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IEU GWAS information

Trait: Waist-to-hip ratio.

name	value
id	ieu-a-75
pmid	25673412
year	2015
mr	1
note	NULL
trait	Waist-to-hip ratio
category	Risk factor
subcategory	Anthropometric
population	European
sex	Females
ncase	NULL
ncontrol	NULL
sample_size	118003
nsnp	2466102
sd	0.07703981045
priority	4
author	Shungin D
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-75
bcf_file	ieu-a-75.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 09:51 BST
build_version	run_igd-8f4f4c9-2020-05-09

Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_plot

beta_std plot

$beta_std_plot$

beta_std_plot

Metadata

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}

LDSC

*********************************************************************
* 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-75/ieu-a-75.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-75/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 10:57:25 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-75/ieu-a-75.vcf.gz ...
Read summary statistics for 2465031 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, 1153117 SNPs remain.
After merging with regression SNP LD, 1153117 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1102 (0.0084)
Lambda GC: 1.0219
Mean Chi^2: 1.0702
Intercept: 0.8943 (0.0072)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 10:57:55 2020
Total time elapsed: 29.42s

QC metrics

Metrics

{
    "af_correlation": 0.9167,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0001,
    "n": 118004,
    "n_snps": 2465031,
    "n_clumped_hits": 23,
    "n_p_sig": 608,
    "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": 8897,
    "n_miss_AF_reference": 20985,
    "n_est": 114466.1697,
    "ratio_se_n": 0.9849,
    "mean_diff": -0,
    "ratio_diff": 7.846,
    "sd_y_est1": 1.2984,
    "sd_y_est2": 1.2788,
    "r2_sum1": 0.0122,
    "r2_sum2": 0.0073,
    "r2_sum3": 0.0075,
    "r2_sum4": 0.0103,
    "ldsc_nsnp_merge_refpanel_ld": 1153117,
    "ldsc_nsnp_merge_regression_ld": 1153117,
    "ldsc_observed_scale_h2_beta": 0.1102,
    "ldsc_observed_scale_h2_se": 0.0084,
    "ldsc_intercept_beta": 0.8943,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.0219,
    "ldsc_mean_chisq": 1.0702,
    "ldsc_ratio": -1.5057
}

Flags

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

Definitions

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 SNPs
n_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:
- alleles other than A, C, G or T.
- P-values < 0 or > 1.
- negative or infinite standard errors (<= 0 or = Infinity).
- infinite beta estimates or allele frequencies < 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.
- $\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)$,
- ${z}_j = \frac{\beta_j}{{se}_j}$,
- and $\beta_j$ is the reported effect size.
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.
- $\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}$
- $\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}$
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.
- $\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}$,
- $C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})$,
- and ${se}_j$ is the reported standard error.
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.
- $\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})$,
- $\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}$,

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 > 0.5
ldsc_intercept_beta: ldsc_intercept_beta > 1.5
n_clumped_hits: n_clumped_hits > 1000
r2_sum<*>: r2_sum<*> > 0.5

Plots

Manhattan plot
- Red line: $-log_{10}^{5 \times 10^{-8}}$
- Blue line: $-log_{10}^{5 \times 10^{-5}}$
QQ plot
AF plot
P-Z plot
beta_std plot: Scatter plot between $\widehat{\beta_j^{std}}$ and $\beta_j$

Diagnostics

Details

Summary stats

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	2465031	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	8.585108e+00	5.656569e+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	7.885599e+07	5.563896e+07	11523.0000	3.272057e+07	7.029249e+07	1.143191e+08	2.49219e+08	▇▇▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	9.930000e-05	1.019030e-02	-0.2000	-4.900000e-03	0.000000e+00	5.000000e-03	2.00000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	8.603300e-03	5.748700e-03	0.0043	5.600000e-03	6.500000e-03	9.100000e-03	8.60000e-02	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.962891e-01	2.908299e-01	0.0000	2.399999e-01	5.000000e-01	7.499995e-01	1.00000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.962114e-01	2.906902e-01	0.0000	2.433450e-01	4.961528e-01	7.478856e-01	1.00000e+00	▇▇▇▇▇
numeric	AF	8897	0.9963907	NA	NA	NA	NA	NA	3.573615e-01	2.750534e-01	0.0083	1.167000e-01	2.917000e-01	5.583000e-01	9.91700e-01	▇▅▃▂▂
numeric	AF_reference	20985	0.9914869	NA	NA	NA	NA	NA	3.606998e-01	2.561419e-01	0.0000	1.451680e-01	2.983230e-01	5.451280e-01	1.00000e+00	▇▆▃▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	8.546765e+04	8.250747e+03	50000.0000	8.388800e+04	8.749600e+04	8.755600e+04	1.18004e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	785050	rs2905062	G	A	0.0048	0.0090	0.5999997	0.5938029	NA	0.626997	61921
1	990380	rs3121561	C	T	0.0027	0.0092	0.7700005	0.7691566	0.26670	0.343450	66409
1	998501	rs3813193	G	C	0.0072	0.0093	0.4400003	0.4388163	0.15000	0.206669	62751
1	1003629	rs4075116	C	T	0.0065	0.0068	0.3400001	0.3391317	0.73730	0.720647	84643
1	1005806	rs3934834	C	T	0.0085	0.0085	0.3200000	0.3173105	0.11670	0.223442	69246
1	1017170	rs3766193	C	G	0.0022	0.0063	0.7300002	0.7269344	0.56670	0.575479	85528
1	1017197	rs3766192	C	T	0.0022	0.0060	0.7099994	0.7138677	0.57630	0.511182	85904
1	1017587	rs3766191	C	T	0.0064	0.0089	0.4700002	0.4720786	0.09649	0.171126	69163
1	1018562	rs9442371	C	T	0.0017	0.0059	0.7700005	0.7732429	0.59170	0.530152	85956
1	1018704	rs9442372	A	G	0.0015	0.0059	0.8000000	0.7993122	0.60170	0.611022	85944

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51216564	rs9616970	T	C	0.0220	0.0120	0.0619998	0.0667530	0.1500	0.1563500	64793
22	51217134	rs117417021	A	G	0.0230	0.0093	0.0120000	0.0133940	0.4417	0.2671730	56769
22	51222100	rs114553188	G	T	-0.0025	0.0150	0.8700001	0.8676323	0.0667	0.0880591	69456
22	51223637	rs375798137	G	A	-0.0026	0.0150	0.8600001	0.8623894	0.0667	0.0788738	69455
22	51229805	rs9616985	T	C	0.0380	0.0180	0.0350002	0.0347628	0.0917	0.0730831	53788
23	35921591	rs2204667	C	G	0.0043	0.0072	0.5500004	0.5503590	0.1667	NA	87529
23	51666786	rs14115	A	G	0.0170	0.0120	0.1499999	0.1565804	0.0250	NA	81067
23	70163799	rs1626496	A	C	-0.0002	0.0100	0.9800000	0.9840434	0.0750	NA	87409
23	91415872	rs6562597	G	A	-0.0380	0.0200	0.0619998	0.0574331	0.0083	0.0021192	76441
23	118495837	rs12882977	G	A	-0.0045	0.0052	0.3900004	0.3868277	0.5167	0.2307280	87556

bcf preview

1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0048:0.009:0.221849:61921:rs2905062
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0027:0.0092:0.113509:0.2667:66409:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0072:0.0093:0.356547:0.15:62751:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0065:0.0068:0.468521:0.7373:84643:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.0085:0.0085:0.49485:0.1167:69246:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0022:0.0063:0.136677:0.5667:85528:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0022:0.006:0.148742:0.5763:85904:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0064:0.0089:0.327902:0.09649:69163:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0017:0.0059:0.113509:0.5917:85956:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0015:0.0059:0.09691:0.6017:85944:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0087:0.0089:0.481486:0.1271:69138:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0051:0.0063:0.376751:0.7167:86275:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0072:0.0091:0.366532:66936:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0058:0.0065:0.431798:0.725:86136:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0002:0.0063:0.0132283:0.5667:80395:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0011:0.0067:0.0604807:0.6:70462:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0089:0.008:0.568636:0.08333:70276:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0055:0.009:0.267606:0.08621:61689:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   0.001:0.0068:0.0555173:0.6583:68447:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0037:0.0095:0.154902:0.05:77643:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0084:0.0086:0.481486:0.075:72434:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.011:0.0089:0.657577:0.06667:75872:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.0033:0.0095:0.136677:0.05172:77587:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.012:0.0088:0.769551:0.06667:75865:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0066:0.01:0.29243:0.05:75409:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0004:0.0088:0.0177288:0.3981:52286:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.019:0.019:0.522879:0.01667:63295:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.005:0.0099:0.21467:0.05833:77557:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.0074:0.01:0.337242:0.05455:77566:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0078:0.01:0.346787:75364:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0022:0.007:0.124939:0.4123:67693:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.027:0.021:0.69897:0.01667:56899:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0037:0.0069:0.229148:0.5517:67231:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.011:0.01:0.552842:0.7542:54409:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.011:0.009:0.69897:0.08333:63881:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.0069:0.0074:0.455932:0.675:65431:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0076:0.008:0.468521:0.6833:62912:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   -0.014:0.012:0.585027:0.92373:76306:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   -0.0082:0.011:0.337242:0.91228:79309:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   -0.015:0.014:0.522879:0.9661:79496:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.94167  ES:SE:LP:AF:SS:ID   -0.0085:0.011:0.366532:0.94167:84634:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94068  ES:SE:LP:AF:SS:ID   -0.0055:0.01:0.221849:0.94068:85842:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.95833  ES:SE:LP:AF:SS:ID   0.0023:0.015:0.0555173:0.95833:84428:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1441   ES:SE:LP:AF:SS:ID   0.0017:0.011:0.0555173:0.1441:51079:rs4970420
1   1113121 rs12092254  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.016:0.015:0.552842:0.1:57472:rs12092254
1   1119858 rs1320565   C   T   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0056:0.012:0.187087:0.09167:53950:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.04167  ES:SE:LP:AF:SS:ID   0.027:0.018:0.920819:0.04167:71210:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.004:0.01:0.154902:0.1121:63101:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0039:0.0085:0.187087:0.125:75950:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0037:0.0064:0.251812:0.2667:85195:rs6684820