22 | 51237063 | rs3896457 | T | C | -0.0043 | 0.0474 | 0.9282001 | 0.9277172 | 0.2761 | 0.2050720 | NA |
22 | 51238249 | rs149733995 | A | C | 0.0980 | 0.0910 | 0.2819000 | 0.2815146 | 0.0718 | NA | NA |
23 | 46256106 | rs12007097 | G | C | -0.0052 | 0.1047 | 0.9602999 | 0.9603888 | 0.9721 | 0.6821190 | NA |
23 | 100784211 | rs188350543 | C | A | -0.0187 | 0.0353 | 0.5956004 | 0.5962887 | 0.7418 | 0.6498010 | NA |
1 662622 rs61769339 G A . PASS AF=0.1293 ES:SE:LP:AF:ID 0.076:0.0613:0.666553:0.1293:rs61769339
1 693731 rs12238997 A G . PASS AF=0.1361 ES:SE:LP:AF:ID 0.0321:0.0592:0.231362:0.1361:rs12238997
1 729679 rs4951859 C G . PASS AF=0.8283 ES:SE:LP:AF:ID -0.0237:0.0544:0.178552:0.8283:rs4951859
1 731718 rs58276399 T C . PASS AF=0.1425 ES:SE:LP:AF:ID 0.0617:0.0564:0.561299:0.1425:rs58276399
1 732809 rs12131618 T C . PASS AF=0.0724 ES:SE:LP:AF:ID 0.0479:0.079:0.264321:0.0724:rs12131618
1 734349 rs141242758 T C . PASS AF=0.141 ES:SE:LP:AF:ID 0.0636:0.0566:0.584192:0.141:rs141242758
1 736289 rs79010578 T A . PASS AF=0.1465 ES:SE:LP:AF:ID 0.0402:0.0611:0.291239:0.1465:rs79010578
1 751756 rs28527770 T C . PASS AF=0.1462 ES:SE:LP:AF:ID 0.0539:0.0474:0.592439:0.1462:rs28527770
1 752566 rs3094315 G A . PASS AF=0.8289 ES:SE:LP:AF:ID -0.0224:0.0423:0.225264:0.8289:rs3094315
1 752721 rs3131972 A G . PASS AF=0.8126 ES:SE:LP:AF:ID -0.0218:0.0429:0.213249:0.8126:rs3131972
1 752894 rs3131971 T C . PASS AF=0.8161 ES:SE:LP:AF:ID -0.0283:0.0446:0.279262:0.8161:rs3131971
1 753405 rs3115860 C A . PASS AF=0.8486 ES:SE:LP:AF:ID -0.0539:0.0455:0.626353:0.8486:rs3115860
1 753474 rs2073814 C G . PASS AF=0.816 ES:SE:LP:AF:ID -0.0349:0.0455:0.3534:0.816:rs2073814
1 753541 rs2073813 G A . PASS AF=0.1512 ES:SE:LP:AF:ID 0.0609:0.048:0.68867:0.1512:rs2073813
1 754182 rs3131969 A G . PASS AF=0.8477 ES:SE:LP:AF:ID -0.0748:0.0479:0.924453:0.8477:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8475 ES:SE:LP:AF:ID -0.0751:0.048:0.929593:0.8475:rs3131968
1 754334 rs3131967 T C . PASS AF=0.8374 ES:SE:LP:AF:ID -0.0594:0.0487:0.652865:0.8374:rs3131967
1 754503 rs3115859 G A . PASS AF=0.8231 ES:SE:LP:AF:ID -0.0314:0.0462:0.304168:0.8231:rs3115859
1 754964 rs3131966 C T . PASS AF=0.8141 ES:SE:LP:AF:ID -0.0185:0.0469:0.158453:0.8141:rs3131966
1 755775 rs3131965 A G . PASS AF=0.7959 ES:SE:LP:AF:ID -0.0042:0.0531:0.0281214:0.7959:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8457 ES:SE:LP:AF:ID -0.0514:0.0468:0.564633:0.8457:rs3115858
1 756604 rs3131962 A G . PASS AF=0.8395 ES:SE:LP:AF:ID -0.0503:0.0485:0.523893:0.8395:rs3131962
1 756912 rs6699990 A G . PASS AF=0.0292 ES:SE:LP:AF:ID 0.1224:0.1381:0.425274:0.0292:rs6699990
1 757640 rs3115853 G A . PASS AF=0.8463 ES:SE:LP:AF:ID -0.0646:0.0485:0.737786:0.8463:rs3115853
1 757734 rs4951929 C T . PASS AF=0.851 ES:SE:LP:AF:ID -0.0656:0.0488:0.747633:0.851:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8482 ES:SE:LP:AF:ID -0.0556:0.0487:0.594483:0.8482:rs4951862
1 758144 rs3131956 A G . PASS AF=0.8373 ES:SE:LP:AF:ID -0.0625:0.0473:0.728856:0.8373:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8498 ES:SE:LP:AF:ID -0.0524:0.0491:0.543786:0.8498:rs3131954
1 759700 rs3115852 T C . PASS AF=0.8093 ES:SE:LP:AF:ID 0.0148:0.0548:0.10397:0.8093:rs3115852
1 759837 rs3115851 T A . PASS AF=0.8518 ES:SE:LP:AF:ID -0.0639:0.0496:0.704873:0.8518:rs3115851
1 760912 rs1048488 C T . PASS AF=0.8136 ES:SE:LP:AF:ID 0.0084:0.0499:0.0619308:0.8136:rs1048488
1 761147 rs3115850 T C . PASS AF=0.8137 ES:SE:LP:AF:ID -0.0212:0.0479:0.181642:0.8137:rs3115850
1 761732 rs2286139 C T . PASS AF=0.8294 ES:SE:LP:AF:ID -0.0647:0.0506:0.697236:0.8294:rs2286139
1 761752 rs1057213 C T . PASS AF=0.8529 ES:SE:LP:AF:ID -0.0469:0.0525:0.430626:0.8529:rs1057213
1 762273 rs3115849 G A . PASS AF=0.8399 ES:SE:LP:AF:ID -0.0751:0.0502:0.870632:0.8399:rs3115849
1 762472 rs145493205 C T . PASS AF=0.1112 ES:SE:LP:AF:ID -0.0453:0.0825:0.234555:0.1112:rs145493205
1 762485 rs12095200 C A . PASS AF=0.116 ES:SE:LP:AF:ID 0.0565:0.063:0.431798:0.116:rs12095200
1 762589 rs3115848 G C . PASS AF=0.8359 ES:SE:LP:AF:ID -0.046:0.0506:0.439496:0.8359:rs3115848
1 762592 rs3131950 C G . PASS AF=0.8354 ES:SE:LP:AF:ID -0.0483:0.0506:0.468266:0.8354:rs3131950
1 762601 rs3131949 T C . PASS AF=0.8346 ES:SE:LP:AF:ID -0.0707:0.0508:0.784891:0.8346:rs3131949
1 762632 rs3131948 T A . PASS AF=0.8348 ES:SE:LP:AF:ID -0.0545:0.051:0.54607:0.8348:rs3131948
1 764191 rs7515915 T G . PASS AF=0.1478 ES:SE:LP:AF:ID 0.0651:0.0508:0.699622:0.1478:rs7515915
1 766007 rs61768174 A C . PASS AF=0.1309 ES:SE:LP:AF:ID 0.0715:0.0553:0.707522:0.1309:rs61768174
1 768253 rs2977608 A C . PASS AF=0.7391 ES:SE:LP:AF:ID -0.0048:0.0376:0.046192:0.7391:rs2977608
1 768448 rs12562034 G A . PASS AF=0.1029 ES:SE:LP:AF:ID -0.0281:0.0459:0.267606:0.1029:rs12562034
1 769223 rs60320384 C G . PASS AF=0.1472 ES:SE:LP:AF:ID 0.0714:0.0514:0.784362:0.1472:rs60320384
1 769963 rs7518545 G A . PASS AF=0.0991 ES:SE:LP:AF:ID -0.0223:0.0486:0.189431:0.0991:rs7518545
1 771823 rs2977605 T C . PASS AF=0.85 ES:SE:LP:AF:ID -0.067:0.0506:0.730954:0.85:rs2977605
1 771967 rs59066358 G A . PASS AF=0.1492 ES:SE:LP:AF:ID 0.0737:0.0508:0.834162:0.1492:rs59066358
1 772755 rs2905039 A C . PASS AF=0.8502 ES:SE:LP:AF:ID -0.0661:0.0506:0.718058:0.8502:rs2905039