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IEU GWAS information

Trait: Waist-to-hip ratio.

name	value
id	ieu-a-78
pmid	25673412
year	2015
mr	1
note	Adjusted for BMI
trait	Waist-to-hip ratio
category	Risk factor
subcategory	Anthropometric
population	Mixed
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	224452
nsnp	2544137
sd	0.07607940864
priority	9
author	Shungin D
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-78
bcf_file	ieu-a-78.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-09 20:59 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-78/ieu-a-78.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-78/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 18:53:05 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-78/ieu-a-78.vcf.gz ...
Read summary statistics for 2511522 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, 1171579 SNPs remain.
After merging with regression SNP LD, 1171579 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0884 (0.0059)
Lambda GC: 1.0219
Mean Chi^2: 1.0927
Intercept: 0.8605 (0.0065)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 18:53:36 2020
Total time elapsed: 31.54s

QC metrics

Metrics

{
    "af_correlation": 0.9178,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0001,
    "n": 224456,
    "n_snps": 2511522,
    "n_clumped_hits": 37,
    "n_p_sig": 687,
    "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": 24946,
    "n_miss_AF_reference": 22184,
    "n_est": 231647.1114,
    "ratio_se_n": 1.0159,
    "mean_diff": -0,
    "ratio_diff": 3.2112,
    "sd_y_est1": 1.4148,
    "sd_y_est2": 1.4373,
    "r2_sum1": 0.0109,
    "r2_sum2": 0.0054,
    "r2_sum3": 0.0053,
    "r2_sum4": 0.0088,
    "ldsc_nsnp_merge_refpanel_ld": 1171579,
    "ldsc_nsnp_merge_regression_ld": 1171579,
    "ldsc_observed_scale_h2_beta": 0.0884,
    "ldsc_observed_scale_h2_se": 0.0059,
    "ldsc_intercept_beta": 0.8605,
    "ldsc_intercept_se": 0.0065,
    "ldsc_lambda_gc": 1.0219,
    "ldsc_mean_chisq": 1.0927,
    "ldsc_ratio": -1.5049
}

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	2511522	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	8.598141e+00	5.663320e+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	7.881053e+07	5.568215e+07	11523.0000	3.264442e+07	7.020837e+07	1.142825e+08	2.49219e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	5.600000e-05	9.271700e-03	-0.2400	-4.100000e-03	0.000000e+00	4.100000e-03	2.50000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	7.328700e-03	6.080600e-03	0.0032	4.500000e-03	5.400000e-03	7.400000e-03	1.30000e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.958869e-01	2.913010e-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	4.958654e-01	2.912904e-01	0.0000	2.433450e-01	4.957706e-01	7.489683e-01	1.00000e+00	▇▇▇▇▇
numeric	AF	24946	0.9900674	NA	NA	NA	NA	NA	3.552798e-01	2.764128e-01	0.0083	1.167000e-01	2.917000e-01	5.583000e-01	9.91700e-01	▇▅▃▂▂
numeric	AF_reference	22184	0.9911671	NA	NA	NA	NA	NA	3.592177e-01	2.572428e-01	0.0000	1.427720e-01	2.959270e-01	5.441290e-01	1.00000e+00	▇▆▃▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	1.385647e+05	2.060481e+04	50001.0000	1.337590e+05	1.423430e+05	1.426770e+05	2.24456e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	721290	rs12565286	G	C	0.0042	0.0170	0.8100000	0.8048627	0.06780	0.0371406	71956
1	723819	rs11804171	T	A	-0.0016	0.0200	0.9400001	0.9362373	0.03704	0.1345850	59668
1	752566	rs3094315	G	A	0.0007	0.0078	0.9299999	0.9284910	0.84480	0.7182510	79849
1	754192	rs3131968	A	G	-0.0011	0.0100	0.9199999	0.9124094	0.87500	0.6785140	59959
1	768448	rs12562034	G	A	-0.0200	0.0130	0.1199999	0.1239358	0.09167	0.1918930	60899
1	775659	rs2905035	A	G	0.0000	0.0084	1.0000000	1.0000000	0.87500	0.7450080	87759
1	777122	rs2980319	A	T	-0.0008	0.0084	0.9199999	0.9241257	0.87500	0.7472040	87751
1	779322	rs4040617	A	G	0.0009	0.0092	0.9199999	0.9220704	0.12500	0.2264380	75954
1	780785	rs2977612	T	A	-0.0015	0.0092	0.8700001	0.8704842	0.86610	0.6693290	76020
1	785050	rs2905062	G	A	0.0031	0.0067	0.6400000	0.6435890	NA	0.6269970	121776

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51217134	rs117417021	A	G	0.0110	0.0074	0.1400000	0.1371505	0.441700	0.2671730	92177
22	51222100	rs114553188	G	T	-0.0022	0.0120	0.8600001	0.8545365	0.066700	0.0880591	113673
22	51223637	rs375798137	G	A	-0.0023	0.0120	0.8499999	0.8480033	0.066700	0.0788738	113672
22	51229805	rs9616985	T	C	0.0200	0.0140	0.1800002	0.1531275	0.091700	0.0730831	90882
23	35921591	rs2204667	C	G	0.0100	0.0058	0.0790005	0.0846829	0.166700	NA	142572
23	51666786	rs14115	A	G	0.0110	0.0095	0.2500000	0.2469070	0.025000	NA	130844
23	70163799	rs1626496	A	C	0.0065	0.0084	0.4400003	0.4390434	0.075000	NA	142515
23	74963352	rs1053838	T	G	-0.0440	0.0590	0.4600002	0.4558108	0.991379	NA	57703
23	91415872	rs6562597	G	A	-0.0350	0.0160	0.0309999	0.0287060	0.008300	0.0021192	123253
23	118495837	rs12882977	G	A	0.0013	0.0043	0.7600007	0.7624039	0.516700	0.2307280	142454

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   0.0042:0.017:0.091515:0.0678:71956:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03704  ES:SE:LP:AF:SS:ID   -0.0016:0.02:0.0268721:0.03704:59668:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   0.0007:0.0078:0.0315171:0.8448:79849:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0011:0.01:0.0362122:0.875:59959:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   -0.02:0.013:0.920819:0.09167:60899:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0:0.0084:-0:0.875:87759:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0008:0.0084:0.0362122:0.875:87751:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0009:0.0092:0.0362122:0.125:75954:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   -0.0015:0.0092:0.0604807:0.8661:76020:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0031:0.0067:0.19382:121776:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   0:0.0092:-0:0.8729:75960:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   0.012:0.016:0.366532:0.9:53796:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   -0.012:0.016:0.356547:0.1083:53718:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   -0.0083:0.0091:0.443698:0.1667:79032:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   -0.01:0.0086:0.638272:0.425:68617:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0054:0.0074:0.327902:0.2667:108226:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.0035:0.0077:0.187087:0.15:100646:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0051:0.0055:0.455932:0.7373:136932:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   -0.0022:0.007:0.124939:0.1167:112564:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0047:0.005:0.455932:0.5667:138296:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0052:0.0048:0.552842:0.5763:138956:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   -0.0043:0.0071:0.267606:0.09649:112432:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0053:0.0047:0.585027:0.5917:139054:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0039:0.0048:0.376751:0.6017:139065:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   -0.0026:0.0072:0.142668:0.1271:112299:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0043:0.005:0.408935:0.7167:139683:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0036:0.0073:0.207608:110190:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0049:0.0052:0.455932:0.725:139394:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0048:0.0051:0.455932:0.5667:127756:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.94737  ES:SE:LP:AF:SS:ID   -0.0005:0.02:0.00877392:0.94737:53179:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   0.0074:0.0056:0.721246:0.6:112123:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0043:0.0067:0.283997:0.08333:113742:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0032:0.0072:0.180456:0.08621:99023:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   0.0078:0.0057:0.769551:0.6583:113948:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   -0.0035:0.008:0.180456:0.05:127907:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0053:0.0072:0.337242:0.075:117968:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.007:0.0074:0.468521:0.06667:124228:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   -0.0049:0.0081:0.259637:0.05172:123811:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0083:0.0073:0.585027:0.06667:124136:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   -0.002:0.0084:0.091515:0.05:125660:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0025:0.007:0.142668:0.3981:83278:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.027:0.015:1.13077:0.01667:106986:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   -0.0029:0.0084:0.136677:0.05833:127783:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   -0.0008:0.0084:0.0362122:0.05455:127797:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0012:0.0085:0.05061:125593:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   -0.0046:0.0057:0.376751:0.4123:112627:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.036:0.017:1.48149:0.01667:95241:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0011:0.0056:0.0757207:0.5517:111869:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.013:0.0082:0.958607:0.7542:90674:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.011:0.0075:0.853872:0.08333:102000:rs2298217