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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_STR/ukb-d-I9_STR_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:35:19.954363",
"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/ukb-d-import/processed/ukb-d-I9_STR/ukb-d-I9_STR.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_STR/ukb-d-I9_STR_data.vcf.gz; Date=Mon Nov 25 16:23:07 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/ukb-d-I9_STR/ukb-d-I9_STR.vcf.gz; Date=Sun May 10 23:23:55 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/ukb-d-import/processed/ukb-d-I9_STR/ukb-d-I9_STR.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/ukb-d-import/processed/ukb-d-I9_STR/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 16:57:44 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_STR/ukb-d-I9_STR.vcf.gz ...
Read summary statistics for 11574898 SNPs.
Dropped 9887 SNPs with duplicated rs numbers.
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, 1282676 SNPs remain.
After merging with regression SNP LD, 1282676 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0016 (0.0012)
Lambda GC: 1.0189
Mean Chi^2: 1.0205
Intercept: 1.0091 (0.0056)
Ratio: 0.4408 (0.2746)
Analysis finished at Mon Nov 25 16:59:27 2019
Total time elapsed: 1.0m:43.1s
{
"af_correlation": 0.9478,
"inflation_factor": 1.0238,
"mean_EFFECT": -1.3655e-07,
"n": 361194,
"n_snps": 11574898,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1165274,
"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": 248572,
"n_est": 361789.0042,
"ratio_se_n": 1.0008,
"mean_diff": -6.2381e-07,
"ratio_diff": 1.0927,
"sd_y_est1": 0.1025,
"sd_y_est2": 0.1026,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1282676,
"ldsc_nsnp_merge_regression_ld": 1282676,
"ldsc_observed_scale_h2_beta": 0.0016,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0091,
"ldsc_intercept_se": 0.0056,
"ldsc_lambda_gc": 1.0189,
"ldsc_mean_chisq": 1.0205,
"ldsc_ratio": 0.4439
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | TRUE |
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 |
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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 11565618 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 52426 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 31779 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.072917e+00 | 6.184028e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.886035e+07 | 5.599487e+07 | 3.02000e+02 | 3.265264e+07 | 6.987371e+07 | 1.147351e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.000000e-07 | 8.560000e-04 | -9.40180e-03 | -3.171000e-04 | -5.400000e-06 | 3.065000e-04 | 1.100590e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.696000e-04 | 5.251000e-04 | 1.98400e-04 | 2.746000e-04 | 4.203000e-04 | 9.122000e-04 | 3.039500e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.962638e-01 | 2.898253e-01 | 1.00000e-07 | 2.442980e-01 | 4.949382e-01 | 7.473276e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.962633e-01 | 2.898256e-01 | 1.00000e-07 | 2.442979e-01 | 4.949372e-01 | 7.473273e-01 | 9.999998e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.221476e-01 | 2.605254e-01 | 3.26200e-03 | 1.868300e-02 | 1.031020e-01 | 3.546160e-01 | 9.967380e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 248572 | 0.9785249 | NA | NA | NA | NA | NA | 2.229057e-01 | 2.518229e-01 | 0.00000e+00 | 1.577480e-02 | 1.218050e-01 | 3.548320e-01 | 1.000000e+00 | ▇▂▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.611940e+05 | 0.000000e+00 | 3.61194e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0006110 | 0.0004226 | 0.1482269 | 0.1482258 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | -0.0005668 | 0.0003993 | 0.1558009 | 0.1557992 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | -0.0003470 | 0.0004489 | 0.4395254 | 0.4395246 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | -0.0004217 | 0.0010712 | 0.6938267 | 0.6938255 | 0.0156880 | 0.0045926 | 361194 |
1 | 730087 | rs148120343 | T | C | -0.0007336 | 0.0005563 | 0.1872669 | 0.1872664 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | -0.0004111 | 0.0003787 | 0.2776540 | 0.2776530 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | -0.0005020 | 0.0004040 | 0.2139681 | 0.2139668 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | -0.0004117 | 0.0003789 | 0.2772158 | 0.2772157 | 0.1209650 | 0.1525560 | 361194 |
1 | 740284 | rs61770167 | C | T | -0.0009230 | 0.0017335 | 0.5944194 | 0.5944192 | 0.0057851 | 0.0023962 | 361194 |
1 | 749963 | rs529266287 | T | TAA | 0.0002780 | 0.0003735 | 0.4567557 | 0.4567550 | 0.8697420 | 0.7641770 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0000604 | 0.0004375 | 0.8901750 | 0.8901747 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | -0.0006378 | 0.0004808 | 0.1846971 | 0.1846950 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | -0.0002747 | 0.0002314 | 0.2351267 | 0.2351257 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | -0.0003162 | 0.0002367 | 0.1815002 | 0.1814988 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | -0.0002144 | 0.0002176 | 0.3243172 | 0.3243158 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | -0.0002814 | 0.0002314 | 0.2240149 | 0.2240148 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | -0.0003690 | 0.0002415 | 0.1265290 | 0.1265287 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | -0.0002808 | 0.0002434 | 0.2485650 | 0.2485655 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | -0.0003209 | 0.0002314 | 0.1655259 | 0.1655256 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | 0.0003621 | 0.0007938 | 0.6483044 | 0.6483057 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID -0.000611015:0.000422606:0.829073:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -0.000566759:0.000399311:0.80743:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID -0.000347005:0.000448909:0.357016:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID -0.000421702:0.00107121:0.158749:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.00073359:0.000556294:0.727539:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID -0.000411128:0.000378708:0.556496:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID -0.00050202:0.000403965:0.669651:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID -0.000411724:0.000378912:0.557182:0.120965:361194:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00578512 ES:SE:LP:AF:SS:ID -0.000923006:0.00173353:0.225907:0.00578512:361194:rs61770167
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID 0.000277994:0.000373547:0.340316:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID -0.000203225:0.00036995:0.234497:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID -0.00025363:0.000365675:0.311635:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID -0.000196373:0.000369435:0.225455:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID 0.000160937:0.000360002:0.183863:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID 0.000170175:0.000365968:0.192511:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID -0.000178656:0.000360905:0.207199:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID -0.000865048:0.000654763:0.729442:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID 0.000166706:0.000359628:0.191809:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID 0.000188867:0.000359792:0.222117:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID 0.000174127:0.000359614:0.201874:0.870481:361194:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00504367 ES:SE:LP:AF:SS:ID 0.00243219:0.00184619:0.726531:0.00504367:361194:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501064 ES:SE:LP:AF:SS:ID 0.0024045:0.00185114:0.712272:0.00501064:361194:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00558665 ES:SE:LP:AF:SS:ID 0.00183012:0.00178808:0.514182:0.00558665:361194:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID 0.000167519:0.000358981:0.193311:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID -0.000226769:0.000366293:0.270953:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID 0.00015984:0.000358117:0.183523:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID 0.000208514:0.000357791:0.25178:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID 0.000181069:0.000358426:0.212233:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID 0.000181203:0.000358451:0.2124:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID 0.000180666:0.000358462:0.211648:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID 0.000160337:0.000359375:0.183437:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID -0.000142554:0.000417616:0.134992:0.0988442:361194:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647588 ES:SE:LP:AF:SS:ID 0.0011948:0.00161536:0.337701:0.00647588:361194:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID 0.000212936:0.000364731:0.25232:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID 0.000295401:0.000357673:0.388421:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID 0.00018057:0.000361146:0.209659:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID 0.000157395:0.000361219:0.178466:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -0.000121778:0.000432446:0.108882:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000232173:0.000365334:0.279761:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000232128:0.000365334:0.279695:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID 0.000232209:0.000365341:0.279807:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID 0.000209001:0.000365549:0.246038:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID -0.000235969:0.000365838:0.284899:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -0.000267969:0.000398264:0.300121:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID 0.000300245:0.000357539:0.396805:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID 0.000832121:0.000352237:1.74093:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID 0.000513166:0.000283486:1.15326:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID -0.000718258:0.000390574:1.18099:0.105921:361194:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00768395 ES:SE:LP:AF:SS:ID 0.00187908:0.00145116:0.709155:0.00768395:361194:rs12562811
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID -0.000169929:0.00036072:0.195464:0.128938:361194:rs762168062