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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-974/ieu-a-974.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-974/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 11:01:42 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-974/ieu-a-974.vcf.gz ...
Read summary statistics for 2493453 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, 1160701 SNPs remain.
After merging with regression SNP LD, 1160701 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.16 (0.007)
Lambda GC: 1.0362
Mean Chi^2: 1.1479
Intercept: 0.7468 (0.0067)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 11:02:11 2020
Total time elapsed: 29.01s
{
"af_correlation": 0.9176,
"inflation_factor": 1.0388,
"mean_EFFECT": 0.0001,
"n": 171977,
"n_snps": 2493453,
"n_clumped_hits": 37,
"n_p_sig": 1129,
"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": 12694,
"n_miss_AF_reference": 21871,
"n_est": 168270.6655,
"ratio_se_n": 0.9892,
"mean_diff": -0,
"ratio_diff": 3.8334,
"sd_y_est1": 1.4052,
"sd_y_est2": 1.3899,
"r2_sum1": 0.0195,
"r2_sum2": 0.0099,
"r2_sum3": 0.0101,
"r2_sum4": 0.0141,
"ldsc_nsnp_merge_refpanel_ld": 1160701,
"ldsc_nsnp_merge_regression_ld": 1160701,
"ldsc_observed_scale_h2_beta": 0.16,
"ldsc_observed_scale_h2_se": 0.007,
"ldsc_intercept_beta": 0.7468,
"ldsc_intercept_se": 0.0067,
"ldsc_lambda_gc": 1.0362,
"ldsc_mean_chisq": 1.1479,
"ldsc_ratio": -1.712
}
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 | TRUE |
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 | 2493453 | 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 | 8.594572e+00 | 5.661433e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.882663e+07 | 5.567007e+07 | 11523.0000 | 3.267591e+07 | 7.023911e+07 | 1.143035e+08 | 2.49219e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.139000e-04 | 9.885500e-03 | -0.3113 | -4.500000e-03 | 0.000000e+00 | 4.600000e-03 | 3.64500e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.059700e-03 | 6.624100e-03 | 0.0039 | 5.000000e-03 | 5.900000e-03 | 8.200000e-03 | 1.63700e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.920300e-01 | 2.929829e-01 | 0.0000 | 2.366001e-01 | 4.918005e-01 | 7.460003e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.920383e-01 | 2.929812e-01 | 0.0000 | 2.366771e-01 | 4.917677e-01 | 7.459807e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | AF | 12694 | 0.9949091 | NA | NA | NA | NA | NA | 3.556387e-01 | 2.762232e-01 | 0.0083 | 1.167000e-01 | 2.917000e-01 | 5.583000e-01 | 9.91700e-01 | ▇▅▃▂▂ |
numeric | AF_reference | 21871 | 0.9912286 | NA | NA | NA | NA | NA | 3.592524e-01 | 2.570326e-01 | 0.0000 | 1.431710e-01 | 2.961260e-01 | 5.439300e-01 | 1.00000e+00 | ▇▆▃▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.287008e+05 | 1.309962e+04 | 50000.8000 | 1.267810e+05 | 1.318830e+05 | 1.320780e+05 | 1.71977e+05 | ▁▁▁▇▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 721290 | rs12565286 | G | C | 0.0128 | 0.0204 | 0.5305997 | 0.5303637 | 0.0678 | 0.0371406 | 51793.0 |
1 | 752566 | rs3094315 | G | A | -0.0008 | 0.0091 | 0.9298999 | 0.9299465 | 0.8448 | 0.7182510 | 63021.2 |
1 | 775659 | rs2905035 | A | G | 0.0046 | 0.0103 | 0.6552002 | 0.6551625 | 0.8750 | 0.7450080 | 69645.8 |
1 | 777122 | rs2980319 | A | T | 0.0051 | 0.0103 | 0.6205003 | 0.6204973 | 0.8750 | 0.7472040 | 69878.8 |
1 | 779322 | rs4040617 | A | G | -0.0010 | 0.0110 | 0.9275999 | 0.9275648 | 0.1250 | 0.2264380 | 63440.6 |
1 | 780785 | rs2977612 | T | A | -0.0007 | 0.0110 | 0.9493000 | 0.9492598 | 0.8661 | 0.6693290 | 63254.6 |
1 | 785050 | rs2905062 | G | A | 0.0008 | 0.0083 | 0.9232999 | 0.9232144 | NA | 0.6269970 | 89910.6 |
1 | 785989 | rs2980300 | T | C | -0.0002 | 0.0109 | 0.9854000 | 0.9853607 | 0.8729 | 0.6269970 | 63430.7 |
1 | 798959 | rs11240777 | G | A | -0.0111 | 0.0111 | 0.3172999 | 0.3173105 | 0.1667 | 0.4099440 | 52556.0 |
1 | 990380 | rs3121561 | C | T | -0.0028 | 0.0081 | 0.7296003 | 0.7295840 | 0.2667 | 0.3434500 | 101314.0 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51217134 | rs117417021 | A | G | 0.0130 | 0.0088 | 0.1395999 | 0.1396025 | 0.441700 | 0.2671730 | 73127.0 |
22 | 51222100 | rs114553188 | G | T | -0.0090 | 0.0136 | 0.5080998 | 0.5081220 | 0.066700 | 0.0880591 | 107282.0 |
22 | 51223637 | rs375798137 | G | A | -0.0092 | 0.0136 | 0.4986996 | 0.4987419 | 0.066700 | 0.0788738 | 107281.0 |
22 | 51229805 | rs9616985 | T | C | 0.0105 | 0.0166 | 0.5270005 | 0.5270405 | 0.091700 | 0.0730831 | 72408.6 |
23 | 35921591 | rs2204667 | C | G | 0.0030 | 0.0065 | 0.6444007 | 0.6444123 | 0.166700 | NA | 132047.0 |
23 | 51666786 | rs14115 | A | G | 0.0185 | 0.0106 | 0.0809394 | 0.0809356 | 0.025000 | NA | 125275.0 |
23 | 70163799 | rs1626496 | A | C | -0.0130 | 0.0091 | 0.1530999 | 0.1531275 | 0.075000 | NA | 131866.0 |
23 | 74963352 | rs1053838 | T | G | -0.0936 | 0.0584 | 0.1089999 | 0.1089921 | 0.991379 | NA | 62799.6 |
23 | 91415872 | rs6562597 | G | A | 0.0115 | 0.0177 | 0.5159006 | 0.5158747 | 0.008300 | 0.0021192 | 118145.0 |
23 | 118495837 | rs12882977 | G | A | 0.0020 | 0.0047 | 0.6704000 | 0.6704490 | 0.516700 | 0.2307280 | 132092.0 |
1 721290 rs12565286 G C . PASS AF=0.0678 ES:SE:LP:AF:SS:ID 0.0128:0.0204:0.275233:0.0678:51793:rs12565286
1 752566 rs3094315 G A . PASS AF=0.8448 ES:SE:LP:AF:SS:ID -0.0008:0.0091:0.0315638:0.8448:63021.2:rs3094315
1 775659 rs2905035 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID 0.0046:0.0103:0.183626:0.875:69645.8:rs2905035
1 777122 rs2980319 A T . PASS AF=0.875 ES:SE:LP:AF:SS:ID 0.0051:0.0103:0.207258:0.875:69878.8:rs2980319
1 779322 rs4040617 A G . PASS AF=0.125 ES:SE:LP:AF:SS:ID -0.001:0.011:0.0326393:0.125:63440.6:rs4040617
1 780785 rs2977612 T A . PASS AF=0.8661 ES:SE:LP:AF:SS:ID -0.0007:0.011:0.0225965:0.8661:63254.6:rs2977612
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID 0.0008:0.0083:0.0346572:89910.6:rs2905062
1 785989 rs2980300 T C . PASS AF=0.8729 ES:SE:LP:AF:SS:ID -0.0002:0.0109:0.00638744:0.8729:63430.7:rs2980300
1 798959 rs11240777 G A . PASS AF=0.1667 ES:SE:LP:AF:SS:ID -0.0111:0.0111:0.49853:0.1667:52556:rs11240777
1 990380 rs3121561 C T . PASS AF=0.2667 ES:SE:LP:AF:SS:ID -0.0028:0.0081:0.136915:0.2667:101314:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:SS:ID 0.0075:0.0081:0.450384:0.15:101183:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.7373 ES:SE:LP:AF:SS:ID 0.0092:0.0061:0.881074:0.7373:127575:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.1167 ES:SE:LP:AF:SS:ID 0.0103:0.0076:0.756218:0.1167:107708:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0042:0.0057:0.336111:0.5667:125586:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5763 ES:SE:LP:AF:SS:ID 0.0044:0.0054:0.381743:0.5763:126537:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.09649 ES:SE:LP:AF:SS:ID 0.0109:0.0079:0.775467:0.09649:108075:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.5917 ES:SE:LP:AF:SS:ID 0.0029:0.0053:0.233364:0.5917:129034:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.6017 ES:SE:LP:AF:SS:ID 0.003:0.0052:0.248721:0.6017:129003:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.1271 ES:SE:LP:AF:SS:ID 0.0117:0.008:0.842846:0.1271:107974:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.7167 ES:SE:LP:AF:SS:ID 0.0087:0.0055:0.94424:0.7167:130346:rs3737728
1 1021583 rs10907178 A C . PASS . ES:SE:LP:SS:ID 0.0118:0.0081:0.838033:104966:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.0095:0.0058:0.993962:0.725:129806:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0032:0.0057:0.24071:0.5667:121254:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:SS:ID -0.007:0.0059:0.628194:0.6:108692:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.08333 ES:SE:LP:AF:SS:ID 0.0049:0.0071:0.309715:0.08333:109994:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.08621 ES:SE:LP:AF:SS:ID 0.0026:0.0077:0.133358:0.08621:98875.6:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.6583 ES:SE:LP:AF:SS:ID -0.0027:0.006:0.185286:0.6583:106125:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0128:0.0084:0.894149:0.05:119834:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.075 ES:SE:LP:AF:SS:ID 0.007:0.0077:0.439735:0.075:114723:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.06667 ES:SE:LP:AF:SS:ID 0.006:0.0077:0.360713:0.06667:118189:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.05172 ES:SE:LP:AF:SS:ID 0.0115:0.0084:0.767004:0.05172:119819:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.06667 ES:SE:LP:AF:SS:ID 0.0046:0.0076:0.263604:0.06667:118203:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0108:0.0088:0.65817:0.05:116574:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.3981 ES:SE:LP:AF:SS:ID -0.0014:0.0073:0.0716554:0.3981:85817.5:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.01667 ES:SE:LP:AF:SS:ID -0.0178:0.0164:0.556268:0.01667:98970.3:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.05833 ES:SE:LP:AF:SS:ID 0.0104:0.0087:0.634699:0.05833:119714:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.05455 ES:SE:LP:AF:SS:ID 0.0107:0.0088:0.649752:0.05455:119731:rs17160826
1 1061152 rs12748370 T C . PASS . ES:SE:LP:SS:ID 0.0116:0.0089:0.715795:116495:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.4123 ES:SE:LP:AF:SS:ID 0.0022:0.0061:0.143634:0.4123:102991:rs11807848
1 1062015 rs9659914 C T . PASS AF=0.01667 ES:SE:LP:AF:SS:ID -0.018:0.0178:0.505985:0.01667:92550.3:rs9659914
1 1062638 rs9442373 C A . PASS AF=0.5517 ES:SE:LP:AF:SS:ID -0.0019:0.006:0.124071:0.5517:102330:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.7542 ES:SE:LP:AF:SS:ID -0.0093:0.0086:0.553618:0.7542:89465.9:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.08333 ES:SE:LP:AF:SS:ID 0.0081:0.0077:0.533429:0.08333:103588:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:SS:ID -0.0002:0.0065:0.0107727:0.675:98390.4:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.6833 ES:SE:LP:AF:SS:ID -0.0012:0.0071:0.0625824:0.6833:94846.1:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.92373 ES:SE:LP:AF:SS:ID -0.0082:0.0111:0.337148:0.92373:117465:rs4970357
1 1079198 rs11260603 T C . PASS AF=0.2241 ES:SE:LP:AF:SS:ID -0.0012:0.0109:0.0398623:0.2241:55928.6:rs11260603
1 1087683 rs9442380 T C . PASS AF=0.91228 ES:SE:LP:AF:SS:ID -0.0119:0.0099:0.639407:0.91228:123134:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.9661 ES:SE:LP:AF:SS:ID -0.0158:0.0128:0.66334:0.9661:124109:rs4970358
1 1094738 rs4970362 A G . PASS AF=0.6667 ES:SE:LP:AF:SS:ID -0.0045:0.0072:0.274088:0.6667:65906.8:rs4970362