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IEU GWAS information

Trait: Waist circumference.

name	value
id	ieu-a-67
pmid	25673412
year	2015
mr	1
note	Adjusted for BMI; effect allele frequecies are missing
trait	Waist circumference
category	Risk factor
subcategory	Anthropometric
population	European
sex	Males and females
ncase	NULL
ncontrol	NULL
sample_size	231353
nsnp	2546074
sd	12.52
priority	10
author	Shungin D
group_name	public
access	public
build	HG19/GRCh37

Report information

name	value
gwas_id	ieu-a-67
bcf_file	ieu-a-67.vcf.gz
qc_metrics_file	qc_metrics.json
metadata	metadata.json
refdata	1kg_v3_nomult.bcf
compile_time	2020-05-10 03:16 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

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-67/ieu-a-67.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-67/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 11:56:04 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-67/ieu-a-67.vcf.gz ...
Read summary statistics for 2513636 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, 1172046 SNPs remain.
After merging with regression SNP LD, 1172046 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1032 (0.0058)
Lambda GC: 1.0291
Mean Chi^2: 1.1339
Intercept: 0.8354 (0.0066)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 11:56:38 2020
Total time elapsed: 34.56s

QC metrics

Metrics

{
    "af_correlation": 0.9179,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0.0001,
    "n": 231355,
    "n_snps": 2513636,
    "n_clumped_hits": 65,
    "n_p_sig": 882,
    "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": 25229,
    "n_miss_AF_reference": 22228,
    "n_est": 229011.4901,
    "ratio_se_n": 0.9949,
    "mean_diff": 0,
    "ratio_diff": 4.7364,
    "sd_y_est1": 1.464,
    "sd_y_est2": 1.4566,
    "r2_sum1": 0.0183,
    "r2_sum2": 0.0085,
    "r2_sum3": 0.0086,
    "r2_sum4": 0.0133,
    "ldsc_nsnp_merge_refpanel_ld": 1172046,
    "ldsc_nsnp_merge_regression_ld": 1172046,
    "ldsc_observed_scale_h2_beta": 0.1032,
    "ldsc_observed_scale_h2_se": 0.0058,
    "ldsc_intercept_beta": 0.8354,
    "ldsc_intercept_se": 0.0066,
    "ldsc_lambda_gc": 1.0291,
    "ldsc_mean_chisq": 1.1339,
    "ldsc_ratio": -1.2293
}

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	2513636	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	8.597717e+00	5.663286e+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	7.881082e+07	5.568353e+07	11523.0000	3.264716e+07	7.020863e+07	1.142758e+08	2.49219e+08	▇▆▅▂▁
numeric	EFFECT	0	1.0000000	NA	NA	NA	NA	NA	-8.760000e-05	9.418100e-03	-0.2800	-4.100000e-03	0.000000e+00	4.100000e-03	2.90000e-01	▁▁▇▁▁
numeric	SE	0	1.0000000	NA	NA	NA	NA	NA	7.357200e-03	6.375100e-03	0.0033	4.500000e-03	5.300000e-03	7.500000e-03	4.60000e-01	▇▁▁▁▁
numeric	PVAL	0	1.0000000	NA	NA	NA	NA	NA	4.942221e-01	2.922193e-01	0.0000	2.399999e-01	4.899999e-01	7.499995e-01	1.00000e+00	▇▇▇▇▇
numeric	PVAL_ztest	0	1.0000000	NA	NA	NA	NA	NA	4.941433e-01	2.921766e-01	0.0000	2.407650e-01	4.946531e-01	7.470129e-01	1.00000e+00	▇▇▇▇▇
numeric	AF	25229	0.9899631	NA	NA	NA	NA	NA	3.551178e-01	2.765300e-01	0.0083	1.167000e-01	2.917000e-01	5.583000e-01	9.91700e-01	▇▅▃▂▂
numeric	AF_reference	22228	0.9911570	NA	NA	NA	NA	NA	3.591245e-01	2.573203e-01	0.0000	1.427720e-01	2.957270e-01	5.441290e-01	1.00000e+00	▇▆▃▃▂
numeric	N	0	1.0000000	NA	NA	NA	NA	NA	1.482723e+05	2.118271e+04	50001.0000	1.434790e+05	1.520210e+05	1.533420e+05	2.31355e+05	▁▁▇▁▁

Head and tail

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
1	721290	rs12565286	G	C	-0.0130	0.0170	0.4299995	0.4444467	0.0678	0.0371406	74152
1	723819	rs11804171	T	A	-0.0180	0.0200	0.3599996	0.3681203	0.0370	0.1345850	59507
1	752566	rs3094315	G	A	0.0012	0.0077	0.8800001	0.8761559	0.8448	0.7182510	85984
1	754192	rs3131968	A	G	-0.0110	0.0100	0.2800000	0.2713321	0.8750	0.6785140	66581
1	768448	rs12562034	G	A	-0.0150	0.0130	0.2599998	0.2485632	0.0917	0.1918930	57189
1	775659	rs2905035	A	G	-0.0046	0.0083	0.5800000	0.5794304	0.8750	0.7450080	95290
1	777122	rs2980319	A	T	-0.0063	0.0083	0.4500005	0.4478309	0.8750	0.7472040	95282
1	779322	rs4040617	A	G	0.0044	0.0090	0.6200004	0.6249204	0.1250	0.2264380	83484
1	780785	rs2977612	T	A	-0.0047	0.0091	0.6100002	0.6055167	0.8661	0.6693290	83550
1	785050	rs2905062	G	A	-0.0059	0.0067	0.3800004	0.3785360	NA	0.6269970	131220

CHROM	POS	ID	REF	ALT	EFFECT	SE	PVAL	PVAL_ztest	AF	AF_reference	N
22	51217134	rs117417021	A	G	0.0074	0.0075	0.3200000	0.3238061	0.4417	0.2671730	93898
22	51222100	rs114553188	G	T	-0.0063	0.0120	0.6100002	0.5995832	0.0667	0.0880591	120158
22	51223637	rs375798137	G	A	-0.0061	0.0120	0.6200004	0.6112196	0.0667	0.0788738	120156
22	51229805	rs9616985	T	C	0.0030	0.0150	0.8400000	0.8414806	0.0917	0.0730831	92602
23	35921591	rs2204667	C	G	0.0100	0.0058	0.0850002	0.0846829	0.1667	NA	153291
23	51666786	rs14115	A	G	0.0087	0.0096	0.3599996	0.3648035	0.0250	NA	139352
23	70163799	rs1626496	A	C	-0.0018	0.0084	0.8300000	0.8303243	0.0750	NA	153234
23	74963352	rs1053838	T	G	-0.0100	0.0580	0.8600001	0.8631122	0.9914	NA	63735
23	91415872	rs6562597	G	A	-0.0320	0.0160	0.0519996	0.0455003	0.0083	0.0021192	133971
23	118495837	rs12882977	G	A	-0.0012	0.0043	0.7800007	0.7801913	0.5167	0.2307280	153172

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   -0.013:0.017:0.366532:0.0678:74152:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.037    ES:SE:LP:AF:SS:ID   -0.018:0.02:0.443698:0.037:59507:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   0.0012:0.0077:0.0555173:0.8448:85984:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.011:0.01:0.552842:0.875:66581:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.0917   ES:SE:LP:AF:SS:ID   -0.015:0.013:0.585027:0.0917:57189:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0046:0.0083:0.236572:0.875:95290:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0063:0.0083:0.346787:0.875:95282:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0044:0.009:0.207608:0.125:83484:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   -0.0047:0.0091:0.21467:0.8661:83550:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0059:0.0067:0.420216:131220:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   -0.0032:0.009:0.142668:0.8729:83490:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   0.01:0.016:0.29243:0.9:50064:rs4951864
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   0.0034:0.0094:0.142668:0.1667:74828:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   -0.0087:0.009:0.481486:0.425:64653:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0067:0.0075:0.431798:0.2667:108819:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.0066:0.0076:0.408935:0.15:101238:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   -0.0008:0.0055:0.0555173:0.7373:147644:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   -0.0078:0.0071:0.568636:0.1167:110907:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0045:0.005:0.431798:0.5667:149015:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0052:0.0048:0.552842:0.5763:148279:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.0965   ES:SE:LP:AF:SS:ID   -0.0084:0.0073:0.60206:0.0965:111629:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0043:0.0047:0.443698:0.5917:149773:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0042:0.0048:0.420216:0.6017:148391:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   -0.0069:0.0073:0.468521:0.1271:111497:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0012:0.0052:0.0861861:0.7167:148149:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0078:0.0074:0.537602:109388:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0014:0.0053:0.102373:0.725:148717:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0028:0.0052:0.229148:0.5667:137569:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.9474   ES:SE:LP:AF:SS:ID   -0.0034:0.02:0.0604807:0.9474:51513:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0002:0.0056:0.0132283:0.6:111322:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.0833   ES:SE:LP:AF:SS:ID   0.0096:0.0067:0.823909:0.0833:112085:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.0862   ES:SE:LP:AF:SS:ID   0.0099:0.0073:0.769551:0.0862:105023:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   0.0048:0.0057:0.39794:0.6583:113686:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0078:0.008:0.481486:0.05:130916:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.012:0.0073:1:0.075:120981:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.0667   ES:SE:LP:AF:SS:ID   0.014:0.0075:1.25964:0.0667:128632:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.0517   ES:SE:LP:AF:SS:ID   0.0049:0.0081:0.259637:0.0517:127358:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.0667   ES:SE:LP:AF:SS:ID   0.013:0.0074:1.11351:0.0667:127682:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.011:0.0084:0.769551:0.05:130065:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0022:0.0071:0.119186:0.3981:87881:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0167   ES:SE:LP:AF:SS:ID   0.014:0.015:0.455932:0.0167:106189:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   0.0093:0.0084:0.568636:0.0583:132188:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.0546   ES:SE:LP:AF:SS:ID   0.012:0.0084:0.823909:0.0546:132201:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.013:0.0085:0.886057:129997:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0029:0.0057:0.21467:0.4123:113222:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0167   ES:SE:LP:AF:SS:ID   0.021:0.017:0.657577:0.0167:95835:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0054:0.0057:0.468521:0.5517:111069:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.018:0.0082:1.5376:0.7542:91246:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.0833   ES:SE:LP:AF:SS:ID   0.015:0.0076:1.30103:0.0833:100344:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.0098:0.0059:1.01323:0.675:111918:rs10907182