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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-93/ieu-a-93.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-93/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 20:27:02 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-93/ieu-a-93.vcf.gz ...
Read summary statistics for 2432135 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, 1147869 SNPs remain.
After merging with regression SNP LD, 1147869 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0873 (0.0045)
Lambda GC: 1.0219
Mean Chi^2: 1.0799
Intercept: 0.8188 (0.0069)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb 4 20:27:33 2020
Total time elapsed: 31.1s
{
"af_correlation": 0.9157,
"inflation_factor": 1.0475,
"mean_EFFECT": -0.0001,
"n": 158855,
"n_snps": 2432135,
"n_clumped_hits": 14,
"n_p_sig": 495,
"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": 4392,
"n_miss_AF_reference": 20518,
"n_est": 157451.6449,
"ratio_se_n": 0.9956,
"mean_diff": 0,
"ratio_diff": 10.7246,
"sd_y_est1": 2.5515,
"sd_y_est2": 2.5402,
"r2_sum1": 0.0343,
"r2_sum2": 0.0053,
"r2_sum3": 0.0053,
"r2_sum4": 0.0054,
"ldsc_nsnp_merge_refpanel_ld": 1147869,
"ldsc_nsnp_merge_regression_ld": 1147869,
"ldsc_observed_scale_h2_beta": 0.0873,
"ldsc_observed_scale_h2_se": 0.0045,
"ldsc_intercept_beta": 0.8188,
"ldsc_intercept_se": 0.0069,
"ldsc_lambda_gc": 1.0219,
"ldsc_mean_chisq": 1.0799,
"ldsc_ratio": -2.2678
}
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 | 2432135 | 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 | 8.584225e+00 | 5.656186e+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 | 7.884085e+07 | 5.563992e+07 | 1.1523e+04 | 3.270070e+07 | 7.026785e+07 | 1.143197e+08 | 2.492107e+08 | ▇▇▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -8.340000e-05 | 1.682730e-02 | -2.7000e-01 | -8.600000e-03 | -1.000000e-04 | 8.400000e-03 | 3.200000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.460930e-02 | 9.308400e-03 | 8.7000e-03 | 9.500000e-03 | 1.100000e-02 | 1.500000e-02 | 1.300000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.946316e-01 | 2.912545e-01 | 0.0000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.944448e-01 | 2.913477e-01 | 0.0000e+00 | 2.372779e-01 | 4.938422e-01 | 7.466370e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 4392 | 0.9981942 | NA | NA | NA | NA | NA | 3.593308e-01 | 2.743894e-01 | 8.0000e-03 | 1.230000e-01 | 2.920000e-01 | 5.590000e-01 | 9.920000e-01 | ▇▅▃▂▂ |
numeric | AF_reference | 20518 | 0.9915638 | NA | NA | NA | NA | NA | 3.628401e-01 | 2.548421e-01 | 1.9970e-04 | 1.485620e-01 | 3.017170e-01 | 5.469250e-01 | 1.000000e+00 | ▇▆▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.499675e+05 | 1.633244e+04 | 7.4199e+04 | 1.524290e+05 | 1.570460e+05 | 1.582780e+05 | 1.588550e+05 | ▁▁▁▁▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 775659 | rs2905035 | A | G | -0.0150 | 0.019 | 0.4500005 | 0.4298352 | 0.875 | 0.745008 | 82842 |
1 | 777122 | rs2980319 | A | T | -0.0150 | 0.019 | 0.4600002 | 0.4298352 | 0.875 | 0.747204 | 82842 |
1 | 779322 | rs4040617 | A | G | 0.0076 | 0.019 | 0.6999999 | 0.6891565 | 0.125 | 0.226438 | 82743 |
1 | 780785 | rs2977612 | T | A | -0.0067 | 0.019 | 0.7300002 | 0.7243647 | 0.866 | 0.669329 | 82842 |
1 | 785050 | rs2905062 | G | A | -0.0073 | 0.020 | 0.7099994 | 0.7151114 | 0.856 | 0.626997 | 82844 |
1 | 785989 | rs2980300 | T | C | -0.0085 | 0.019 | 0.6600001 | 0.6546091 | 0.873 | 0.626997 | 82717 |
1 | 990380 | rs3121561 | C | T | -0.0001 | 0.016 | 0.9900000 | 0.9950133 | 0.267 | 0.343450 | 117954 |
1 | 998501 | rs3813193 | G | C | 0.0200 | 0.016 | 0.2099999 | 0.2112995 | 0.150 | 0.206669 | 110598 |
1 | 1003629 | rs4075116 | C | T | 0.0150 | 0.012 | 0.2099999 | 0.2112995 | 0.737 | 0.720647 | 153331 |
1 | 1005806 | rs3934834 | C | T | 0.0210 | 0.015 | 0.1700000 | 0.1615133 | 0.119 | 0.223442 | 110581 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51216564 | rs9616970 | T | C | 0.0007 | 0.021 | 0.9699999 | 0.9734088 | 0.150 | 0.1563500 | 105130.0 |
22 | 51217134 | rs117417021 | A | G | 0.0130 | 0.017 | 0.4400003 | 0.4444467 | 0.442 | 0.2671730 | 82510.0 |
22 | 51222100 | rs114553188 | G | T | -0.0053 | 0.026 | 0.8400000 | 0.8384737 | 0.067 | 0.0880591 | 131442.0 |
22 | 51223637 | rs375798137 | G | A | -0.0072 | 0.026 | 0.7800007 | 0.7818392 | 0.067 | 0.0788738 | 131442.0 |
22 | 51229805 | rs9616985 | T | C | 0.0230 | 0.032 | 0.4600002 | 0.4722950 | 0.092 | 0.0730831 | 83684.0 |
23 | 35921591 | rs2204667 | C | G | -0.0039 | 0.012 | 0.7499995 | 0.7451811 | 0.167 | NA | 157372.0 |
23 | 51666786 | rs14115 | A | G | 0.0180 | 0.021 | 0.3800004 | 0.3913659 | 0.025 | NA | 144266.0 |
23 | 70163799 | rs1626496 | A | C | -0.0410 | 0.018 | 0.0219999 | 0.0227398 | 0.075 | NA | 148075.0 |
23 | 91415872 | rs6562597 | G | A | 0.0520 | 0.039 | 0.1900002 | 0.1824224 | 0.008 | 0.0021192 | 98130.8 |
23 | 118495837 | rs12882977 | G | A | 0.0098 | 0.009 | 0.2700001 | 0.2762029 | 0.509 | 0.2307280 | 158813.0 |
1 775659 rs2905035 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.015:0.019:0.346787:0.875:82842:rs2905035
1 777122 rs2980319 A T . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.015:0.019:0.337242:0.875:82842:rs2980319
1 779322 rs4040617 A G . PASS AF=0.125 ES:SE:LP:AF:SS:ID 0.0076:0.019:0.154902:0.125:82743:rs4040617
1 780785 rs2977612 T A . PASS AF=0.866 ES:SE:LP:AF:SS:ID -0.0067:0.019:0.136677:0.866:82842:rs2977612
1 785050 rs2905062 G A . PASS AF=0.856 ES:SE:LP:AF:SS:ID -0.0073:0.02:0.148742:0.856:82844:rs2905062
1 785989 rs2980300 T C . PASS AF=0.873 ES:SE:LP:AF:SS:ID -0.0085:0.019:0.180456:0.873:82717:rs2980300
1 990380 rs3121561 C T . PASS AF=0.267 ES:SE:LP:AF:SS:ID -0.0001:0.016:0.00436481:0.267:117954:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:SS:ID 0.02:0.016:0.677781:0.15:110598:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.737 ES:SE:LP:AF:SS:ID 0.015:0.012:0.677781:0.737:153331:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.119 ES:SE:LP:AF:SS:ID 0.021:0.015:0.769551:0.119:110581:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.569 ES:SE:LP:AF:SS:ID 0.0018:0.011:0.0604807:0.569:152313:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.576 ES:SE:LP:AF:SS:ID 0.0032:0.011:0.119186:0.576:153163:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.096 ES:SE:LP:AF:SS:ID 0.021:0.016:0.721246:0.096:110190:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.592 ES:SE:LP:AF:SS:ID 0.0037:0.01:0.142668:0.592:153346:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.602 ES:SE:LP:AF:SS:ID 0.0036:0.01:0.136677:0.602:153340:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.127 ES:SE:LP:AF:SS:ID 0.021:0.016:0.721246:0.127:109993:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.717 ES:SE:LP:AF:SS:ID 0.011:0.011:0.508638:0.717:154945:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.113 ES:SE:LP:AF:SS:ID 0.021:0.017:0.69897:0.113:110077:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.014:0.011:0.638272:0.725:154325:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.567 ES:SE:LP:AF:SS:ID 0.004:0.011:0.142668:0.567:137895:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:SS:ID 0.0028:0.012:0.091515:0.6:113403:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.083 ES:SE:LP:AF:SS:ID 0.012:0.015:0.376751:0.083:113635:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.086 ES:SE:LP:AF:SS:ID 0.0055:0.016:0.136677:0.086:96149.6:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.658 ES:SE:LP:AF:SS:ID 0.01:0.012:0.387216:0.658:111723:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.015:0.018:0.420216:0.05:128605:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.075 ES:SE:LP:AF:SS:ID 0.013:0.016:0.387216:0.075:121289:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.067 ES:SE:LP:AF:SS:ID 0.012:0.016:0.356547:0.067:131262:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.052 ES:SE:LP:AF:SS:ID 0.014:0.018:0.376751:0.052:127463:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.067 ES:SE:LP:AF:SS:ID 0.0097:0.015:0.283997:0.067:131206:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.013:0.018:0.346787:0.05:127496:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.398 ES:SE:LP:AF:SS:ID -0.0023:0.015:0.0555173:0.398:86260.2:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.017 ES:SE:LP:AF:SS:ID 0.005:0.034:0.0555173:0.017:91346:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.058 ES:SE:LP:AF:SS:ID 0.012:0.018:0.309804:0.058:128564:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.055 ES:SE:LP:AF:SS:ID 0.014:0.018:0.376751:0.055:127453:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.015:0.018:0.408935:0.05:127453:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.412 ES:SE:LP:AF:SS:ID 0.0037:0.013:0.113509:0.412:107231:rs11807848
1 1062015 rs9659914 C T . PASS AF=0.017 ES:SE:LP:AF:SS:ID 0.0069:0.036:0.0705811:0.017:91321.7:rs9659914
1 1062638 rs9442373 C A . PASS AF=0.552 ES:SE:LP:AF:SS:ID 0.0015:0.013:0.0457575:0.552:106204:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.754 ES:SE:LP:AF:SS:ID -0.016:0.017:0.481486:0.754:103360:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.083 ES:SE:LP:AF:SS:ID 0.0082:0.015:0.221849:0.083:113000:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:SS:ID 0.011:0.014:0.346787:0.675:103165:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.683 ES:SE:LP:AF:SS:ID 0.014:0.015:0.481486:0.683:98877.5:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.924 ES:SE:LP:AF:SS:ID 0.023:0.021:0.552842:0.924:135677:rs4970357
1 1087683 rs9442380 T C . PASS AF=0.912 ES:SE:LP:AF:SS:ID 0.019:0.019:0.508638:0.912:151585:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.966 ES:SE:LP:AF:SS:ID 0.0044:0.026:0.0604807:0.966:133529:rs4970358
1 1097335 rs9442385 T G . PASS AF=0.942 ES:SE:LP:AF:SS:ID 0.017:0.018:0.431798:0.942:147198:rs9442385
1 1099342 rs9660710 A C . PASS AF=0.941 ES:SE:LP:AF:SS:ID 0.012:0.018:0.30103:0.941:148158:rs9660710
1 1100217 rs1891905 C T . PASS AF=0.958 ES:SE:LP:AF:SS:ID 0.029:0.028:0.522879:0.958:133423:rs1891905
1 1106473 rs4970420 G A . PASS AF=0.144 ES:SE:LP:AF:SS:ID -0.015:0.016:0.468521:0.144:100171:rs4970420
1 1119858 rs1320565 C T . PASS AF=0.092 ES:SE:LP:AF:SS:ID -0.0084:0.02:0.173925:0.092:106172:rs1320565