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}
*********************************************************************
* 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-91/ieu-a-91.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-91/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Wed Feb 5 11:23:43 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-91/ieu-a-91.vcf.gz ...
Read summary statistics for 2328688 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, 1118400 SNPs remain.
After merging with regression SNP LD, 1118400 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1624 (0.0091)
Lambda GC: 1.0291
Mean Chi^2: 1.0771
Intercept: 0.8717 (0.0068)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 11:24:11 2020
Total time elapsed: 27.78s
{
"af_correlation": 0.9101,
"inflation_factor": 1.0475,
"mean_EFFECT": 0.0011,
"n": 72546,
"n_snps": 2328688,
"n_clumped_hits": 11,
"n_p_sig": 335,
"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": 3098,
"n_miss_AF_reference": 19094,
"n_est": 68596.8534,
"ratio_se_n": 0.9724,
"mean_diff": -0.0008,
"ratio_diff": 131.473,
"sd_y_est1": 3.8175,
"sd_y_est2": 3.7121,
"r2_sum1": 0.1173,
"r2_sum2": 0.0081,
"r2_sum3": 0.0085,
"r2_sum4": 0.0094,
"ldsc_nsnp_merge_refpanel_ld": 1118400,
"ldsc_nsnp_merge_regression_ld": 1118400,
"ldsc_observed_scale_h2_beta": 0.1624,
"ldsc_observed_scale_h2_se": 0.0091,
"ldsc_intercept_beta": 0.8717,
"ldsc_intercept_se": 0.0068,
"ldsc_lambda_gc": 1.0291,
"ldsc_mean_chisq": 1.0771,
"ldsc_ratio": -1.6641
}
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 |
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 | 42 | 0 | 2328688 | 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 | 8.579384e+00 | 5.655840e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.884627e+07 | 5.565200e+07 | 1.15230e+04 | 3.268457e+07 | 7.025224e+07 | 1.143796e+08 | 2.491722e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.123100e-03 | 3.396810e-02 | -3.70000e-01 | -1.700000e-02 | 8.000000e-04 | 1.900000e-02 | 4.100000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.019660e-02 | 1.584440e-02 | 1.80000e-02 | 2.000000e-02 | 2.400000e-02 | 3.300000e-02 | 1.800000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.923219e-01 | 2.920883e-01 | 0.00000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.923636e-01 | 2.920938e-01 | 0.00000e+00 | 2.372779e-01 | 4.938422e-01 | 7.460822e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 3098 | 0.9986696 | NA | NA | NA | NA | NA | 3.680300e-01 | 2.679996e-01 | 8.00000e-03 | 1.340000e-01 | 3.080000e-01 | 5.670000e-01 | 9.920000e-01 | ▇▆▃▃▂ |
numeric | AF_reference | 19094 | 0.9918005 | NA | NA | NA | NA | NA | 3.701374e-01 | 2.502366e-01 | 1.99700e-04 | 1.599440e-01 | 3.130990e-01 | 5.523160e-01 | 1.000000e+00 | ▇▇▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.218866e+04 | 1.164639e+04 | 2.79669e+04 | 5.522060e+04 | 6.768500e+04 | 7.120100e+04 | 7.254600e+04 | ▁▂▁▂▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 990380 | rs3121561 | C | T | 0.0008 | 0.033 | 0.9800000 | 0.9806592 | 0.267 | 0.343450 | 54027.8 |
1 | 998501 | rs3813193 | G | C | 0.0590 | 0.034 | 0.0810009 | 0.0826887 | 0.150 | 0.206669 | 48235.8 |
1 | 1003629 | rs4075116 | C | T | 0.0470 | 0.026 | 0.0649995 | 0.0706544 | 0.737 | 0.720647 | 66954.0 |
1 | 1005806 | rs3934834 | C | T | 0.0650 | 0.034 | 0.0569994 | 0.0559064 | 0.119 | 0.223442 | 45178.0 |
1 | 1017170 | rs3766193 | C | G | 0.0110 | 0.024 | 0.6499995 | 0.6467130 | 0.569 | 0.575479 | 69418.1 |
1 | 1017197 | rs3766192 | C | T | 0.0110 | 0.022 | 0.6300007 | 0.6170751 | 0.576 | 0.511182 | 70076.3 |
1 | 1017587 | rs3766191 | C | T | 0.0610 | 0.036 | 0.0890000 | 0.0901809 | 0.096 | 0.171126 | 45085.2 |
1 | 1018562 | rs9442371 | C | T | 0.0110 | 0.022 | 0.5999997 | 0.6170751 | 0.592 | 0.530152 | 68747.5 |
1 | 1018704 | rs9442372 | A | G | 0.0110 | 0.022 | 0.6200004 | 0.6170751 | 0.602 | 0.611022 | 68744.6 |
1 | 1021346 | rs10907177 | A | G | 0.0570 | 0.036 | 0.1199999 | 0.1133455 | 0.127 | 0.178914 | 45011.5 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51212875 | rs2238837 | A | C | 0.037 | 0.033 | 0.2599998 | 0.2621976 | 0.392 | 0.3724040 | 40723.0 |
22 | 51216564 | rs9616970 | T | C | -0.032 | 0.047 | 0.5000000 | 0.4959657 | 0.150 | 0.1563500 | 46042.6 |
22 | 51217134 | rs117417021 | A | G | 0.012 | 0.034 | 0.7099994 | 0.7241325 | 0.442 | 0.2671730 | 39020.0 |
22 | 51222100 | rs114553188 | G | T | -0.170 | 0.067 | 0.0120000 | 0.0111707 | 0.067 | 0.0880591 | 40017.5 |
22 | 51223637 | rs375798137 | G | A | -0.140 | 0.066 | 0.0329997 | 0.0339040 | 0.067 | 0.0788738 | 42190.3 |
23 | 35921591 | rs2204667 | C | G | -0.025 | 0.027 | 0.3599996 | 0.3544845 | 0.167 | NA | 65080.9 |
23 | 51666786 | rs14115 | A | G | -0.047 | 0.055 | 0.3900004 | 0.3928028 | 0.025 | NA | 40295.0 |
23 | 70163799 | rs1626496 | A | C | -0.058 | 0.043 | 0.1800002 | 0.1773893 | 0.075 | NA | 45423.4 |
23 | 91415872 | rs6562597 | G | A | 0.057 | 0.093 | 0.5400003 | 0.5399403 | 0.008 | 0.0021192 | 34675.9 |
23 | 118495837 | rs12882977 | G | A | 0.022 | 0.019 | 0.2500000 | 0.2469070 | 0.509 | 0.2307280 | 72369.7 |
1 990380 rs3121561 C T . PASS AF=0.267 ES:SE:LP:AF:SS:ID 0.0008:0.033:0.00877392:0.267:54027.8:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:SS:ID 0.059:0.034:1.09151:0.15:48235.8:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.737 ES:SE:LP:AF:SS:ID 0.047:0.026:1.18709:0.737:66954:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.119 ES:SE:LP:AF:SS:ID 0.065:0.034:1.24413:0.119:45178:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.569 ES:SE:LP:AF:SS:ID 0.011:0.024:0.187087:0.569:69418.1:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.576 ES:SE:LP:AF:SS:ID 0.011:0.022:0.200659:0.576:70076.3:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.096 ES:SE:LP:AF:SS:ID 0.061:0.036:1.05061:0.096:45085.2:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.592 ES:SE:LP:AF:SS:ID 0.011:0.022:0.221849:0.592:68747.5:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.602 ES:SE:LP:AF:SS:ID 0.011:0.022:0.207608:0.602:68744.6:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.127 ES:SE:LP:AF:SS:ID 0.057:0.036:0.920819:0.127:45011.5:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.717 ES:SE:LP:AF:SS:ID 0.028:0.024:0.60206:0.717:68399:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.113 ES:SE:LP:AF:SS:ID 0.056:0.037:0.920819:0.113:45034.1:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.027:0.025:0.552842:0.725:68068.4:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.567 ES:SE:LP:AF:SS:ID 0.014:0.024:0.251812:0.567:65424.8:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:SS:ID -0.014:0.026:0.244125:0.6:53713.8:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.083 ES:SE:LP:AF:SS:ID -0.014:0.033:0.173925:0.083:46958:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.086 ES:SE:LP:AF:SS:ID -0.016:0.035:0.19382:0.086:42018.8:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.658 ES:SE:LP:AF:SS:ID -0.015:0.027:0.229148:0.658:52260:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.029:0.042:0.30103:0.05:44776.8:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.075 ES:SE:LP:AF:SS:ID 0.013:0.035:0.154902:0.075:51484.4:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.067 ES:SE:LP:AF:SS:ID 0.023:0.035:0.29243:0.067:52590.3:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.052 ES:SE:LP:AF:SS:ID 0.042:0.042:0.49485:0.052:43300:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.067 ES:SE:LP:AF:SS:ID 0.02:0.034:0.251812:0.067:53608:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.027:0.042:0.283997:0.05:44972.6:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.398 ES:SE:LP:AF:SS:ID -0.0036:0.034:0.0362122:0.398:40946.1:rs7548798
1 1060608 rs17160824 G A . PASS AF=0.058 ES:SE:LP:AF:SS:ID 0.027:0.042:0.275724:0.058:45627.9:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.055 ES:SE:LP:AF:SS:ID 0.026:0.042:0.275724:0.055:44971.7:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.029:0.043:0.30103:0.05:44971.7:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.412 ES:SE:LP:AF:SS:ID -0.0087:0.028:0.124939:0.412:50937.1:rs11807848
1 1062638 rs9442373 C A . PASS AF=0.552 ES:SE:LP:AF:SS:ID 0.019:0.027:0.318759:0.552:50519.7:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.754 ES:SE:LP:AF:SS:ID -0.0037:0.037:0.0362122:0.754:47178.9:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.083 ES:SE:LP:AF:SS:ID -0.018:0.035:0.221849:0.083:45831:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:SS:ID 0.038:0.03:0.677781:0.675:48362:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.683 ES:SE:LP:AF:SS:ID 0.049:0.033:0.853872:0.683:46266.3:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.924 ES:SE:LP:AF:SS:ID -0.012:0.051:0.0861861:0.924:44719.1:rs4970357
1 1087683 rs9442380 T C . PASS AF=0.912 ES:SE:LP:AF:SS:ID -0.04:0.047:0.39794:0.912:48051.2:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.966 ES:SE:LP:AF:SS:ID -0.11:0.067:0.920819:0.966:42196.6:rs4970358
1 1097335 rs9442385 T G . PASS AF=0.942 ES:SE:LP:AF:SS:ID -0.057:0.045:0.677781:0.942:45035.4:rs9442385
1 1099342 rs9660710 A C . PASS AF=0.941 ES:SE:LP:AF:SS:ID -0.057:0.044:0.69897:0.941:47342:rs9660710
1 1100217 rs1891905 C T . PASS AF=0.958 ES:SE:LP:AF:SS:ID -0.1:0.069:0.853872:0.958:42196.8:rs1891905
1 1106473 rs4970420 G A . PASS AF=0.144 ES:SE:LP:AF:SS:ID -0.11:0.036:2.65758:0.144:43802:rs4970420
1 1119858 rs1320565 C T . PASS AF=0.092 ES:SE:LP:AF:SS:ID 0.013:0.047:0.113509:0.092:36861:rs1320565
1 1120431 rs1320571 G A . PASS AF=0.042 ES:SE:LP:AF:SS:ID 0.012:0.073:0.0604807:0.042:33301.2:rs1320571
1 1121014 rs3813204 G A . PASS AF=0.112 ES:SE:LP:AF:SS:ID -0.015:0.043:0.136677:0.112:37338.7:rs3813204
1 1121794 rs11260549 G A . PASS AF=0.125 ES:SE:LP:AF:SS:ID -0.0056:0.035:0.0604807:0.125:49576:rs11260549
1 1124663 rs6684820 G A . PASS AF=0.267 ES:SE:LP:AF:SS:ID -0.004:0.024:0.0604807:0.267:67590.7:rs6684820
1 1125553 rs10907174 A T . PASS AF=0.225 ES:SE:LP:AF:SS:ID -0.0073:0.026:0.107905:0.225:62807.5:rs10907174
1 1129672 rs11260554 G T . PASS AF=0.125 ES:SE:LP:AF:SS:ID -0.0085:0.035:0.091515:0.125:48127.6:rs11260554
1 1130727 rs10907175 A C . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.018:0.038:0.19382:0.1:47449.2:rs10907175
1 1135242 rs9729550 A C . PASS AF=0.275 ES:SE:LP:AF:SS:ID -0.0051:0.023:0.0809219:0.275:67505:rs9729550