docs/meta-analysis.md
In perishky/dmrff: Identifying differentially methylated regions efficiently with power and control
title: "Meta-analysis using dmrff"
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Meta-analysis using dmrff
Download and prepare DNA methylation datasets
We'll use a couple of small cord blood DNA methylation datasets
available on GEO: GSE79056, GSE62924.
Loading each dataset takes about 1 minute.
accessions <- c("GSE79056", "GSE62924")
library(geograbi) ## https://github.com/yousefi138
## Loading required package: XML
## Loading required package: data.table
samples <- sapply(accessions, geograbi.get.samples, simplify=F)
## Tue Dec 12 19:02:41 2023 reading
## Tue Dec 12 19:02:42 2023 reading
vars <- sapply(samples, geograbi.extract.characteristics, simplify=F)
system.time(methylation <- sapply(accessions, geograbi.get.data, simplify=F))
## Tue Dec 12 19:02:44 2023 reading
## Tue Dec 12 19:02:53 2023 reading
## user system elapsed
## 15.290 1.666 15.312
Remove non-CpG probes from the datasets.
for (acc in accessions)
methylation[[acc]] <- methylation[[acc]][grepl("^c", rownames(methylation[[acc]])),]
Extract the variable of interest from each dataset.
variable <- sapply(accessions, function(acc) {
idx <- grep("(ga weeks|gestational_age|gestational age)", colnames(vars[[acc]]))
stopifnot(length(idx) == 1)
as.numeric(vars[[acc]][,idx])
}, simplify=F)
Remove samples with incomplete data.
for (acc in accessions) {
idx <- which(!is.na(variable[[acc]]))
samples[[acc]] <- samples[[acc]][idx,]
vars[[acc]] <- vars[[acc]][idx,]
variable[[acc]] <- variable[[acc]][idx]
methylation[[acc]] <- methylation[[acc]][,idx]
}
Calculate surrogate variables to handle unknown confounding
SVA takes a few seconds for each dataset.
library(sva, quietly=T)
## This is mgcv 1.8-41. For overview type 'help("mgcv-package")'.
set.seed(20191029)
covariates <- sapply(accessions, function(acc) {
mod <- model.matrix(~ var, data.frame(var=variable[[acc]]))
mod0 <- mod[,1,drop=F]
random.idx <- sample(1:nrow(methylation[[acc]]), 5000)
meth.sva <- methylation[[acc]][random.idx,]
meth.mean <- rowMeans(meth.sva, na.rm=T)
idx <- which(is.na(meth.sva), arr.ind=T)
if (nrow(idx) > 0)
meth.sva[idx] <- meth.mean[idx[,1]]
sva(meth.sva, mod=mod, mod0=mod0)$sv
}, simplify=F)
## Number of significant surrogate variables is: 3
## Iteration (out of 5 ):1 2 3 4 5 Number of significant surrogate variables is: 2
## Iteration (out of 5 ):1 2 3 4 5
Test the associations with gestational age
Testing associations takes a few seconds for each dataset.
library(limma)
stats <- sapply(accessions, function(acc) {
mod <- model.matrix(~ ., data.frame(ga=variable[[acc]],
covariates[[acc]]))
fit <- lmFit(methylation[[acc]], mod)
fit <- eBayes(fit)
data.frame(estimate=fit$coefficients[,"ga"],
se=sqrt(fit$s2.post) * fit$stdev.unscaled[,"ga"],
p.value=fit$p.value[,"ga"])
},simplify=F)
Now we check the agreement between the datasets.
kable(sapply(stats, function(a) sapply(stats, function(b) {
sites <- intersect(rownames(a), rownames(b))
sites <- sites[order(a[sites,"p.value"])[1:100]]
cor(a[sites,"estimate"], b[sites,"estimate"])
})))
| | GSE79056| GSE62924|
|:--------|---------:|---------:|
|GSE79056 | 1.0000000| 0.5844022|
|GSE62924 | 0.8681764| 1.0000000|
A previous study reported thousands of associations with gestational age:
Bohlin J, et al.
Prediction of gestational age based on genome-wide
differentially methylated regions.
Genome Biol. 2016;17(1):207.
The effect estimates are strongly associated.
bohlin <- read.csv("bohlin.csv",stringsAsFactors=F,row.names=1)
kable(sapply(stats, function(stats) {
cor(bohlin$estimate, stats[rownames(bohlin),"estimate"], use="p")
}))
| | x|
|:--------|---------:|
|GSE79056 | 0.7631472|
|GSE62924 | 0.5647381|
Annotate summary statistics with genomic locations
If your data was generated using one of the Illumina BeadChips, then it is possible
to annotate your EWAS summary statistics using the appropriate
Bioconductor annotation package.
For the Illumina 450K microaray, we use the
IlluminaHumanMethylation450kanno.ilmn12.hg19 package.
if (!require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly=T)) {
install.packages("BiocManager")
BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19")
}
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## locfit 1.5-9.6 2022-07-11
## Setting options('download.file.method.GEOquery'='auto')
## Setting options('GEOquery.inmemory.gpl'=FALSE)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
If we were using the more recent Illumina MethylationEPIC BeadChip,
then we would load the IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package instead.
We construct an annotation data frame as follows:
data(list="IlluminaHumanMethylation450kanno.ilmn12.hg19")
data(Locations)
data(Other)
annotation <- cbind(as.data.frame(Locations), as.data.frame(Other))
We then add the annotation to the stats object
(Warning: we assume that the row names of the stats object
are the Illumina CpG site identifiers, e.g. cg05775921).
stats <- sapply(stats, function(stats) {
annotation <- annotation[match(rownames(stats), rownames(annotation)),]
cbind(stats, annotation)
}, simplify=F)
Construct 'pre' objects for DMR meta-analysis
Takes about 2 minutes per dataset to calculate CpG site correlations.
library(dmrff)
pre <- sapply(accessions, function(acc) {
cat(date(), "pre", acc, "\n")
with(stats[[acc]], dmrff.pre(estimate, se, methylation[[acc]], chr, pos))
}, simplify=F)
## Tue Dec 12 19:04:18 2023 pre GSE79056
## Tue Dec 12 19:05:22 2023 pre GSE62924
Perform DMR meta-analysis
There are hundreds of DMRs for this phenotype,
so the final meta-analysis takes about 15 minutes
with a single processor.
options(mc.cores=20) ## if you have 20 processors available
meta <- dmrff.meta(pre)
## [dmrff.candidates] Tue Dec 12 19:06:45 2023 Found 92222 candidate regions.
The output contains a data frame of the meta-analysed regions
and the EWAS meta-analysis on which it was based.
kable(meta$dmrs[1:2,])
|chr | start| end| n|B |S | estimate| se| z| p.value| p.adjust|
|:----|--------:|--------:|--:|:--|:--|---------:|---------:|---------:|-------:|---------:|
|chr6 | 32120203| 32121113| 18|NA |NA | 0.1363391| 0.0104200| 13.084374| 0e+00| 0.0000000|
|chr6 | 32119874| 32119874| 1|NA |NA | 0.1136654| 0.0209026| 5.437861| 1e-07| 0.0368855|
kable(meta$ewas[1:2,])
| | estimate| se| z| p.value|chr | pos|
|:----------|----------:|---------:|----------:|---------:|:----|-----:|
|cg13869341 | 0.0196382| 0.0270016| 0.7272998| 0.4670423|chr1 | 15865|
|cg14008030 | -0.0030598| 0.0201270| -0.1520225| 0.8791692|chr1 | 18827|
Here we add the CpG sites and gene names to the EWAS sites:
idx <- match(with(meta$ewas, paste(chr,pos)),
with(annotation, paste(chr,pos)))
meta$ewas$cpg <- rownames(annotation)[idx]
meta$ewas$gene <- annotation$UCSC_RefGene_Name[idx]
Meta-analyzed DMRs
dmrs <- meta$dmrs[which(meta$dmrs$p.adjust < 0.05 & meta$dmrs$n >= 2), ]
We've identified 1987 DMRs with Bonferroni adjusted p < 0.05.
For convenience, we'll just look at DMRs on chromosome 6 with at least 5 CpG sites.
dmrs6 <- meta$dmrs[which(meta$dmrs$p.adjust < 0.05
& meta$dmrs$n >= 5
& meta$dmrs$chr == "chr6"), ]
dmrs6 <- dmrs6[order(dmrs6$start),]
kable(dmrs6[,c("chr","start","end","n","estimate","se","p.value","p.adjust")])
| |chr | start| end| n| estimate| se| p.value| p.adjust|
|:-----|:----|---------:|---------:|--:|----------:|---------:|-------:|---------:|
|3259 |chr6 | 1635611| 1635847| 5| 0.1027082| 0.0078696| 0e+00| 0.0000000|
|1218 |chr6 | 15504844| 15506085| 9| -0.1462422| 0.0121251| 0e+00| 0.0000000|
|2159 |chr6 | 25652383| 25652602| 7| 0.0880595| 0.0162855| 1e-07| 0.0437835|
|5135 |chr6 | 28543262| 28543670| 5| 0.0989848| 0.0152585| 0e+00| 0.0000598|
|3266 |chr6 | 29520752| 29521046| 6| 0.1262316| 0.0185271| 0e+00| 0.0000065|
|2164 |chr6 | 29571363| 29571693| 8| 0.0801718| 0.0070362| 0e+00| 0.0000000|
|3272 |chr6 | 29576987| 29577348| 5| 0.0433758| 0.0042732| 0e+00| 0.0000000|
|8281 |chr6 | 29577916| 29578423| 5| 0.0311143| 0.0056372| 0e+00| 0.0232597|
|643 |chr6 | 29589573| 29589729| 5| 0.0352142| 0.0060229| 0e+00| 0.0034298|
|88 |chr6 | 29599012| 29599836| 10| 0.1287574| 0.0118910| 0e+00| 0.0000000|
|1219 |chr6 | 29911295| 29911550| 7| -0.1202450| 0.0151196| 0e+00| 0.0000000|
|264 |chr6 | 30127760| 30128775| 15| 0.0328547| 0.0031879| 0e+00| 0.0000000|
|66 |chr6 | 30458158| 30459317| 12| -0.1553172| 0.0110948| 0e+00| 0.0000000|
|67 |chr6 | 30459540| 30460600| 9| -0.1038827| 0.0125606| 0e+00| 0.0000000|
|3918 |chr6 | 30581820| 30582416| 6| -0.1515777| 0.0125543| 0e+00| 0.0000000|
|221 |chr6 | 30652771| 30653530| 9| -0.1228585| 0.0147872| 0e+00| 0.0000000|
|2221 |chr6 | 30850543| 30850977| 8| 0.0708181| 0.0120973| 0e+00| 0.0032814|
|238 |chr6 | 30854161| 30854551| 5| 0.1272353| 0.0190420| 0e+00| 0.0000161|
|3299 |chr6 | 30955992| 30956440| 5| 0.0511286| 0.0066766| 0e+00| 0.0000000|
|14716 |chr6 | 31079110| 31079617| 5| 0.0936230| 0.0068468| 0e+00| 0.0000000|
|249 |chr6 | 31127159| 31127863| 8| -0.0618254| 0.0094440| 0e+00| 0.0000403|
|1820 |chr6 | 31549480| 31550090| 7| -0.1139919| 0.0093255| 0e+00| 0.0000000|
|3320 |chr6 | 31646236| 31646625| 5| 0.0718148| 0.0110119| 0e+00| 0.0000476|
|562 |chr6 | 31744391| 31744831| 10| -0.1243364| 0.0169747| 0e+00| 0.0000002|
|5186 |chr6 | 31846797| 31846970| 6| 0.0662870| 0.0122338| 1e-07| 0.0411449|
|52 |chr6 | 31867945| 31868470| 14| -0.0694588| 0.0065306| 0e+00| 0.0000000|
|170 |chr6 | 31937758| 31938533| 12| -0.0721526| 0.0126389| 0e+00| 0.0077834|
|169 |chr6 | 31939059| 31939319| 8| -0.0813310| 0.0137086| 0e+00| 0.0020366|
|179 |chr6 | 32013699| 32014739| 19| 0.0724101| 0.0047237| 0e+00| 0.0000000|
|3326 |chr6 | 32020425| 32020750| 8| 0.0575820| 0.0073172| 0e+00| 0.0000000|
|2223 |chr6 | 32022898| 32023650| 13| 0.0625395| 0.0097437| 0e+00| 0.0000942|
|21 |chr6 | 32037018| 32037800| 17| 0.0666399| 0.0083409| 0e+00| 0.0000000|
|85 |chr6 | 32042200| 32044254| 20| 0.0597093| 0.0043667| 0e+00| 0.0000000|
|86 |chr6 | 32044384| 32045323| 6| 0.0389959| 0.0069651| 0e+00| 0.0147658|
|187 |chr6 | 32048449| 32049845| 20| 0.0559469| 0.0060904| 0e+00| 0.0000000|
|1518 |chr6 | 32060791| 32061478| 7| 0.1054549| 0.0066597| 0e+00| 0.0000000|
|1024 |chr6 | 32086755| 32086893| 8| 0.0979195| 0.0167033| 0e+00| 0.0031226|
|1 |chr6 | 32120203| 32121113| 18| 0.1363391| 0.0104200| 0e+00| 0.0000000|
|10 |chr6 | 32121143| 32121475| 14| 0.0993614| 0.0096535| 0e+00| 0.0000000|
|1824 |chr6 | 32122736| 32122864| 5| -0.1028521| 0.0164666| 0e+00| 0.0002878|
|1520 |chr6 | 32135241| 32135803| 13| 0.0629867| 0.0044176| 0e+00| 0.0000000|
|14783 |chr6 | 32150404| 32150716| 5| 0.0442438| 0.0077106| 0e+00| 0.0065511|
|566 |chr6 | 32154416| 32154715| 6| -0.0954617| 0.0109209| 0e+00| 0.0000000|
|824 |chr6 | 32158927| 32160074| 8| -0.1059600| 0.0100092| 0e+00| 0.0000000|
|8386 |chr6 | 32171796| 32172124| 6| 0.0435022| 0.0072622| 0e+00| 0.0014331|
|1258 |chr6 | 32805398| 32805684| 5| -0.1578966| 0.0142437| 0e+00| 0.0000000|
|351 |chr6 | 32812933| 32813448| 9| -0.1547065| 0.0088548| 0e+00| 0.0000000|
|70 |chr6 | 32820355| 32820577| 6| -0.1703108| 0.0153020| 0e+00| 0.0000000|
|675 |chr6 | 32825701| 32826197| 5| 0.0464334| 0.0067413| 0e+00| 0.0000039|
|236 |chr6 | 32908567| 32909523| 13| -0.1486117| 0.0100272| 0e+00| 0.0000000|
|573 |chr6 | 32942063| 32943025| 11| -0.1361098| 0.0150253| 0e+00| 0.0000000|
|1829 |chr6 | 33043841| 33044510| 7| -0.1374565| 0.0212478| 0e+00| 0.0000674|
|213 |chr6 | 33132163| 33132318| 5| 0.0876268| 0.0147821| 0e+00| 0.0020991|
|212 |chr6 | 33132650| 33134078| 19| 0.0319455| 0.0050725| 0e+00| 0.0002065|
|42 |chr6 | 33245488| 33245553| 6| -0.1782523| 0.0143561| 0e+00| 0.0000000|
|47 |chr6 | 33245706| 33245804| 7| -0.0949201| 0.0136651| 0e+00| 0.0000026|
|44 |chr6 | 33245893| 33246094| 7| -0.1385954| 0.0148995| 0e+00| 0.0000000|
|3338 |chr6 | 41010111| 41010654| 6| 0.0394107| 0.0045998| 0e+00| 0.0000000|
|3339 |chr6 | 53530503| 53530628| 6| 0.1001493| 0.0159807| 0e+00| 0.0002519|
|585 |chr6 | 149805995| 149806732| 11| -0.1157892| 0.0081252| 0e+00| 0.0000000|
|5317 |chr6 | 152702330| 152702463| 5| 0.1032869| 0.0074051| 0e+00| 0.0000000|
|2651 |chr6 | 170580947| 170581690| 8| -0.0842003| 0.0128133| 0e+00| 0.0000341|
Below we use the dmrff.sites function to show the CpG sites in each DMR and their
meta-analysed summary statistics.
sites <- dmrff.sites(dmrs6, meta$ewas$chr, meta$ewas$pos)
sites <- cbind(sites[,c("region","chr","pos")],
meta$ewas[sites$site,c("cpg", "estimate","se","p.value")])
kable(sites,row.names=F)
| region|chr | pos|cpg | estimate| se| p.value|
|------:|:----|---------:|:----------|----------:|---------:|---------:|
| 1|chr6 | 1635611|cg07714812 | 0.1325816| 0.0161031| 0.0000000|
| 1|chr6 | 1635640|cg19295314 | 0.0976020| 0.0125669| 0.0000000|
| 1|chr6 | 1635808|cg13394216 | 0.1330165| 0.0128689| 0.0000000|
| 1|chr6 | 1635818|cg26908825 | 0.1246750| 0.0161058| 0.0000000|
| 1|chr6 | 1635847|cg10707788 | 0.1219806| 0.0111667| 0.0000000|
| 2|chr6 | 15504844|cg10975897 | -0.1515391| 0.0129587| 0.0000000|
| 2|chr6 | 15504872|cg13027183 | -0.1431798| 0.0135442| 0.0000000|
| 2|chr6 | 15504923|cg20052079 | -0.1618406| 0.0143556| 0.0000000|
| 2|chr6 | 15505094|cg18188328 | -0.1427320| 0.0129587| 0.0000000|
| 2|chr6 | 15505345|cg03173502 | -0.0992715| 0.0246547| 0.0000566|
| 2|chr6 | 15505452|cg23850913 | -0.1082715| 0.0246992| 0.0000117|
| 2|chr6 | 15505460|cg13500852 | -0.1251692| 0.0209455| 0.0000000|
| 2|chr6 | 15505949|cg14058851 | -0.1135978| 0.0231285| 0.0000009|
| 2|chr6 | 15506085|cg24408769 | -0.1431592| 0.0186050| 0.0000000|
| 3|chr6 | 25652383|cg13586599 | 0.0985821| 0.0177986| 0.0000000|
| 3|chr6 | 25652390|cg04200224 | 0.0835931| 0.0270537| 0.0020023|
| 3|chr6 | 25652395|cg15562220 | 0.0598369| 0.0258873| 0.0208088|
| 3|chr6 | 25652405|cg10721149 | 0.0658864| 0.0264927| 0.0128838|
| 3|chr6 | 25652407|cg13834623 | 0.0347019| 0.0297161| 0.2428950|
| 3|chr6 | 25652531|cg26718511 | 0.0564228| 0.0307144| 0.0662074|
| 3|chr6 | 25652602|cg06493994 | 0.0758429| 0.0288685| 0.0086093|
| 4|chr6 | 28543262|cg18214570 | 0.0273951| 0.0281027| 0.3296477|
| 4|chr6 | 28543508|cg04113450 | 0.0414187| 0.0259925| 0.1110509|
| 4|chr6 | 28543514|cg06280322 | 0.0746264| 0.0210831| 0.0004007|
| 4|chr6 | 28543667|cg01254034 | 0.0971941| 0.0163355| 0.0000000|
| 4|chr6 | 28543670|cg07031070 | 0.1028115| 0.0159255| 0.0000000|
| 5|chr6 | 29520752|cg11935738 | 0.0855872| 0.0254399| 0.0007674|
| 5|chr6 | 29520774|cg08065408 | 0.1288810| 0.0200188| 0.0000000|
| 5|chr6 | 29520965|cg09641376 | 0.1043260| 0.0248782| 0.0000275|
| 5|chr6 | 29521013|cg12749246 | 0.1097796| 0.0202969| 0.0000001|
| 5|chr6 | 29521023|cg06343355 | 0.0930443| 0.0212854| 0.0000124|
| 5|chr6 | 29521046|cg18342026 | 0.0876552| 0.0276076| 0.0014982|
| 6|chr6 | 29571363|cg18656132 | 0.0540814| 0.0090586| 0.0000000|
| 6|chr6 | 29571419|cg07169712 | 0.0471520| 0.0235234| 0.0450191|
| 6|chr6 | 29571429|cg12166917 | -0.0049779| 0.0160092| 0.7558444|
| 6|chr6 | 29571432|cg00806253 | 0.0258679| 0.0207753| 0.2130837|
| 6|chr6 | 29571438|cg12083232 | 0.0053564| 0.0254470| 0.8332830|
| 6|chr6 | 29571468|cg15136600 | 0.0224261| 0.0160977| 0.1635830|
| 6|chr6 | 29571483|cg21652192 | -0.0188971| 0.0180588| 0.2953669|
| 6|chr6 | 29571693|cg20067272 | 0.0028609| 0.0148239| 0.8469628|
| 7|chr6 | 29576987|cg15154411 | 0.0351587| 0.0064316| 0.0000000|
| 7|chr6 | 29577006|cg04960880 | -0.0031858| 0.0129476| 0.8056420|
| 7|chr6 | 29577082|cg20642417 | 0.0208238| 0.0086763| 0.0163920|
| 7|chr6 | 29577223|cg03258475 | 0.0243484| 0.0111411| 0.0288550|
| 7|chr6 | 29577348|cg05972518 | 0.0356577| 0.0148130| 0.0160761|
| 8|chr6 | 29577916|cg24962941 | 0.0387238| 0.0192038| 0.0437511|
| 8|chr6 | 29578124|cg23801674 | -0.0098085| 0.0278039| 0.7242565|
| 8|chr6 | 29578144|cg22783999 | 0.0522605| 0.0240929| 0.0300734|
| 8|chr6 | 29578313|cg26569800 | 0.0371461| 0.0108821| 0.0006413|
| 8|chr6 | 29578423|cg21552290 | 0.0303105| 0.0073074| 0.0000336|
| 9|chr6 | 29589573|cg13730341 | -0.0073799| 0.0220999| 0.7384307|
| 9|chr6 | 29589631|cg01373089 | 0.0042720| 0.0172564| 0.8044751|
| 9|chr6 | 29589707|cg06266853 | 0.0259628| 0.0071999| 0.0003110|
| 9|chr6 | 29589714|cg24430207 | 0.0093660| 0.0121189| 0.4396148|
| 9|chr6 | 29589729|cg18004110 | 0.0044864| 0.0134167| 0.7380879|
| 10|chr6 | 29599012|cg23306453 | 0.1207457| 0.0158933| 0.0000000|
| 10|chr6 | 29599160|cg01765653 | 0.1269653| 0.0140006| 0.0000000|
| 10|chr6 | 29599178|cg20139800 | 0.1414558| 0.0182363| 0.0000000|
| 10|chr6 | 29599226|cg06519422 | 0.1285017| 0.0133170| 0.0000000|
| 10|chr6 | 29599250|cg03127104 | 0.1345549| 0.0164055| 0.0000000|
| 10|chr6 | 29599259|cg12991385 | 0.1442089| 0.0154134| 0.0000000|
| 10|chr6 | 29599319|cg17806418 | 0.1430834| 0.0165113| 0.0000000|
| 10|chr6 | 29599331|cg22679406 | 0.1331319| 0.0175590| 0.0000000|
| 10|chr6 | 29599390|cg06512249 | 0.1434446| 0.0172208| 0.0000000|
| 10|chr6 | 29599836|cg07839627 | 0.0542492| 0.0231074| 0.0188901|
| 11|chr6 | 29911295|cg09535358 | -0.0890083| 0.0265383| 0.0007967|
| 11|chr6 | 29911334|cg08039587 | -0.1139279| 0.0221143| 0.0000003|
| 11|chr6 | 29911339|cg00082981 | -0.0998774| 0.0249472| 0.0000624|
| 11|chr6 | 29911366|cg16742075 | -0.1416403| 0.0179065| 0.0000000|
| 11|chr6 | 29911494|cg20408505 | -0.0587967| 0.0294647| 0.0459885|
| 11|chr6 | 29911542|cg25637655 | -0.1136482| 0.0224943| 0.0000004|
| 11|chr6 | 29911550|cg17608381 | -0.1207630| 0.0222267| 0.0000001|
| 12|chr6 | 30127760|cg04560098 | 0.0401264| 0.0113225| 0.0003942|
| 12|chr6 | 30127997|cg03189075 | 0.0327587| 0.0067979| 0.0000014|
| 12|chr6 | 30128219|cg24449136 | 0.0491391| 0.0171271| 0.0041165|
| 12|chr6 | 30128238|cg15118780 | 0.0478123| 0.0173236| 0.0057811|
| 12|chr6 | 30128254|cg18765127 | 0.0356384| 0.0176748| 0.0437645|
| 12|chr6 | 30128385|cg17232861 | 0.0250335| 0.0092835| 0.0070060|
| 12|chr6 | 30128404|cg24679043 | 0.0402768| 0.0088223| 0.0000050|
| 12|chr6 | 30128427|cg15109860 | 0.0272555| 0.0117868| 0.0207577|
| 12|chr6 | 30128511|cg10391909 | 0.0253172| 0.0091443| 0.0056292|
| 12|chr6 | 30128526|cg22733580 | 0.0153087| 0.0082243| 0.0626860|
| 12|chr6 | 30128542|cg03266377 | 0.0062717| 0.0116496| 0.5903261|
| 12|chr6 | 30128548|cg20136460 | 0.0212401| 0.0083472| 0.0109408|
| 12|chr6 | 30128558|cg07738839 | 0.0368983| 0.0096792| 0.0001378|
| 12|chr6 | 30128686|cg11334822 | 0.0458124| 0.0154149| 0.0029591|
| 12|chr6 | 30128775|cg21126020 | 0.0351664| 0.0067421| 0.0000002|
| 13|chr6 | 30458158|cg21176130 | -0.1187951| 0.0247921| 0.0000017|
| 13|chr6 | 30458161|cg09326440 | -0.1279226| 0.0225586| 0.0000000|
| 13|chr6 | 30458237|cg12700271 | -0.1475024| 0.0199043| 0.0000000|
| 13|chr6 | 30458519|cg13007871 | -0.1490487| 0.0154139| 0.0000000|
| 13|chr6 | 30458586|cg00340855 | -0.1577606| 0.0130459| 0.0000000|
| 13|chr6 | 30458601|cg11594821 | -0.1466365| 0.0142721| 0.0000000|
| 13|chr6 | 30458730|cg21758773 | -0.1130846| 0.0145080| 0.0000000|
| 13|chr6 | 30458998|cg25786265 | -0.0724191| 0.0262484| 0.0057980|
| 13|chr6 | 30459139|cg05201185 | -0.1186304| 0.0168037| 0.0000000|
| 13|chr6 | 30459255|cg02188225 | -0.0937755| 0.0211501| 0.0000093|
| 13|chr6 | 30459295|cg20652371 | -0.0980952| 0.0194738| 0.0000005|
| 13|chr6 | 30459317|cg04907849 | -0.0678662| 0.0263028| 0.0098747|
| 14|chr6 | 30459540|cg23235965 | -0.1008510| 0.0291446| 0.0005394|
| 14|chr6 | 30459595|cg27486585 | -0.0878102| 0.0169830| 0.0000002|
| 14|chr6 | 30459867|cg17615629 | -0.0841319| 0.0186010| 0.0000061|
| 14|chr6 | 30460244|cg20105257 | -0.0966510| 0.0214485| 0.0000066|
| 14|chr6 | 30460322|cg02678305 | -0.0790670| 0.0188239| 0.0000267|
| 14|chr6 | 30460484|cg19109457 | -0.0108955| 0.0262903| 0.6785587|
| 14|chr6 | 30460548|cg09569347 | -0.0922902| 0.0194441| 0.0000021|
| 14|chr6 | 30460576|cg13036546 | -0.1021893| 0.0134941| 0.0000000|
| 14|chr6 | 30460600|cg16535080 | -0.0767010| 0.0173629| 0.0000100|
| 15|chr6 | 30581820|cg13522406 | -0.1540336| 0.0134155| 0.0000000|
| 15|chr6 | 30582174|cg05235540 | -0.1331640| 0.0204797| 0.0000000|
| 15|chr6 | 30582241|cg08677140 | -0.1462982| 0.0200799| 0.0000000|
| 15|chr6 | 30582333|cg23583454 | -0.1278021| 0.0197341| 0.0000000|
| 15|chr6 | 30582352|cg04694022 | -0.1133670| 0.0184513| 0.0000000|
| 15|chr6 | 30582416|cg10977734 | -0.1577487| 0.0164834| 0.0000000|
| 16|chr6 | 30652771|cg11414821 | -0.1226349| 0.0206328| 0.0000000|
| 16|chr6 | 30652829|cg00278359 | -0.1349316| 0.0165676| 0.0000000|
| 16|chr6 | 30652907|cg12036303 | -0.1437066| 0.0176865| 0.0000000|
| 16|chr6 | 30653167|cg00010853 | -0.1255908| 0.0164041| 0.0000000|
| 16|chr6 | 30653191|cg11554650 | -0.0818081| 0.0211529| 0.0001100|
| 16|chr6 | 30653242|cg08253704 | -0.1141914| 0.0180993| 0.0000000|
| 16|chr6 | 30653407|cg12105190 | -0.1148872| 0.0208874| 0.0000000|
| 16|chr6 | 30653512|cg25980484 | -0.1206877| 0.0210263| 0.0000000|
| 16|chr6 | 30653530|cg03052182 | -0.1253747| 0.0227586| 0.0000000|
| 17|chr6 | 30850543|cg08951271 | 0.1071200| 0.0184280| 0.0000000|
| 17|chr6 | 30850581|cg19178509 | -0.0092858| 0.0318039| 0.7703079|
| 17|chr6 | 30850718|cg13396738 | 0.0621029| 0.0220589| 0.0048729|
| 17|chr6 | 30850829|cg17604312 | 0.1115154| 0.0207763| 0.0000001|
| 17|chr6 | 30850868|cg24727290 | 0.1061909| 0.0213050| 0.0000006|
| 17|chr6 | 30850876|cg13329862 | 0.0696142| 0.0192965| 0.0003090|
| 17|chr6 | 30850913|cg19215110 | 0.0400965| 0.0238290| 0.0924369|
| 17|chr6 | 30850977|cg02696067 | 0.0938655| 0.0169445| 0.0000000|
| 18|chr6 | 30854161|cg07187855 | 0.1007622| 0.0254437| 0.0000749|
| 18|chr6 | 30854164|cg24566261 | 0.1226748| 0.0218724| 0.0000000|
| 18|chr6 | 30854186|cg09965419 | 0.0852155| 0.0242037| 0.0004303|
| 18|chr6 | 30854233|cg17091577 | 0.0834024| 0.0257151| 0.0011815|
| 18|chr6 | 30854551|cg15656686 | 0.1179877| 0.0191640| 0.0000000|
| 19|chr6 | 30955992|cg05123447 | 0.0459193| 0.0185740| 0.0134271|
| 19|chr6 | 30956214|cg26556020 | 0.0469319| 0.0285778| 0.1005376|
| 19|chr6 | 30956221|cg07491399 | 0.0337318| 0.0220895| 0.1267479|
| 19|chr6 | 30956397|cg24067150 | 0.0465228| 0.0078675| 0.0000000|
| 19|chr6 | 30956440|cg25159149 | 0.0458519| 0.0100622| 0.0000052|
| 20|chr6 | 31079110|cg17323974 | 0.0534675| 0.0107817| 0.0000007|
| 20|chr6 | 31079152|cg08951273 | 0.0715681| 0.0087428| 0.0000000|
| 20|chr6 | 31079306|cg15993401 | 0.0217831| 0.0176159| 0.2162510|
| 20|chr6 | 31079555|cg10185489 | 0.0228372| 0.0132467| 0.0847102|
| 20|chr6 | 31079617|cg17784811 | 0.0393704| 0.0181017| 0.0296334|
| 21|chr6 | 31127159|cg23679615 | -0.0885155| 0.0228118| 0.0001043|
| 21|chr6 | 31127173|cg21863888 | -0.0874801| 0.0238761| 0.0002484|
| 21|chr6 | 31127178|cg09045681 | -0.0785239| 0.0248822| 0.0016005|
| 21|chr6 | 31127271|cg10094358 | -0.1115438| 0.0258876| 0.0000164|
| 21|chr6 | 31127357|cg09329266 | -0.0940475| 0.0283812| 0.0009206|
| 21|chr6 | 31127379|cg21799473 | -0.0915739| 0.0256380| 0.0003545|
| 21|chr6 | 31127527|cg23654219 | -0.0594847| 0.0149943| 0.0000727|
| 21|chr6 | 31127863|cg16095155 | -0.0687672| 0.0146127| 0.0000025|
| 22|chr6 | 31549480|cg22934035 | -0.0926485| 0.0225478| 0.0000397|
| 22|chr6 | 31549563|cg26311932 | -0.0991315| 0.0140378| 0.0000000|
| 22|chr6 | 31549625|cg24479522 | -0.0720174| 0.0298864| 0.0159654|
| 22|chr6 | 31549631|cg21055528 | -0.1077615| 0.0108198| 0.0000000|
| 22|chr6 | 31549853|cg26724726 | -0.1432887| 0.0152955| 0.0000000|
| 22|chr6 | 31549929|cg06526741 | -0.0943205| 0.0119944| 0.0000000|
| 22|chr6 | 31550090|cg19279042 | -0.0865161| 0.0154381| 0.0000000|
| 23|chr6 | 31646236|cg00621943 | 0.0748559| 0.0122366| 0.0000000|
| 23|chr6 | 31646262|cg15039036 | 0.0573391| 0.0120663| 0.0000020|
| 23|chr6 | 31646366|cg27334499 | 0.0028921| 0.0159384| 0.8560097|
| 23|chr6 | 31646377|cg17187990 | 0.0170122| 0.0174635| 0.3299779|
| 23|chr6 | 31646625|cg12632549 | 0.0731516| 0.0231392| 0.0015703|
| 24|chr6 | 31744391|cg16672203 | -0.1329963| 0.0180809| 0.0000000|
| 24|chr6 | 31744398|cg15369633 | -0.0949400| 0.0252150| 0.0001664|
| 24|chr6 | 31744524|cg12988118 | -0.1012584| 0.0272224| 0.0001995|
| 24|chr6 | 31744545|cg23916646 | -0.1270805| 0.0231574| 0.0000000|
| 24|chr6 | 31744612|cg12383352 | -0.1185445| 0.0248924| 0.0000019|
| 24|chr6 | 31744628|cg27143082 | -0.0902251| 0.0275646| 0.0010633|
| 24|chr6 | 31744636|cg27574980 | -0.1179906| 0.0245011| 0.0000015|
| 24|chr6 | 31744735|cg24065328 | -0.1385544| 0.0221587| 0.0000000|
| 24|chr6 | 31744816|cg19868593 | -0.0939086| 0.0258975| 0.0002877|
| 24|chr6 | 31744831|cg05447916 | -0.1131832| 0.0254600| 0.0000088|
| 25|chr6 | 31846797|cg07357081 | 0.0596000| 0.0138991| 0.0000180|
| 25|chr6 | 31846813|cg23431175 | 0.0243320| 0.0245092| 0.3208223|
| 25|chr6 | 31846899|cg21236501 | 0.0739955| 0.0172653| 0.0000182|
| 25|chr6 | 31846924|cg24529722 | 0.0849608| 0.0199092| 0.0000198|
| 25|chr6 | 31846956|cg04567302 | 0.0477799| 0.0190684| 0.0122206|
| 25|chr6 | 31846970|cg03045620 | 0.0418653| 0.0183732| 0.0226909|
| 26|chr6 | 31867945|cg17243044 | -0.0755680| 0.0181911| 0.0000327|
| 26|chr6 | 31867956|cg00058449 | -0.0991778| 0.0127343| 0.0000000|
| 26|chr6 | 31867995|cg07249939 | -0.1080695| 0.0136897| 0.0000000|
| 26|chr6 | 31868021|cg12484688 | -0.0930608| 0.0153543| 0.0000000|
| 26|chr6 | 31868025|cg25110523 | -0.1148973| 0.0147600| 0.0000000|
| 26|chr6 | 31868133|cg00889295 | -0.0723599| 0.0297440| 0.0149846|
| 26|chr6 | 31868144|cg05680710 | -0.0238520| 0.0241229| 0.3227749|
| 26|chr6 | 31868162|cg07910050 | -0.0404111| 0.0219174| 0.0652134|
| 26|chr6 | 31868169|cg17766150 | -0.0571946| 0.0272606| 0.0358991|
| 26|chr6 | 31868207|cg06169557 | -0.0652424| 0.0258276| 0.0115346|
| 26|chr6 | 31868368|cg12229403 | -0.0439614| 0.0197288| 0.0258615|
| 26|chr6 | 31868418|cg03537740 | -0.0597538| 0.0244753| 0.0146307|
| 26|chr6 | 31868452|cg13464142 | -0.0625777| 0.0287193| 0.0293356|
| 26|chr6 | 31868470|cg20159839 | -0.0538207| 0.0252013| 0.0327092|
| 27|chr6 | 31937758|cg14666908 | -0.0923688| 0.0246890| 0.0001831|
| 27|chr6 | 31937906|cg22283528 | -0.0674884| 0.0140519| 0.0000016|
| 27|chr6 | 31937968|cg08721491 | -0.0400322| 0.0261884| 0.1263581|
| 27|chr6 | 31937973|cg15010006 | -0.0854724| 0.0235559| 0.0002851|
| 27|chr6 | 31938090|cg04654261 | -0.0545310| 0.0234533| 0.0200670|
| 27|chr6 | 31938176|cg00620476 | -0.0272449| 0.0191201| 0.1541751|
| 27|chr6 | 31938187|cg17587998 | -0.0152135| 0.0271285| 0.5749374|
| 27|chr6 | 31938207|cg20510378 | -0.0373073| 0.0202105| 0.0649021|
| 27|chr6 | 31938358|cg09346993 | -0.0091692| 0.0246650| 0.7100784|
| 27|chr6 | 31938372|cg01449563 | -0.0622017| 0.0206789| 0.0026299|
| 27|chr6 | 31938527|cg10201402 | -0.0632100| 0.0184577| 0.0006158|
| 27|chr6 | 31938533|cg23514417 | -0.0364712| 0.0225217| 0.1053658|
| 28|chr6 | 31939059|cg12776033 | -0.0875861| 0.0152930| 0.0000000|
| 28|chr6 | 31939085|cg26029547 | -0.0245157| 0.0271835| 0.3671311|
| 28|chr6 | 31939106|cg16190718 | -0.0414330| 0.0279153| 0.1377455|
| 28|chr6 | 31939112|cg23906067 | -0.0843669| 0.0240844| 0.0004601|
| 28|chr6 | 31939181|cg04142955 | -0.0669547| 0.0267664| 0.0123689|
| 28|chr6 | 31939224|cg10914467 | -0.0732949| 0.0274490| 0.0075801|
| 28|chr6 | 31939280|cg20194050 | -0.0922175| 0.0232613| 0.0000736|
| 28|chr6 | 31939319|cg04149916 | -0.0669540| 0.0280619| 0.0170354|
| 29|chr6 | 32013699|cg10967176 | 0.0578634| 0.0082523| 0.0000000|
| 29|chr6 | 32013710|cg14070039 | 0.0627561| 0.0075186| 0.0000000|
| 29|chr6 | 32013845|cg20621471 | 0.0550659| 0.0169361| 0.0011484|
| 29|chr6 | 32013974|cg13739666 | 0.0311762| 0.0218473| 0.1535798|
| 29|chr6 | 32014003|cg03819671 | 0.0141546| 0.0206556| 0.4931753|
| 29|chr6 | 32014059|cg26537323 | 0.0073518| 0.0258693| 0.7762629|
| 29|chr6 | 32014096|cg25522795 | 0.0174326| 0.0227670| 0.4438562|
| 29|chr6 | 32014100|cg18178844 | 0.0307302| 0.0224183| 0.1704485|
| 29|chr6 | 32014148|cg06824720 | 0.0509557| 0.0287177| 0.0760027|
| 29|chr6 | 32014189|cg16385684 | 0.0752194| 0.0182385| 0.0000372|
| 29|chr6 | 32014300|cg04182226 | 0.0188578| 0.0243463| 0.4385966|
| 29|chr6 | 32014381|cg22616343 | 0.0063350| 0.0161042| 0.6940419|
| 29|chr6 | 32014476|cg13409674 | 0.0175369| 0.0304824| 0.5650800|
| 29|chr6 | 32014484|cg14630748 | 0.0252643| 0.0285488| 0.3761814|
| 29|chr6 | 32014510|cg07481886 | 0.0348800| 0.0292591| 0.2332197|
| 29|chr6 | 32014605|cg09115485 | 0.0190211| 0.0158274| 0.2294474|
| 29|chr6 | 32014663|cg09423875 | 0.0466589| 0.0206613| 0.0239289|
| 29|chr6 | 32014674|cg08972588 | 0.0254215| 0.0186169| 0.1720938|
| 29|chr6 | 32014739|cg25375757 | 0.0723296| 0.0169683| 0.0000202|
| 30|chr6 | 32020425|cg07122553 | 0.0414882| 0.0096718| 0.0000179|
| 30|chr6 | 32020477|cg22800959 | 0.0652162| 0.0163215| 0.0000645|
| 30|chr6 | 32020479|cg00705156 | 0.0542607| 0.0108547| 0.0000006|
| 30|chr6 | 32020489|cg21554399 | 0.0502569| 0.0151791| 0.0009299|
| 30|chr6 | 32020498|cg01630940 | 0.0033497| 0.0179897| 0.8522878|
| 30|chr6 | 32020572|cg23285599 | 0.0384311| 0.0164462| 0.0194509|
| 30|chr6 | 32020587|cg05499272 | 0.0216049| 0.0169106| 0.2013937|
| 30|chr6 | 32020750|cg22259126 | 0.0561279| 0.0174840| 0.0013262|
| 31|chr6 | 32022898|cg25270367 | 0.0521446| 0.0125787| 0.0000339|
| 31|chr6 | 32022929|cg05598103 | 0.0595188| 0.0119202| 0.0000006|
| 31|chr6 | 32023102|cg11223361 | 0.0348962| 0.0140642| 0.0130939|
| 31|chr6 | 32023142|cg01054725 | 0.0268959| 0.0161439| 0.0957121|
| 31|chr6 | 32023246|cg14200543 | 0.0274669| 0.0168365| 0.1028078|
| 31|chr6 | 32023249|cg07910408 | 0.0432637| 0.0225178| 0.0546919|
| 31|chr6 | 32023251|cg09102573 | 0.0304399| 0.0210556| 0.1482642|
| 31|chr6 | 32023283|cg11815438 | 0.0646882| 0.0197018| 0.0010258|
| 31|chr6 | 32023332|cg02600478 | 0.0076457| 0.0244752| 0.7547475|
| 31|chr6 | 32023383|cg14011611 | 0.0040272| 0.0223974| 0.8573050|
| 31|chr6 | 32023409|cg16651678 | 0.0690415| 0.0233394| 0.0030949|
| 31|chr6 | 32023527|cg10750010 | 0.0299052| 0.0160993| 0.0632324|
| 31|chr6 | 32023650|cg06418131 | 0.0565061| 0.0125174| 0.0000064|
| 32|chr6 | 32037018|cg13069985 | 0.0568268| 0.0101261| 0.0000000|
| 32|chr6 | 32037097|cg15846590 | -0.0203538| 0.0293228| 0.4876016|
| 32|chr6 | 32037148|cg19644336 | 0.0301327| 0.0246112| 0.2208210|
| 32|chr6 | 32037290|cg05227556 | 0.0544538| 0.0142427| 0.0001317|
| 32|chr6 | 32037339|cg07139946 | 0.0585110| 0.0162122| 0.0003073|
| 32|chr6 | 32037342|cg01886385 | 0.0651169| 0.0149918| 0.0000140|
| 32|chr6 | 32037421|cg23858197 | 0.0250787| 0.0155224| 0.1061706|
| 32|chr6 | 32037426|cg08277291 | 0.0380627| 0.0191002| 0.0462847|
| 32|chr6 | 32037453|cg09381582 | 0.0452096| 0.0154411| 0.0034129|
| 32|chr6 | 32037474|cg21386904 | 0.0180316| 0.0142395| 0.2054043|
| 32|chr6 | 32037587|cg02571560 | 0.0410477| 0.0178117| 0.0211927|
| 32|chr6 | 32037602|cg02969214 | 0.0154629| 0.0160582| 0.3355837|
| 32|chr6 | 32037632|cg14698808 | 0.0116169| 0.0141993| 0.4132799|
| 32|chr6 | 32037653|cg21830122 | 0.0387630| 0.0152443| 0.0109969|
| 32|chr6 | 32037735|cg16416464 | 0.0665907| 0.0252700| 0.0084096|
| 32|chr6 | 32037751|cg24506088 | 0.0205561| 0.0189513| 0.2780633|
| 32|chr6 | 32037800|cg05596841 | 0.0042574| 0.0205186| 0.8356263|
| 33|chr6 | 32042200|cg03144708 | 0.0353414| 0.0124635| 0.0045741|
| 33|chr6 | 32042344|cg13308063 | 0.0387898| 0.0213276| 0.0689480|
| 33|chr6 | 32042351|cg13205613 | 0.0631600| 0.0182999| 0.0005577|
| 33|chr6 | 32042430|cg02927981 | 0.0052016| 0.0154604| 0.7365348|
| 33|chr6 | 32042518|cg03169843 | -0.0293359| 0.0264765| 0.2678632|
| 33|chr6 | 32042526|cg26950876 | 0.0301300| 0.0338511| 0.3734258|
| 33|chr6 | 32042534|cg07460894 | 0.0017347| 0.0280651| 0.9507137|
| 33|chr6 | 32042658|cg00013543 | -0.0244076| 0.0246059| 0.3212247|
| 33|chr6 | 32042797|cg23623681 | 0.0424775| 0.0129319| 0.0010209|
| 33|chr6 | 32042947|cg20170809 | 0.0548336| 0.0094096| 0.0000000|
| 33|chr6 | 32043029|cg14173662 | 0.0553816| 0.0193324| 0.0041739|
| 33|chr6 | 32043191|cg06878311 | 0.0198667| 0.0098425| 0.0435443|
| 33|chr6 | 32043561|cg22825871 | 0.0513585| 0.0083843| 0.0000000|
| 33|chr6 | 32043676|cg25962829 | 0.0451832| 0.0153327| 0.0032104|
| 33|chr6 | 32043739|cg04492496 | 0.0728570| 0.0091460| 0.0000000|
| 33|chr6 | 32044104|cg15318957 | 0.0224676| 0.0138420| 0.1045586|
| 33|chr6 | 32044163|cg08660959 | 0.0425730| 0.0205270| 0.0380790|
| 33|chr6 | 32044179|cg07485305 | 0.0707318| 0.0180229| 0.0000869|
| 33|chr6 | 32044203|cg20407792 | 0.0041450| 0.0145242| 0.7753506|
| 33|chr6 | 32044254|cg05423418 | 0.0464549| 0.0130002| 0.0003524|
| 34|chr6 | 32044384|cg05569328 | 0.0632515| 0.0168732| 0.0001778|
| 34|chr6 | 32044404|cg22851080 | 0.0918711| 0.0199763| 0.0000042|
| 34|chr6 | 32044496|cg27428104 | 0.0651064| 0.0215196| 0.0024827|
| 34|chr6 | 32044869|cg23164535 | 0.0510180| 0.0166487| 0.0021812|
| 34|chr6 | 32044959|cg02133510 | 0.0158587| 0.0143360| 0.2686349|
| 34|chr6 | 32045323|cg04076535 | 0.0423971| 0.0116441| 0.0002715|
| 35|chr6 | 32048449|cg18431489 | 0.0604830| 0.0128694| 0.0000026|
| 35|chr6 | 32048463|cg15212833 | 0.0654139| 0.0213765| 0.0022127|
| 35|chr6 | 32048632|cg06696874 | 0.0377689| 0.0135462| 0.0053009|
| 35|chr6 | 32048679|cg02550722 | 0.0601228| 0.0147345| 0.0000450|
| 35|chr6 | 32049053|cg27624229 | 0.0571857| 0.0230224| 0.0129948|
| 35|chr6 | 32049177|cg00661399 | 0.0490283| 0.0264692| 0.0639859|
| 35|chr6 | 32049196|cg13199127 | 0.0713010| 0.0281338| 0.0112656|
| 35|chr6 | 32049235|cg17031787 | 0.0769871| 0.0219826| 0.0004615|
| 35|chr6 | 32049263|cg15712520 | 0.0174487| 0.0216647| 0.4205907|
| 35|chr6 | 32049322|cg09975576 | 0.0585593| 0.0116761| 0.0000005|
| 35|chr6 | 32049354|cg07306331 | 0.0238488| 0.0207991| 0.2515368|
| 35|chr6 | 32049373|cg15048806 | 0.0213092| 0.0192680| 0.2687527|
| 35|chr6 | 32049376|cg14218053 | 0.0364012| 0.0204221| 0.0746769|
| 35|chr6 | 32049513|cg17295739 | 0.0579886| 0.0284546| 0.0415565|
| 35|chr6 | 32049516|cg10303653 | 0.0409066| 0.0235653| 0.0825851|
| 35|chr6 | 32049622|cg08753391 | 0.0958057| 0.0218816| 0.0000120|
| 35|chr6 | 32049699|cg04872123 | 0.0663145| 0.0182384| 0.0002769|
| 35|chr6 | 32049825|cg20116929 | 0.0344560| 0.0164789| 0.0365355|
| 35|chr6 | 32049829|cg11289677 | 0.0601781| 0.0218992| 0.0059967|
| 35|chr6 | 32049845|cg05471725 | 0.0014822| 0.0220097| 0.9463090|
| 36|chr6 | 32060791|cg02151997 | 0.0942577| 0.0241650| 0.0000960|
| 36|chr6 | 32060794|cg04757901 | 0.0726107| 0.0237271| 0.0022115|
| 36|chr6 | 32060816|cg23145336 | 0.1308970| 0.0166251| 0.0000000|
| 36|chr6 | 32061084|cg15642307 | 0.1245957| 0.0218110| 0.0000000|
| 36|chr6 | 32061160|cg07148038 | 0.0606021| 0.0144964| 0.0000291|
| 36|chr6 | 32061318|cg23641899 | 0.0681344| 0.0094939| 0.0000000|
| 36|chr6 | 32061478|cg24504289 | 0.0982410| 0.0078538| 0.0000000|
| 37|chr6 | 32086755|cg25065981 | 0.0880026| 0.0257344| 0.0006270|
| 37|chr6 | 32086758|cg27001603 | 0.1049990| 0.0284150| 0.0002197|
| 37|chr6 | 32086779|cg04962282 | 0.0473999| 0.0276648| 0.0866461|
| 37|chr6 | 32086782|cg06111526 | 0.0822598| 0.0249918| 0.0009966|
| 37|chr6 | 32086818|cg10089357 | 0.0959562| 0.0261365| 0.0002413|
| 37|chr6 | 32086857|cg07986385 | 0.0919125| 0.0255865| 0.0003279|
| 37|chr6 | 32086878|cg17396404 | 0.0867368| 0.0233334| 0.0002014|
| 37|chr6 | 32086893|cg19004565 | 0.1020329| 0.0178593| 0.0000000|
| 38|chr6 | 32120203|cg04749507 | 0.1198729| 0.0210175| 0.0000000|
| 38|chr6 | 32120324|cg19048176 | 0.1256765| 0.0152671| 0.0000000|
| 38|chr6 | 32120584|cg06814287 | 0.1260252| 0.0212687| 0.0000000|
| 38|chr6 | 32120623|cg18235088 | 0.1353823| 0.0194376| 0.0000000|
| 38|chr6 | 32120625|cg08045906 | 0.1523929| 0.0174620| 0.0000000|
| 38|chr6 | 32120773|cg12883279 | 0.1521650| 0.0182417| 0.0000000|
| 38|chr6 | 32120783|cg12626589 | 0.1453301| 0.0180123| 0.0000000|
| 38|chr6 | 32120826|cg25426302 | 0.1421975| 0.0178451| 0.0000000|
| 38|chr6 | 32120863|cg06025456 | 0.1338643| 0.0165478| 0.0000000|
| 38|chr6 | 32120878|cg13934406 | 0.1395729| 0.0138750| 0.0000000|
| 38|chr6 | 32120895|cg17113856 | 0.1269924| 0.0174787| 0.0000000|
| 38|chr6 | 32120899|cg06108383 | 0.1275164| 0.0150833| 0.0000000|
| 38|chr6 | 32120901|cg02956248 | 0.1351876| 0.0166930| 0.0000000|
| 38|chr6 | 32120907|cg23359665 | 0.1316898| 0.0176902| 0.0000000|
| 38|chr6 | 32120933|cg10551329 | 0.1316254| 0.0155450| 0.0000000|
| 38|chr6 | 32120955|cg16481280 | 0.1206437| 0.0145211| 0.0000000|
| 38|chr6 | 32121055|cg01111041 | 0.1320252| 0.0150413| 0.0000000|
| 38|chr6 | 32121113|cg20328456 | 0.1215476| 0.0141210| 0.0000000|
| 39|chr6 | 32121143|cg03570994 | 0.1095963| 0.0112578| 0.0000000|
| 39|chr6 | 32121156|cg11386011 | 0.1113099| 0.0121279| 0.0000000|
| 39|chr6 | 32121204|cg12738718 | 0.1161463| 0.0188377| 0.0000000|
| 39|chr6 | 32121225|cg14130039 | 0.1262075| 0.0179329| 0.0000000|
| 39|chr6 | 32121249|cg05133205 | 0.1261820| 0.0165417| 0.0000000|
| 39|chr6 | 32121259|cg17329164 | 0.1225339| 0.0163152| 0.0000000|
| 39|chr6 | 32121261|cg18049167 | 0.1125958| 0.0185609| 0.0000000|
| 39|chr6 | 32121355|cg04105091 | 0.1160281| 0.0188530| 0.0000000|
| 39|chr6 | 32121368|cg12585943 | 0.1145624| 0.0151163| 0.0000000|
| 39|chr6 | 32121393|cg13102294 | 0.1197061| 0.0157364| 0.0000000|
| 39|chr6 | 32121420|cg00552704 | 0.1117626| 0.0194779| 0.0000000|
| 39|chr6 | 32121433|cg06264679 | 0.1134183| 0.0173969| 0.0000000|
| 39|chr6 | 32121471|cg00933538 | 0.0603220| 0.0228462| 0.0082819|
| 39|chr6 | 32121475|cg23470939 | 0.0752624| 0.0282451| 0.0077076|
| 40|chr6 | 32122736|cg21241317 | -0.0940792| 0.0272468| 0.0005547|
| 40|chr6 | 32122738|cg04877280 | -0.0913755| 0.0275097| 0.0008951|
| 40|chr6 | 32122753|cg06832687 | -0.1184888| 0.0195084| 0.0000000|
| 40|chr6 | 32122779|cg27070869 | -0.0633859| 0.0275227| 0.0212767|
| 40|chr6 | 32122864|cg03995156 | -0.1012236| 0.0166360| 0.0000000|
| 41|chr6 | 32135241|cg16681436 | 0.0380111| 0.0129310| 0.0032871|
| 41|chr6 | 32135285|cg12508392 | 0.0139004| 0.0204100| 0.4958368|
| 41|chr6 | 32135321|cg00359087 | 0.0078081| 0.0196024| 0.6903941|
| 41|chr6 | 32135326|cg26687830 | 0.0019283| 0.0262969| 0.9415444|
| 41|chr6 | 32135370|cg10262770 | 0.0209381| 0.0190779| 0.2724211|
| 41|chr6 | 32135379|cg07754347 | -0.0052812| 0.0200649| 0.7923923|
| 41|chr6 | 32135384|cg16006963 | 0.0104801| 0.0214948| 0.6258590|
| 41|chr6 | 32135396|cg06024540 | 0.0017704| 0.0278038| 0.9492295|
| 41|chr6 | 32135715|cg12305588 | 0.0487057| 0.0073939| 0.0000000|
| 41|chr6 | 32135718|cg08759957 | 0.0567178| 0.0077728| 0.0000000|
| 41|chr6 | 32135728|cg12827283 | 0.0674969| 0.0115235| 0.0000000|
| 41|chr6 | 32135776|cg11356887 | 0.0455947| 0.0100301| 0.0000055|
| 41|chr6 | 32135803|cg26785234 | 0.0590164| 0.0091618| 0.0000000|
| 42|chr6 | 32150404|cg08321684 | 0.0317791| 0.0084644| 0.0001737|
| 42|chr6 | 32150577|cg23177883 | 0.0082737| 0.0115063| 0.4721083|
| 42|chr6 | 32150585|cg11105830 | 0.0124544| 0.0103557| 0.2291065|
| 42|chr6 | 32150656|cg26505596 | 0.0243330| 0.0324130| 0.4528236|
| 42|chr6 | 32150716|cg26653489 | -0.0166842| 0.0177231| 0.3465108|
| 43|chr6 | 32154416|cg18057469 | -0.0650918| 0.0205330| 0.0015238|
| 43|chr6 | 32154447|cg14635654 | -0.1158400| 0.0209838| 0.0000000|
| 43|chr6 | 32154454|cg18809947 | -0.0651060| 0.0261868| 0.0129111|
| 43|chr6 | 32154568|cg03422527 | -0.0994093| 0.0213716| 0.0000033|
| 43|chr6 | 32154613|cg01940915 | -0.0724621| 0.0223119| 0.0011634|
| 43|chr6 | 32154715|cg20765522 | -0.1057901| 0.0139633| 0.0000000|
| 44|chr6 | 32158927|cg17851795 | -0.0634730| 0.0262394| 0.0155636|
| 44|chr6 | 32158953|cg03280235 | -0.0645184| 0.0223107| 0.0038302|
| 44|chr6 | 32159036|cg16609995 | -0.0991986| 0.0183662| 0.0000001|
| 44|chr6 | 32159527|cg21386484 | -0.1405397| 0.0184502| 0.0000000|
| 44|chr6 | 32159604|cg19555708 | -0.1147191| 0.0228179| 0.0000005|
| 44|chr6 | 32159607|cg06194738 | -0.1290303| 0.0224632| 0.0000000|
| 44|chr6 | 32159933|cg19321684 | -0.1487378| 0.0157545| 0.0000000|
| 44|chr6 | 32160074|cg00442389 | -0.1422843| 0.0151954| 0.0000000|
| 45|chr6 | 32171796|cg14996490 | 0.0336560| 0.0134619| 0.0124162|
| 45|chr6 | 32171823|cg05380127 | 0.0257353| 0.0088432| 0.0036123|
| 45|chr6 | 32172007|cg13336485 | 0.0045858| 0.0122188| 0.7074334|
| 45|chr6 | 32172013|cg27597473 | -0.0067288| 0.0176515| 0.7030529|
| 45|chr6 | 32172027|cg16642360 | -0.0018143| 0.0158587| 0.9089182|
| 45|chr6 | 32172124|cg22022067 | 0.0401365| 0.0099830| 0.0000581|
| 46|chr6 | 32805398|cg12854186 | -0.1513757| 0.0150578| 0.0000000|
| 46|chr6 | 32805548|cg03438552 | -0.1426522| 0.0177625| 0.0000000|
| 46|chr6 | 32805554|cg22940798 | -0.1581847| 0.0164751| 0.0000000|
| 46|chr6 | 32805570|cg08998192 | -0.1475779| 0.0188510| 0.0000000|
| 46|chr6 | 32805684|cg13563634 | -0.1146810| 0.0221911| 0.0000002|
| 47|chr6 | 32812933|cg05697726 | -0.1267054| 0.0124278| 0.0000000|
| 47|chr6 | 32812953|cg16483840 | -0.1160184| 0.0193411| 0.0000000|
| 47|chr6 | 32812965|cg02657012 | -0.1461522| 0.0140874| 0.0000000|
| 47|chr6 | 32813084|cg16890093 | -0.1692340| 0.0112045| 0.0000000|
| 47|chr6 | 32813154|cg11706729 | -0.0774957| 0.0156555| 0.0000007|
| 47|chr6 | 32813211|cg07218288 | -0.0535592| 0.0329116| 0.1036598|
| 47|chr6 | 32813337|cg19136673 | -0.1617629| 0.0137228| 0.0000000|
| 47|chr6 | 32813441|cg05693489 | 0.0110656| 0.0259386| 0.6696656|
| 47|chr6 | 32813448|cg12253437 | -0.0440842| 0.0214105| 0.0394945|
| 48|chr6 | 32820355|cg08818207 | -0.1206501| 0.0223959| 0.0000001|
| 48|chr6 | 32820410|cg04773990 | -0.1622381| 0.0159072| 0.0000000|
| 48|chr6 | 32820421|cg24154161 | -0.1310339| 0.0231500| 0.0000000|
| 48|chr6 | 32820546|cg23880953 | -0.1491729| 0.0203307| 0.0000000|
| 48|chr6 | 32820553|cg26700949 | -0.1247669| 0.0267352| 0.0000031|
| 48|chr6 | 32820577|cg15926590 | -0.1422087| 0.0182045| 0.0000000|
| 49|chr6 | 32825701|cg02878284 | 0.0431232| 0.0083064| 0.0000002|
| 49|chr6 | 32825852|cg19994157 | 0.0095956| 0.0095798| 0.3165110|
| 49|chr6 | 32825897|cg00045690 | 0.0322623| 0.0123032| 0.0087349|
| 49|chr6 | 32826171|cg04913118 | 0.0424573| 0.0083450| 0.0000004|
| 49|chr6 | 32826197|cg06043617 | 0.0262839| 0.0109621| 0.0164979|
| 50|chr6 | 32908567|cg10310595 | -0.1324225| 0.0227564| 0.0000000|
| 50|chr6 | 32908605|cg16236263 | -0.1433555| 0.0215182| 0.0000000|
| 50|chr6 | 32908642|cg00575744 | -0.1351980| 0.0219912| 0.0000000|
| 50|chr6 | 32908718|cg12840248 | -0.1329792| 0.0227719| 0.0000000|
| 50|chr6 | 32908794|cg25247351 | -0.1312033| 0.0237725| 0.0000000|
| 50|chr6 | 32908901|cg10714284 | -0.1429521| 0.0224331| 0.0000000|
| 50|chr6 | 32908980|cg16300030 | -0.1676273| 0.0150704| 0.0000000|
| 50|chr6 | 32909003|cg20392842 | -0.1598784| 0.0169428| 0.0000000|
| 50|chr6 | 32909282|cg20600379 | -0.1404678| 0.0202167| 0.0000000|
| 50|chr6 | 32909397|cg00862588 | -0.1205997| 0.0173209| 0.0000000|
| 50|chr6 | 32909440|cg10518264 | -0.1094457| 0.0163014| 0.0000000|
| 50|chr6 | 32909493|cg21470947 | -0.1094288| 0.0137516| 0.0000000|
| 50|chr6 | 32909523|cg07623567 | -0.1350158| 0.0190329| 0.0000000|
| 51|chr6 | 32942063|cg11439393 | -0.1165383| 0.0234906| 0.0000007|
| 51|chr6 | 32942205|cg18918417 | -0.1316404| 0.0227900| 0.0000000|
| 51|chr6 | 32942358|cg16416715 | -0.1340703| 0.0224418| 0.0000000|
| 51|chr6 | 32942400|cg26264318 | -0.1063840| 0.0258753| 0.0000393|
| 51|chr6 | 32942429|cg25158622 | -0.1444292| 0.0186863| 0.0000000|
| 51|chr6 | 32942494|cg26953232 | -0.1526354| 0.0190591| 0.0000000|
| 51|chr6 | 32942541|cg24275356 | -0.1114375| 0.0251043| 0.0000090|
| 51|chr6 | 32942710|cg27395200 | -0.1336472| 0.0157469| 0.0000000|
| 51|chr6 | 32942714|cg07275218 | -0.1278996| 0.0183328| 0.0000000|
| 51|chr6 | 32942808|cg17451586 | -0.1454581| 0.0210295| 0.0000000|
| 51|chr6 | 32943025|cg02471378 | -0.1317711| 0.0201084| 0.0000000|
| 52|chr6 | 33043841|cg02286081 | -0.1337190| 0.0230865| 0.0000000|
| 52|chr6 | 33043849|cg22483030 | -0.1296716| 0.0229438| 0.0000000|
| 52|chr6 | 33043868|cg26350754 | -0.1189423| 0.0252242| 0.0000024|
| 52|chr6 | 33043976|cg12365667 | -0.0930881| 0.0274477| 0.0006952|
| 52|chr6 | 33044012|cg12939283 | -0.1348687| 0.0220010| 0.0000000|
| 52|chr6 | 33044345|cg14356799 | -0.1094301| 0.0256268| 0.0000195|
| 52|chr6 | 33044510|cg00750366 | -0.0952827| 0.0279658| 0.0006565|
| 53|chr6 | 33132163|cg04820679 | 0.0800563| 0.0160236| 0.0000006|
| 53|chr6 | 33132181|cg07570257 | 0.0624801| 0.0221740| 0.0048367|
| 53|chr6 | 33132192|cg14147420 | 0.0474335| 0.0179623| 0.0082726|
| 53|chr6 | 33132241|cg12945707 | 0.0890059| 0.0151261| 0.0000000|
| 53|chr6 | 33132318|cg10537192 | 0.0416781| 0.0206160| 0.0432140|
| 54|chr6 | 33132650|cg13478289 | 0.0623967| 0.0190634| 0.0010637|
| 54|chr6 | 33132693|cg19887293 | 0.0368220| 0.0175806| 0.0362184|
| 54|chr6 | 33132705|cg01828813 | 0.0621322| 0.0226616| 0.0061115|
| 54|chr6 | 33132727|cg17578548 | 0.0095940| 0.0253775| 0.7053936|
| 54|chr6 | 33132943|cg20506659 | 0.0302774| 0.0192878| 0.1164694|
| 54|chr6 | 33132996|cg15047502 | 0.0203154| 0.0133922| 0.1292778|
| 54|chr6 | 33133039|cg26144659 | 0.0151949| 0.0100293| 0.1297575|
| 54|chr6 | 33133083|cg17790159 | 0.0308606| 0.0080224| 0.0001197|
| 54|chr6 | 33133329|cg24483785 | 0.0186437| 0.0114476| 0.1033937|
| 54|chr6 | 33133370|cg23332813 | 0.0141153| 0.0146426| 0.3350509|
| 54|chr6 | 33133485|cg06049932 | 0.0595455| 0.0171565| 0.0005190|
| 54|chr6 | 33133517|cg02667414 | 0.0254879| 0.0180811| 0.1586442|
| 54|chr6 | 33133531|cg00324223 | 0.0250070| 0.0161946| 0.1225495|
| 54|chr6 | 33133535|cg24213189 | 0.0049175| 0.0214155| 0.8183834|
| 54|chr6 | 33133538|cg22370716 | 0.0126669| 0.0180955| 0.4839249|
| 54|chr6 | 33133675|cg01701055 | 0.0448536| 0.0101642| 0.0000102|
| 54|chr6 | 33133752|cg15081128 | 0.0278885| 0.0105656| 0.0083013|
| 54|chr6 | 33134045|cg06924878 | 0.0309625| 0.0157284| 0.0490022|
| 54|chr6 | 33134078|cg23945333 | 0.0349533| 0.0139671| 0.0123307|
| 55|chr6 | 33245488|cg06753439 | -0.1322913| 0.0199100| 0.0000000|
| 55|chr6 | 33245490|cg03108070 | -0.1468223| 0.0187034| 0.0000000|
| 55|chr6 | 33245516|cg19241689 | -0.1433868| 0.0209017| 0.0000000|
| 55|chr6 | 33245537|cg16396284 | -0.1578083| 0.0176820| 0.0000000|
| 55|chr6 | 33245541|cg17416730 | -0.1662809| 0.0145976| 0.0000000|
| 55|chr6 | 33245553|cg26270195 | -0.1255039| 0.0246871| 0.0000004|
| 56|chr6 | 33245706|cg03721978 | -0.0999077| 0.0175918| 0.0000000|
| 56|chr6 | 33245717|cg09349343 | -0.1014203| 0.0205029| 0.0000008|
| 56|chr6 | 33245721|cg17103217 | -0.1046379| 0.0202272| 0.0000002|
| 56|chr6 | 33245739|cg23950233 | -0.0855352| 0.0231036| 0.0002137|
| 56|chr6 | 33245770|cg21618521 | -0.0915700| 0.0176115| 0.0000002|
| 56|chr6 | 33245779|cg19882268 | -0.0246106| 0.0283363| 0.3851114|
| 56|chr6 | 33245804|cg00052772 | -0.1124515| 0.0163070| 0.0000000|
| 57|chr6 | 33245893|cg06362282 | -0.1471256| 0.0167391| 0.0000000|
| 57|chr6 | 33245895|cg24605046 | -0.1352626| 0.0197275| 0.0000000|
| 57|chr6 | 33245990|cg26055446 | -0.1388379| 0.0213931| 0.0000000|
| 57|chr6 | 33246008|cg03169472 | -0.1472251| 0.0203723| 0.0000000|
| 57|chr6 | 33246043|cg16090881 | -0.1000398| 0.0189134| 0.0000001|
| 57|chr6 | 33246091|cg16226644 | -0.1307261| 0.0200605| 0.0000000|
| 57|chr6 | 33246094|cg13882090 | -0.1377345| 0.0168440| 0.0000000|
| 58|chr6 | 41010111|cg25533211 | 0.0474561| 0.0066796| 0.0000000|
| 58|chr6 | 41010217|cg20377447 | 0.0401030| 0.0070032| 0.0000000|
| 58|chr6 | 41010223|cg13983640 | 0.0524027| 0.0123288| 0.0000213|
| 58|chr6 | 41010316|cg22801217 | 0.0390960| 0.0059316| 0.0000000|
| 58|chr6 | 41010375|cg22815409 | 0.0316286| 0.0080956| 0.0000935|
| 58|chr6 | 41010654|cg04904815 | 0.0536667| 0.0193641| 0.0055808|
| 59|chr6 | 53530503|cg00536792 | 0.0575961| 0.0249095| 0.0207659|
| 59|chr6 | 53530538|cg15658676 | 0.0764135| 0.0187394| 0.0000455|
| 59|chr6 | 53530570|cg19801120 | 0.0816580| 0.0191154| 0.0000194|
| 59|chr6 | 53530600|cg06485521 | 0.0743545| 0.0231992| 0.0013504|
| 59|chr6 | 53530624|cg26980034 | 0.0661843| 0.0233828| 0.0046481|
| 59|chr6 | 53530628|cg13840445 | 0.0994877| 0.0172199| 0.0000000|
| 60|chr6 | 149805995|cg15132169 | -0.1421403| 0.0180800| 0.0000000|
| 60|chr6 | 149806077|cg18951352 | -0.1573447| 0.0143688| 0.0000000|
| 60|chr6 | 149806081|cg09678939 | -0.1582970| 0.0141131| 0.0000000|
| 60|chr6 | 149806131|cg13136655 | -0.1593556| 0.0127474| 0.0000000|
| 60|chr6 | 149806235|cg02464487 | -0.1654364| 0.0146566| 0.0000000|
| 60|chr6 | 149806273|cg04275695 | -0.1607989| 0.0149558| 0.0000000|
| 60|chr6 | 149806331|cg17501395 | -0.1619124| 0.0139751| 0.0000000|
| 60|chr6 | 149806339|cg18082788 | -0.1565043| 0.0142206| 0.0000000|
| 60|chr6 | 149806502|cg00073460 | -0.0965617| 0.0247094| 0.0000931|
| 60|chr6 | 149806635|cg06762457 | -0.0436767| 0.0158661| 0.0059081|
| 60|chr6 | 149806732|cg14030904 | -0.0843969| 0.0139906| 0.0000000|
| 61|chr6 | 152702330|cg00041666 | 0.0477057| 0.0136213| 0.0004613|
| 61|chr6 | 152702365|cg07604117 | 0.0420085| 0.0163071| 0.0099925|
| 61|chr6 | 152702387|cg19827346 | 0.0435096| 0.0198885| 0.0286934|
| 61|chr6 | 152702444|cg20187047 | 0.0427556| 0.0134452| 0.0014728|
| 61|chr6 | 152702463|cg13806292 | 0.0875492| 0.0082688| 0.0000000|
| 62|chr6 | 170580947|cg24039042 | -0.0921876| 0.0250976| 0.0002396|
| 62|chr6 | 170580966|cg01766850 | -0.0748875| 0.0274486| 0.0063665|
| 62|chr6 | 170581039|cg05973084 | -0.0874901| 0.0273323| 0.0013696|
| 62|chr6 | 170581085|cg09344348 | -0.0212537| 0.0316357| 0.5016956|
| 62|chr6 | 170581248|cg18555277 | -0.0576516| 0.0198330| 0.0036508|
| 62|chr6 | 170581355|cg01209642 | -0.0589026| 0.0255071| 0.0209289|
| 62|chr6 | 170581502|cg21138542 | -0.1174579| 0.0191805| 0.0000000|
| 62|chr6 | 170581690|cg03899510 | -0.0532274| 0.0254434| 0.0364393|
best6 <- dmrs6[which.min(dmrs6$p.value),]
dmrff.plot(
best6$chr, best6$start, best6$end,
meta$ewas$estimate, meta$ewas$se, meta$ewas$chr, meta$ewas$pos)
## Loading required package: ggplot2
We can use the same function to show the summary statistics for these sites
from one of the original studies.
acc <- "GSE79056"
sites <- dmrff.sites(dmrs6, stats[[acc]]$chr, stats[[acc]]$pos)
sites <- cbind(sites[,c("region","chr","pos")],
stats[[acc]][sites$site,c("estimate","se","p.value")])
kable(sites,row.names=F)
| region|chr | pos| estimate| se| p.value|
|------:|:----|---------:|----------:|---------:|---------:|
| 1|chr6 | 1635611| 0.0053363| 0.0006958| 0.0000000|
| 1|chr6 | 1635640| 0.0063335| 0.0008181| 0.0000000|
| 1|chr6 | 1635808| 0.0073781| 0.0007358| 0.0000000|
| 1|chr6 | 1635818| 0.0064351| 0.0008352| 0.0000000|
| 1|chr6 | 1635847| 0.0083883| 0.0007770| 0.0000000|
| 2|chr6 | 15504844| -0.0113105| 0.0009718| 0.0000000|
| 2|chr6 | 15504872| -0.0100702| 0.0009470| 0.0000000|
| 2|chr6 | 15504923| -0.0109958| 0.0009858| 0.0000000|
| 2|chr6 | 15505094| -0.0184816| 0.0016960| 0.0000000|
| 2|chr6 | 15505345| -0.0023223| 0.0005873| 0.0003840|
| 2|chr6 | 15505452| -0.0017037| 0.0004356| 0.0004337|
| 2|chr6 | 15505460| -0.0038243| 0.0006648| 0.0000020|
| 2|chr6 | 15505949| -0.0049969| 0.0009589| 0.0000099|
| 2|chr6 | 15506085| -0.0111326| 0.0014722| 0.0000000|
| 3|chr6 | 25652383| 0.0029570| 0.0004757| 0.0000005|
| 3|chr6 | 25652390| 0.0020246| 0.0005783| 0.0013540|
| 3|chr6 | 25652395| 0.0011633| 0.0005708| 0.0496633|
| 3|chr6 | 25652405| 0.0014082| 0.0005784| 0.0204916|
| 3|chr6 | 25652407| 0.0005231| 0.0004102| 0.2111513|
| 3|chr6 | 25652531| 0.0008247| 0.0003650| 0.0305841|
| 3|chr6 | 25652602| 0.0010391| 0.0003115| 0.0021187|
| 4|chr6 | 28543262| 0.0007349| 0.0006114| 0.2379327|
| 4|chr6 | 28543508| 0.0010910| 0.0006956| 0.1266460|
| 4|chr6 | 28543514| 0.0021095| 0.0005610| 0.0006616|
| 4|chr6 | 28543667| 0.0083357| 0.0014310| 0.0000016|
| 4|chr6 | 28543670| 0.0083497| 0.0013315| 0.0000004|
| 5|chr6 | 29520752| 0.0051044| 0.0016067| 0.0032272|
| 5|chr6 | 29520774| 0.0120810| 0.0019128| 0.0000004|
| 5|chr6 | 29520965| 0.0038275| 0.0009041| 0.0001729|
| 5|chr6 | 29521013| 0.0045393| 0.0008581| 0.0000086|
| 5|chr6 | 29521023| 0.0039910| 0.0009063| 0.0001060|
| 5|chr6 | 29521046| 0.0030241| 0.0011091| 0.0104404|
| 6|chr6 | 29571363| 0.0027398| 0.0004724| 0.0000017|
| 6|chr6 | 29571419| 0.0006992| 0.0006111| 0.2607553|
| 6|chr6 | 29571429| -0.0001876| 0.0005052| 0.7127723|
| 6|chr6 | 29571432| 0.0008405| 0.0006006| 0.1710513|
| 6|chr6 | 29571438| 0.0001579| 0.0005151| 0.7611272|
| 6|chr6 | 29571468| 0.0005212| 0.0003924| 0.1932056|
| 6|chr6 | 29571483| -0.0008368| 0.0007880| 0.2960132|
| 6|chr6 | 29571693| 0.0000680| 0.0004994| 0.8925189|
| 7|chr6 | 29576987| 0.0021864| 0.0004052| 0.0000058|
| 7|chr6 | 29577006| -0.0000740| 0.0004983| 0.8828218|
| 7|chr6 | 29577082| 0.0009482| 0.0004277| 0.0336305|
| 7|chr6 | 29577223| 0.0015588| 0.0007135| 0.0361197|
| 7|chr6 | 29577348| 0.0019153| 0.0007907| 0.0210915|
| 8|chr6 | 29577916| 0.0011126| 0.0007108| 0.1270934|
| 8|chr6 | 29578124| -0.0001449| 0.0009887| 0.8844037|
| 8|chr6 | 29578144| 0.0015863| 0.0007730| 0.0481615|
| 8|chr6 | 29578313| 0.0025291| 0.0007500| 0.0019188|
| 8|chr6 | 29578423| 0.0019701| 0.0004786| 0.0002421|
| 9|chr6 | 29589573| -0.0001670| 0.0005581| 0.7666850|
| 9|chr6 | 29589631| 0.0001497| 0.0005547| 0.7888916|
| 9|chr6 | 29589707| 0.0012088| 0.0003386| 0.0011217|
| 9|chr6 | 29589714| 0.0003982| 0.0004516| 0.3842728|
| 9|chr6 | 29589729| 0.0004549| 0.0007802| 0.5638605|
| 10|chr6 | 29599012| 0.0046057| 0.0006266| 0.0000000|
| 10|chr6 | 29599160| 0.0090858| 0.0010374| 0.0000000|
| 10|chr6 | 29599178| 0.0090018| 0.0012280| 0.0000000|
| 10|chr6 | 29599226| 0.0108933| 0.0011754| 0.0000000|
| 10|chr6 | 29599250| 0.0109745| 0.0013997| 0.0000000|
| 10|chr6 | 29599259| 0.0102835| 0.0011497| 0.0000000|
| 10|chr6 | 29599319| 0.0140782| 0.0016932| 0.0000000|
| 10|chr6 | 29599331| 0.0099653| 0.0013887| 0.0000000|
| 10|chr6 | 29599390| 0.0113110| 0.0014083| 0.0000000|
| 10|chr6 | 29599836| 0.0016739| 0.0007429| 0.0310341|
| 11|chr6 | 29911295| -0.0046014| 0.0013833| 0.0021706|
| 11|chr6 | 29911334| -0.0055718| 0.0010543| 0.0000080|
| 11|chr6 | 29911339| -0.0038322| 0.0010044| 0.0005674|
| 11|chr6 | 29911366| -0.0087870| 0.0010933| 0.0000000|
| 11|chr6 | 29911494| -0.0028189| 0.0016230| 0.0917497|
| 11|chr6 | 29911542| -0.0082911| 0.0015855| 0.0000094|
| 11|chr6 | 29911550| -0.0055508| 0.0010538| 0.0000084|
| 12|chr6 | 30127760| 0.0034895| 0.0009843| 0.0012340|
| 12|chr6 | 30127997| 0.0029891| 0.0006232| 0.0000337|
| 12|chr6 | 30128219| 0.0018831| 0.0006779| 0.0089632|
| 12|chr6 | 30128238| 0.0021771| 0.0007528| 0.0067290|
| 12|chr6 | 30128254| 0.0012274| 0.0006494| 0.0675670|
| 12|chr6 | 30128385| 0.0014351| 0.0005207| 0.0094515|
| 12|chr6 | 30128404| 0.0028702| 0.0006394| 0.0000827|
| 12|chr6 | 30128427| 0.0014605| 0.0007050| 0.0461996|
| 12|chr6 | 30128511| 0.0020327| 0.0007291| 0.0087386|
| 12|chr6 | 30128526| 0.0009337| 0.0005204| 0.0819474|
| 12|chr6 | 30128542| 0.0003235| 0.0006045| 0.5961825|
| 12|chr6 | 30128548| 0.0012666| 0.0004980| 0.0158615|
| 12|chr6 | 30128558| 0.0020794| 0.0005404| 0.0005179|
| 12|chr6 | 30128686| 0.0033997| 0.0011544| 0.0058861|
| 12|chr6 | 30128775| 0.0037394| 0.0007283| 0.0000125|
| 13|chr6 | 30458158| -0.0010364| 0.0002062| 0.0000171|
| 13|chr6 | 30458161| -0.0052931| 0.0009179| 0.0000019|
| 13|chr6 | 30458237| -0.0063287| 0.0009044| 0.0000001|
| 13|chr6 | 30458519| -0.0087248| 0.0009109| 0.0000000|
| 13|chr6 | 30458586| -0.0078358| 0.0006527| 0.0000000|
| 13|chr6 | 30458601| -0.0108134| 0.0010658| 0.0000000|
| 13|chr6 | 30458730| -0.0055093| 0.0007080| 0.0000000|
| 13|chr6 | 30458998| -0.0034406| 0.0013169| 0.0134299|
| 13|chr6 | 30459139| -0.0067699| 0.0009491| 0.0000000|
| 13|chr6 | 30459255| -0.0034567| 0.0007771| 0.0000930|
| 13|chr6 | 30459295| -0.0048622| 0.0009776| 0.0000200|
| 13|chr6 | 30459317| -0.0022834| 0.0008987| 0.0159493|
| 14|chr6 | 30459540| -0.0055945| 0.0018240| 0.0044619|
| 14|chr6 | 30459595| -0.0065842| 0.0012847| 0.0000128|
| 14|chr6 | 30459867| -0.0053297| 0.0012047| 0.0000998|
| 14|chr6 | 30460244| -0.0031765| 0.0007381| 0.0001414|
| 14|chr6 | 30460322| -0.0034656| 0.0008761| 0.0003823|
| 14|chr6 | 30460484| -0.0007314| 0.0023526| 0.7578311|
| 14|chr6 | 30460548| -0.0056734| 0.0012089| 0.0000456|
| 14|chr6 | 30460576| -0.0071095| 0.0009408| 0.0000000|
| 14|chr6 | 30460600| -0.0052924| 0.0011727| 0.0000771|
| 15|chr6 | 30581820| -0.0072376| 0.0006511| 0.0000000|
| 15|chr6 | 30582174| -0.0046628| 0.0007254| 0.0000003|
| 15|chr6 | 30582241| -0.0087080| 0.0012550| 0.0000001|
| 15|chr6 | 30582333| -0.0079857| 0.0012664| 0.0000004|
| 15|chr6 | 30582352| -0.0046817| 0.0007966| 0.0000014|
| 15|chr6 | 30582416| -0.0050133| 0.0005547| 0.0000000|
| 16|chr6 | 30652771| -0.0036735| 0.0006103| 0.0000009|
| 16|chr6 | 30652829| -0.0082523| 0.0010218| 0.0000000|
| 16|chr6 | 30652907| -0.0067420| 0.0008282| 0.0000000|
| 16|chr6 | 30653167| -0.0091442| 0.0012343| 0.0000000|
| 16|chr6 | 30653191| -0.0039108| 0.0010121| 0.0004953|
| 16|chr6 | 30653242| -0.0026327| 0.0004126| 0.0000003|
| 16|chr6 | 30653407| -0.0062780| 0.0011103| 0.0000027|
| 16|chr6 | 30653512| -0.0050652| 0.0008696| 0.0000016|
| 16|chr6 | 30653530| -0.0059723| 0.0010842| 0.0000041|
| 17|chr6 | 30850543| 0.0080152| 0.0013483| 0.0000011|
| 17|chr6 | 30850581| -0.0031452| 0.0053412| 0.5599735|
| 17|chr6 | 30850718| 0.0023579| 0.0007733| 0.0045015|
| 17|chr6 | 30850829| 0.0048777| 0.0009207| 0.0000077|
| 17|chr6 | 30850868| 0.0070721| 0.0014112| 0.0000179|
| 17|chr6 | 30850876| 0.0027450| 0.0007419| 0.0007826|
| 17|chr6 | 30850913| 0.0015332| 0.0008513| 0.0808466|
| 17|chr6 | 30850977| 0.0081431| 0.0014615| 0.0000034|
| 18|chr6 | 30854161| 0.0071258| 0.0017536| 0.0002815|
| 18|chr6 | 30854164| 0.0051399| 0.0009032| 0.0000024|
| 18|chr6 | 30854186| 0.0059085| 0.0016669| 0.0012016|
| 18|chr6 | 30854233| 0.0049327| 0.0014393| 0.0016544|
| 18|chr6 | 30854551| 0.0074110| 0.0011912| 0.0000005|
| 19|chr6 | 30955992| 0.0013819| 0.0005706| 0.0211023|
| 19|chr6 | 30956214| 0.0017557| 0.0011167| 0.1254763|
| 19|chr6 | 30956221| 0.0009545| 0.0006868| 0.1739330|
| 19|chr6 | 30956397| 0.0046973| 0.0007931| 0.0000012|
| 19|chr6 | 30956440| 0.0046062| 0.0010511| 0.0001128|
| 20|chr6 | 31079110| 0.0021681| 0.0004168| 0.0000102|
| 20|chr6 | 31079152| 0.0034412| 0.0004245| 0.0000000|
| 20|chr6 | 31079306| 0.0006828| 0.0005854| 0.2518531|
| 20|chr6 | 31079555| 0.0009611| 0.0005674| 0.0997232|
| 20|chr6 | 31079617| 0.0012210| 0.0005581| 0.0358930|
| 21|chr6 | 31127159| -0.0031986| 0.0008677| 0.0008135|
| 21|chr6 | 31127173| -0.0028072| 0.0007980| 0.0012939|
| 21|chr6 | 31127178| -0.0027491| 0.0009275| 0.0056065|
| 21|chr6 | 31127271| -0.0029349| 0.0007459| 0.0004054|
| 21|chr6 | 31127357| -0.0023601| 0.0008021| 0.0059212|
| 21|chr6 | 31127379| -0.0028426| 0.0008402| 0.0018635|
| 21|chr6 | 31127527| -0.0015685| 0.0004125| 0.0005893|
| 21|chr6 | 31127863| -0.0021863| 0.0004672| 0.0000475|
| 22|chr6 | 31549480| -0.0015810| 0.0003835| 0.0002382|
| 22|chr6 | 31549563| -0.0043659| 0.0006342| 0.0000001|
| 22|chr6 | 31549625| -0.0021442| 0.0009244| 0.0267130|
| 22|chr6 | 31549631| -0.0058549| 0.0005927| 0.0000000|
| 22|chr6 | 31549853| -0.0058183| 0.0006280| 0.0000000|
| 22|chr6 | 31549929| -0.0047272| 0.0006038| 0.0000000|
| 22|chr6 | 31550090| -0.0049884| 0.0009083| 0.0000048|
| 23|chr6 | 31646236| 0.0043452| 0.0007266| 0.0000010|
| 23|chr6 | 31646262| 0.0025956| 0.0005409| 0.0000335|
| 23|chr6 | 31646366| 0.0000296| 0.0004468| 0.9475834|
| 23|chr6 | 31646377| 0.0004806| 0.0004894| 0.3332814|
| 23|chr6 | 31646625| 0.0025643| 0.0007651| 0.0020295|
| 24|chr6 | 31744391| -0.0050457| 0.0006990| 0.0000000|
| 24|chr6 | 31744398| -0.0018473| 0.0005261| 0.0013156|
| 24|chr6 | 31744524| -0.0030812| 0.0008451| 0.0009093|
| 24|chr6 | 31744545| -0.0046108| 0.0008439| 0.0000047|
| 24|chr6 | 31744612| -0.0044627| 0.0009478| 0.0000436|
| 24|chr6 | 31744628| -0.0034480| 0.0010534| 0.0025021|
| 24|chr6 | 31744636| -0.0053844| 0.0011241| 0.0000343|
| 24|chr6 | 31744735| -0.0065323| 0.0010509| 0.0000005|
| 24|chr6 | 31744816| -0.0033457| 0.0009076| 0.0008133|
| 24|chr6 | 31744831| -0.0031882| 0.0007461| 0.0001543|
| 25|chr6 | 31846797| 0.0027906| 0.0006335| 0.0001055|
| 25|chr6 | 31846813| 0.0011288| 0.0008538| 0.1955051|
| 25|chr6 | 31846899| 0.0038241| 0.0008466| 0.0000762|
| 25|chr6 | 31846924| 0.0040218| 0.0009684| 0.0002181|
| 25|chr6 | 31846956| 0.0045979| 0.0017440| 0.0126826|
| 25|chr6 | 31846970| 0.0018120| 0.0007503| 0.0214568|
| 26|chr6 | 31867945| -0.0021363| 0.0005188| 0.0002410|
| 26|chr6 | 31867956| -0.0092438| 0.0011713| 0.0000000|
| 26|chr6 | 31867995| -0.0076270| 0.0009856| 0.0000000|
| 26|chr6 | 31868021| -0.0041524| 0.0006997| 0.0000012|
| 26|chr6 | 31868025| -0.0077718| 0.0010175| 0.0000000|
| 26|chr6 | 31868133| -0.0023261| 0.0010224| 0.0295304|
| 26|chr6 | 31868144| -0.0007071| 0.0007210| 0.3338497|
| 26|chr6 | 31868162| -0.0008090| 0.0004455| 0.0785049|
| 26|chr6 | 31868169| -0.0012835| 0.0005928| 0.0377116|
| 26|chr6 | 31868207| -0.0011950| 0.0004271| 0.0085196|
| 26|chr6 | 31868368| -0.0008705| 0.0004044| 0.0387621|
| 26|chr6 | 31868418| -0.0010511| 0.0004663| 0.0309463|
| 26|chr6 | 31868452| -0.0009970| 0.0003899| 0.0153497|
| 26|chr6 | 31868470| -0.0011890| 0.0004890| 0.0206447|
| 27|chr6 | 31937758| -0.0024101| 0.0006967| 0.0015157|
| 27|chr6 | 31937906| -0.0023675| 0.0005143| 0.0000593|
| 27|chr6 | 31937968| -0.0007674| 0.0005002| 0.1345344|
| 27|chr6 | 31937973| -0.0018000| 0.0005101| 0.0012542|
| 27|chr6 | 31938090| -0.0009554| 0.0005194| 0.0748506|
| 27|chr6 | 31938176| -0.0007199| 0.0004237| 0.0987293|
| 27|chr6 | 31938187| -0.0003214| 0.0005346| 0.5517659|
| 27|chr6 | 31938207| -0.0010164| 0.0005838| 0.0912894|
| 27|chr6 | 31938358| -0.0003664| 0.0005078| 0.4756917|
| 27|chr6 | 31938372| -0.0015409| 0.0005593| 0.0094789|
| 27|chr6 | 31938527| -0.0015529| 0.0004554| 0.0017341|
| 27|chr6 | 31938533| -0.0010392| 0.0006738| 0.1325230|
| 28|chr6 | 31939059| -0.0027433| 0.0004824| 0.0000024|
| 28|chr6 | 31939085| -0.0008313| 0.0008125| 0.3137230|
| 28|chr6 | 31939106| -0.0020200| 0.0010173| 0.0554381|
| 28|chr6 | 31939112| -0.0039003| 0.0010390| 0.0006968|
| 28|chr6 | 31939181| -0.0031801| 0.0010732| 0.0056176|
| 28|chr6 | 31939224| -0.0030100| 0.0010536| 0.0073586|
| 28|chr6 | 31939280| -0.0044583| 0.0010547| 0.0001763|
| 28|chr6 | 31939319| -0.0033072| 0.0011398| 0.0065710|
| 29|chr6 | 32013699| 0.0059543| 0.0008817| 0.0000001|
| 29|chr6 | 32013710| 0.0066619| 0.0008109| 0.0000000|
| 29|chr6 | 32013845| 0.0018667| 0.0006313| 0.0057110|
| 29|chr6 | 32013974| 0.0006072| 0.0004168| 0.1546392|
| 29|chr6 | 32014003| 0.0003136| 0.0006145| 0.6131548|
| 29|chr6 | 32014059| 0.0001794| 0.0006347| 0.7791855|
| 29|chr6 | 32014096| 0.0002089| 0.0003722| 0.5784243|
| 29|chr6 | 32014100| 0.0004546| 0.0004554| 0.3254209|
| 29|chr6 | 32014148| 0.0013972| 0.0008293| 0.1014986|
| 29|chr6 | 32014189| 0.0025051| 0.0006349| 0.0003933|
| 29|chr6 | 32014300| 0.0005311| 0.0006692| 0.4330893|
| 29|chr6 | 32014381| 0.0001677| 0.0006949| 0.8108247|
| 29|chr6 | 32014476| 0.0011984| 0.0018292| 0.5169125|
| 29|chr6 | 32014484| 0.0010834| 0.0011520| 0.3538185|
| 29|chr6 | 32014510| 0.0014252| 0.0010947| 0.2019818|
| 29|chr6 | 32014605| 0.0006342| 0.0005843| 0.2856641|
| 29|chr6 | 32014663| 0.0018555| 0.0008157| 0.0295622|
| 29|chr6 | 32014674| 0.0011431| 0.0008564| 0.1911191|
| 29|chr6 | 32014739| 0.0029281| 0.0007009| 0.0002030|
| 30|chr6 | 32020425| 0.0020827| 0.0005039| 0.0002306|
| 30|chr6 | 32020477| 0.0015273| 0.0004015| 0.0005851|
| 30|chr6 | 32020479| 0.0021571| 0.0004397| 0.0000244|
| 30|chr6 | 32020489| 0.0015262| 0.0004735| 0.0028541|
| 30|chr6 | 32020498| -0.0000017| 0.0005183| 0.9973686|
| 30|chr6 | 32020572| 0.0009896| 0.0004088| 0.0211588|
| 30|chr6 | 32020587| 0.0006498| 0.0004170| 0.1287077|
| 30|chr6 | 32020750| 0.0024541| 0.0008160| 0.0050132|
| 31|chr6 | 32022898| 0.0022802| 0.0005643| 0.0003002|
| 31|chr6 | 32022929| 0.0022027| 0.0004470| 0.0000229|
| 31|chr6 | 32023102| 0.0016554| 0.0006389| 0.0141459|
| 31|chr6 | 32023142| 0.0008489| 0.0005198| 0.1119170|
| 31|chr6 | 32023246| 0.0008791| 0.0005057| 0.0914957|
| 31|chr6 | 32023249| 0.0012437| 0.0006695| 0.0721889|
| 31|chr6 | 32023251| 0.0005900| 0.0004299| 0.1791401|
| 31|chr6 | 32023283| 0.0017482| 0.0005553| 0.0034788|
| 31|chr6 | 32023332| 0.0002324| 0.0007577| 0.7610253|
| 31|chr6 | 32023383| 0.0003477| 0.0007625| 0.6513856|
| 31|chr6 | 32023409| 0.0022897| 0.0007285| 0.0035287|
| 31|chr6 | 32023527| 0.0014054| 0.0007570| 0.0723335|
| 31|chr6 | 32023650| 0.0017740| 0.0003961| 0.0000851|
| 32|chr6 | 32037018| 0.0026723| 0.0004962| 0.0000059|
| 32|chr6 | 32037097| -0.0013256| 0.0025792| 0.6107074|
| 32|chr6 | 32037148| 0.0010102| 0.0006431| 0.1257408|
| 32|chr6 | 32037290| 0.0020436| 0.0005277| 0.0004836|
| 32|chr6 | 32037339| 0.0012885| 0.0004185| 0.0041670|
| 32|chr6 | 32037342| 0.0018824| 0.0004367| 0.0001458|
| 32|chr6 | 32037421| 0.0007300| 0.0004808| 0.1384573|
| 32|chr6 | 32037426| 0.0011939| 0.0006062| 0.0573444|
| 32|chr6 | 32037453| 0.0013684| 0.0004575| 0.0052290|
| 32|chr6 | 32037474| 0.0005452| 0.0005051| 0.2884926|
| 32|chr6 | 32037587| 0.0011717| 0.0005700| 0.0480694|
| 32|chr6 | 32037602| 0.0007434| 0.0006194| 0.2386053|
| 32|chr6 | 32037632| 0.0003933| 0.0005328| 0.4656375|
| 32|chr6 | 32037653| 0.0012443| 0.0005433| 0.0285275|
| 32|chr6 | 32037735| 0.0016637| 0.0006331| 0.0129396|
| 32|chr6 | 32037751| 0.0005364| 0.0005487| 0.3354639|
| 32|chr6 | 32037800| 0.0000891| 0.0010872| 0.9352074|
| 33|chr6 | 32042200| 0.0014293| 0.0004842| 0.0057855|
| 33|chr6 | 32042344| 0.0011513| 0.0006680| 0.0941661|
| 33|chr6 | 32042351| 0.0026276| 0.0007252| 0.0009681|
| 33|chr6 | 32042430| 0.0000574| 0.0005808| 0.9219081|
| 33|chr6 | 32042518| -0.0007150| 0.0005161| 0.1752731|
| 33|chr6 | 32042526| 0.0001437| 0.0002279| 0.5325884|
| 33|chr6 | 32042534| 0.0002357| 0.0003114| 0.4544765|
| 33|chr6 | 32042658| -0.0005557| 0.0004400| 0.2154079|
| 33|chr6 | 32042797| 0.0016001| 0.0005211| 0.0043381|
| 33|chr6 | 32042947| 0.0028341| 0.0004951| 0.0000022|
| 33|chr6 | 32043029| 0.0022139| 0.0008258| 0.0113761|
| 33|chr6 | 32043191| 0.0010731| 0.0005525| 0.0607045|
| 33|chr6 | 32043561| 0.0025143| 0.0004325| 0.0000017|
| 33|chr6 | 32043676| 0.0017213| 0.0005664| 0.0046229|
| 33|chr6 | 32043739| 0.0036167| 0.0004596| 0.0000000|
| 33|chr6 | 32044104| 0.0010326| 0.0005928| 0.0908754|
| 33|chr6 | 32044163| 0.0012238| 0.0005234| 0.0256076|
| 33|chr6 | 32044179| 0.0023767| 0.0006243| 0.0005812|
| 33|chr6 | 32044203| 0.0000922| 0.0003763| 0.8079619|
| 33|chr6 | 32044254| 0.0021710| 0.0006306| 0.0015861|
| 34|chr6 | 32044384| 0.0024851| 0.0006693| 0.0007805|
| 34|chr6 | 32044404| 0.0020356| 0.0004539| 0.0000836|
| 34|chr6 | 32044496| 0.0027983| 0.0009480| 0.0057832|
| 34|chr6 | 32044869| 0.0021456| 0.0007448| 0.0069241|
| 34|chr6 | 32044959| 0.0005330| 0.0004470| 0.2415568|
| 34|chr6 | 32045323| 0.0016298| 0.0004460| 0.0008879|
| 35|chr6 | 32048449| 0.0024789| 0.0005231| 0.0000399|
| 35|chr6 | 32048463| 0.0013852| 0.0004396| 0.0034536|
| 35|chr6 | 32048632| 0.0014067| 0.0005307| 0.0122437|
| 35|chr6 | 32048679| 0.0023866| 0.0005699| 0.0001975|
| 35|chr6 | 32049053| 0.0019867| 0.0008200| 0.0210623|
| 35|chr6 | 32049177| 0.0015486| 0.0010356| 0.1446383|
| 35|chr6 | 32049196| 0.0020956| 0.0009048| 0.0269247|
| 35|chr6 | 32049235| 0.0022859| 0.0007026| 0.0026370|
| 35|chr6 | 32049263| 0.0002777| 0.0007076| 0.6972357|
| 35|chr6 | 32049322| 0.0022113| 0.0004534| 0.0000265|
| 35|chr6 | 32049354| 0.0007787| 0.0006394| 0.2319110|
| 35|chr6 | 32049373| 0.0004675| 0.0006475| 0.4753871|
| 35|chr6 | 32049376| 0.0007720| 0.0004805| 0.1176681|
| 35|chr6 | 32049513| 0.0044872| 0.0019918| 0.0310568|
| 35|chr6 | 32049516| 0.0018892| 0.0009905| 0.0652198|
| 35|chr6 | 32049622| 0.0054246| 0.0013535| 0.0003297|
| 35|chr6 | 32049699| 0.0020965| 0.0005851| 0.0010812|
| 35|chr6 | 32049825| 0.0009969| 0.0005786| 0.0942450|
| 35|chr6 | 32049829| 0.0015914| 0.0006348| 0.0172882|
| 35|chr6 | 32049845| -0.0000463| 0.0004556| 0.9196930|
| 36|chr6 | 32060791| 0.0018855| 0.0005010| 0.0006560|
| 36|chr6 | 32060794| 0.0020018| 0.0006337| 0.0033841|
| 36|chr6 | 32060816| 0.0058113| 0.0007286| 0.0000000|
| 36|chr6 | 32061084| 0.0055124| 0.0010282| 0.0000064|
| 36|chr6 | 32061160| 0.0016416| 0.0004351| 0.0006386|
| 36|chr6 | 32061318| 0.0034423| 0.0004940| 0.0000001|
| 36|chr6 | 32061478| 0.0067209| 0.0005456| 0.0000000|
| 37|chr6 | 32086755| 0.0015567| 0.0004910| 0.0032805|
| 37|chr6 | 32086758| 0.0013796| 0.0004483| 0.0041843|
| 37|chr6 | 32086779| 0.0004479| 0.0003126| 0.1613656|
| 37|chr6 | 32086782| 0.0012962| 0.0004033| 0.0029276|
| 37|chr6 | 32086818| 0.0017141| 0.0004723| 0.0009513|
| 37|chr6 | 32086857| 0.0034127| 0.0009315| 0.0008933|
| 37|chr6 | 32086878| 0.0027513| 0.0007137| 0.0005076|
| 37|chr6 | 32086893| 0.0026092| 0.0004671| 0.0000033|
| 38|chr6 | 32120203| 0.0047441| 0.0008483| 0.0000032|
| 38|chr6 | 32120324| 0.0070977| 0.0009075| 0.0000000|
| 38|chr6 | 32120584| 0.0123171| 0.0021697| 0.0000025|
| 38|chr6 | 32120623| 0.0071143| 0.0010378| 0.0000001|
| 38|chr6 | 32120625| 0.0129119| 0.0015077| 0.0000000|
| 38|chr6 | 32120773| 0.0164555| 0.0020453| 0.0000000|
| 38|chr6 | 32120783| 0.0143953| 0.0018676| 0.0000000|
| 38|chr6 | 32120826| 0.0141621| 0.0018371| 0.0000000|
| 38|chr6 | 32120863| 0.0214823| 0.0027928| 0.0000000|
| 38|chr6 | 32120878| 0.0205448| 0.0020839| 0.0000000|
| 38|chr6 | 32120895| 0.0083636| 0.0011945| 0.0000001|
| 38|chr6 | 32120899| 0.0103226| 0.0012918| 0.0000000|
| 38|chr6 | 32120901| 0.0196434| 0.0025588| 0.0000000|
| 38|chr6 | 32120907| 0.0166847| 0.0023794| 0.0000001|
| 38|chr6 | 32120933| 0.0170291| 0.0021530| 0.0000000|
| 38|chr6 | 32120955| 0.0127698| 0.0015906| 0.0000000|
| 38|chr6 | 32121055| 0.0094295| 0.0011082| 0.0000000|
| 38|chr6 | 32121113| 0.0097364| 0.0011803| 0.0000000|
| 39|chr6 | 32121143| 0.0109729| 0.0011602| 0.0000000|
| 39|chr6 | 32121156| 0.0099459| 0.0011021| 0.0000000|
| 39|chr6 | 32121204| 0.0032973| 0.0005583| 0.0000013|
| 39|chr6 | 32121225| 0.0053628| 0.0008030| 0.0000001|
| 39|chr6 | 32121249| 0.0099222| 0.0013729| 0.0000000|
| 39|chr6 | 32121259| 0.0070243| 0.0010034| 0.0000001|
| 39|chr6 | 32121261| 0.0043735| 0.0007757| 0.0000028|
| 39|chr6 | 32121355| 0.0046116| 0.0007507| 0.0000006|
| 39|chr6 | 32121368| 0.0046871| 0.0006328| 0.0000000|
| 39|chr6 | 32121393| 0.0057123| 0.0007757| 0.0000000|
| 39|chr6 | 32121420| 0.0038576| 0.0007068| 0.0000048|
| 39|chr6 | 32121433| 0.0057492| 0.0009363| 0.0000006|
| 39|chr6 | 32121471| 0.0016624| 0.0006661| 0.0177519|
| 39|chr6 | 32121475| 0.0009150| 0.0003760| 0.0205303|
| 40|chr6 | 32122736| -0.0019809| 0.0005945| 0.0021386|
| 40|chr6 | 32122738| -0.0017221| 0.0005213| 0.0023083|
| 40|chr6 | 32122753| -0.0054938| 0.0009396| 0.0000015|
| 40|chr6 | 32122779| -0.0021445| 0.0008217| 0.0135258|
| 40|chr6 | 32122864| -0.0042917| 0.0007076| 0.0000008|
| 41|chr6 | 32135241| 0.0025645| 0.0009279| 0.0092807|
| 41|chr6 | 32135285| 0.0004048| 0.0006879| 0.5602335|
| 41|chr6 | 32135321| 0.0001307| 0.0005663| 0.8189223|
| 41|chr6 | 32135326| 0.0002122| 0.0004804| 0.6616047|
| 41|chr6 | 32135370| 0.0005473| 0.0004846| 0.2668586|
| 41|chr6 | 32135379| -0.0000150| 0.0003912| 0.9696503|
| 41|chr6 | 32135384| 0.0003727| 0.0004929| 0.4550117|
| 41|chr6 | 32135396| 0.0001756| 0.0008316| 0.8340676|
| 41|chr6 | 32135715| 0.0046879| 0.0007164| 0.0000002|
| 41|chr6 | 32135718| 0.0046263| 0.0006358| 0.0000000|
| 41|chr6 | 32135728| 0.0057995| 0.0010419| 0.0000035|
| 41|chr6 | 32135776| 0.0041579| 0.0009441| 0.0001057|
| 41|chr6 | 32135803| 0.0050413| 0.0007966| 0.0000004|
| 42|chr6 | 32150404| 0.0025165| 0.0006867| 0.0008637|
| 42|chr6 | 32150577| 0.0003203| 0.0005143| 0.5376663|
| 42|chr6 | 32150585| 0.0004927| 0.0003992| 0.2257965|
| 42|chr6 | 32150656| 0.0002132| 0.0003881| 0.5865275|
| 42|chr6 | 32150716| -0.0003987| 0.0004324| 0.3632602|
| 43|chr6 | 32154416| -0.0016134| 0.0004878| 0.0022828|
| 43|chr6 | 32154447| -0.0037112| 0.0006244| 0.0000011|
| 43|chr6 | 32154454| -0.0025579| 0.0008551| 0.0052262|
| 43|chr6 | 32154568| -0.0023963| 0.0004999| 0.0000340|
| 43|chr6 | 32154613| -0.0018532| 0.0005691| 0.0026145|
| 43|chr6 | 32154715| -0.0061503| 0.0007977| 0.0000000|
| 44|chr6 | 32158927| -0.0023200| 0.0008853| 0.0131813|
| 44|chr6 | 32158953| -0.0025423| 0.0008705| 0.0062623|
| 44|chr6 | 32159036| -0.0059181| 0.0010988| 0.0000059|
| 44|chr6 | 32159527| -0.0086710| 0.0011671| 0.0000000|
| 44|chr6 | 32159604| -0.0049000| 0.0009847| 0.0000199|
| 44|chr6 | 32159607| -0.0065540| 0.0011702| 0.0000031|
| 44|chr6 | 32159933| -0.0137602| 0.0014807| 0.0000000|
| 44|chr6 | 32160074| -0.0089959| 0.0009821| 0.0000000|
| 45|chr6 | 32171796| 0.0014813| 0.0006109| 0.0209610|
| 45|chr6 | 32171823| 0.0018818| 0.0006666| 0.0080082|
| 45|chr6 | 32172007| 0.0000657| 0.0004591| 0.8870551|
| 45|chr6 | 32172013| -0.0001783| 0.0005026| 0.7250002|
| 45|chr6 | 32172027| -0.0000996| 0.0004899| 0.8401518|
| 45|chr6 | 32172124| 0.0020267| 0.0005030| 0.0003105|
| 46|chr6 | 32805398| -0.0052602| 0.0005470| 0.0000000|
| 46|chr6 | 32805548| -0.0056497| 0.0007112| 0.0000000|
| 46|chr6 | 32805554| -0.0064121| 0.0006925| 0.0000000|
| 46|chr6 | 32805570| -0.0052904| 0.0007072| 0.0000000|
| 46|chr6 | 32805684| -0.0032412| 0.0006549| 0.0000215|
| 47|chr6 | 32812933| -0.0062452| 0.0006269| 0.0000000|
| 47|chr6 | 32812953| -0.0026982| 0.0004877| 0.0000039|
| 47|chr6 | 32812965| -0.0081845| 0.0008237| 0.0000000|
| 47|chr6 | 32813084| -0.0149186| 0.0010165| 0.0000000|
| 47|chr6 | 32813154| -0.0029333| 0.0006178| 0.0000388|
| 47|chr6 | 32813211| -0.0002499| 0.0002206| 0.2653142|
| 47|chr6 | 32813337| -0.0136689| 0.0011875| 0.0000000|
| 47|chr6 | 32813441| 0.0001788| 0.0003417| 0.6043078|
| 47|chr6 | 32813448| -0.0007677| 0.0003414| 0.0313178|
| 48|chr6 | 32820355| -0.0056831| 0.0010883| 0.0000096|
| 48|chr6 | 32820410| -0.0087937| 0.0008914| 0.0000000|
| 48|chr6 | 32820421| -0.0056739| 0.0011000| 0.0000116|
| 48|chr6 | 32820546| -0.0064499| 0.0009647| 0.0000001|
| 48|chr6 | 32820553| -0.0028039| 0.0007199| 0.0004542|
| 48|chr6 | 32820577| -0.0044637| 0.0005969| 0.0000000|
| 49|chr6 | 32825701| 0.0036795| 0.0007241| 0.0000146|
| 49|chr6 | 32825852| 0.0006878| 0.0007489| 0.3652902|
| 49|chr6 | 32825897| 0.0028278| 0.0010861| 0.0137263|
| 49|chr6 | 32826171| 0.0024772| 0.0004859| 0.0000139|
| 49|chr6 | 32826197| 0.0012497| 0.0005665| 0.0344650|
| 50|chr6 | 32908567| -0.0077758| 0.0014040| 0.0000038|
| 50|chr6 | 32908605| -0.0089481| 0.0013805| 0.0000003|
| 50|chr6 | 32908642| -0.0079963| 0.0013258| 0.0000009|
| 50|chr6 | 32908718| -0.0059827| 0.0010752| 0.0000035|
| 50|chr6 | 32908794| -0.0028700| 0.0005460| 0.0000087|
| 50|chr6 | 32908901| -0.0049536| 0.0008100| 0.0000007|
| 50|chr6 | 32908980| -0.0111032| 0.0010072| 0.0000000|
| 50|chr6 | 32909003| -0.0151386| 0.0016320| 0.0000000|
| 50|chr6 | 32909282| -0.0096443| 0.0014176| 0.0000001|
| 50|chr6 | 32909397| -0.0029869| 0.0004300| 0.0000001|
| 50|chr6 | 32909440| -0.0040748| 0.0006100| 0.0000001|
| 50|chr6 | 32909493| -0.0075823| 0.0009612| 0.0000000|
| 50|chr6 | 32909523| -0.0081156| 0.0011620| 0.0000001|
| 51|chr6 | 32942063| -0.0040017| 0.0008592| 0.0000506|
| 51|chr6 | 32942205| -0.0029352| 0.0005267| 0.0000038|
| 51|chr6 | 32942358| -0.0044676| 0.0008093| 0.0000040|
| 51|chr6 | 32942400| -0.0026140| 0.0008169| 0.0030381|
| 51|chr6 | 32942429| -0.0054339| 0.0007539| 0.0000000|
| 51|chr6 | 32942494| -0.0076144| 0.0010191| 0.0000000|
| 51|chr6 | 32942541| -0.0026536| 0.0007427| 0.0011115|
| 51|chr6 | 32942710| -0.0062878| 0.0007592| 0.0000000|
| 51|chr6 | 32942714| -0.0052184| 0.0007741| 0.0000001|
| 51|chr6 | 32942808| -0.0051455| 0.0008107| 0.0000004|
| 51|chr6 | 32943025| -0.0068885| 0.0011701| 0.0000014|
| 52|chr6 | 33043841| -0.0089592| 0.0016461| 0.0000050|
| 52|chr6 | 33043849| -0.0049225| 0.0008960| 0.0000043|
| 52|chr6 | 33043868| -0.0048543| 0.0011048| 0.0001090|
| 52|chr6 | 33043976| -0.0040812| 0.0013144| 0.0038955|
| 52|chr6 | 33044012| -0.0075230| 0.0012858| 0.0000015|
| 52|chr6 | 33044345| -0.0076685| 0.0019056| 0.0003148|
| 52|chr6 | 33044510| -0.0090305| 0.0029214| 0.0040381|
| 53|chr6 | 33132163| 0.0044894| 0.0009285| 0.0000301|
| 53|chr6 | 33132181| 0.0026369| 0.0009792| 0.0113280|
| 53|chr6 | 33132192| 0.0023092| 0.0007936| 0.0064369|
| 53|chr6 | 33132241| 0.0039578| 0.0007188| 0.0000042|
| 53|chr6 | 33132318| 0.0016570| 0.0007374| 0.0314602|
| 54|chr6 | 33132650| 0.0029044| 0.0008988| 0.0027934|
| 54|chr6 | 33132693| 0.0014578| 0.0007445| 0.0587333|
| 54|chr6 | 33132705| 0.0018258| 0.0006080| 0.0050709|
| 54|chr6 | 33132727| 0.0005718| 0.0010938| 0.6046186|
| 54|chr6 | 33132943| 0.0013510| 0.0009483| 0.1636810|
| 54|chr6 | 33132996| 0.0010484| 0.0006467| 0.1145411|
| 54|chr6 | 33133039| 0.0008051| 0.0005092| 0.1233940|
| 54|chr6 | 33133083| 0.0022452| 0.0005955| 0.0006438|
| 54|chr6 | 33133329| 0.0009322| 0.0005292| 0.0874075|
| 54|chr6 | 33133370| 0.0005597| 0.0006001| 0.3578041|
| 54|chr6 | 33133485| 0.0013197| 0.0003820| 0.0015343|
| 54|chr6 | 33133517| 0.0006703| 0.0006335| 0.2984729|
| 54|chr6 | 33133531| 0.0006133| 0.0004131| 0.1471008|
| 54|chr6 | 33133535| 0.0001841| 0.0007781| 0.8144606|
| 54|chr6 | 33133538| 0.0004572| 0.0006730| 0.5016341|
| 54|chr6 | 33133675| 0.0018501| 0.0004255| 0.0001246|
| 54|chr6 | 33133752| 0.0013819| 0.0005242| 0.0126865|
| 54|chr6 | 33134045| 0.0014330| 0.0008152| 0.0880898|
| 54|chr6 | 33134078| 0.0013833| 0.0005912| 0.0254883|
| 55|chr6 | 33245488| -0.0063308| 0.0009790| 0.0000002|
| 55|chr6 | 33245490| -0.0072472| 0.0009477| 0.0000000|
| 55|chr6 | 33245516| -0.0027005| 0.0004193| 0.0000003|
| 55|chr6 | 33245537| -0.0059599| 0.0006817| 0.0000000|
| 55|chr6 | 33245541| -0.0066055| 0.0005880| 0.0000000|
| 55|chr6 | 33245553| -0.0020256| 0.0004237| 0.0000353|
| 56|chr6 | 33245706| -0.0034841| 0.0006308| 0.0000040|
| 56|chr6 | 33245717| -0.0031527| 0.0006644| 0.0000392|
| 56|chr6 | 33245721| -0.0040674| 0.0008277| 0.0000239|
| 56|chr6 | 33245739| -0.0061758| 0.0016666| 0.0007708|
| 56|chr6 | 33245770| -0.0033426| 0.0006525| 0.0000129|
| 56|chr6 | 33245779| -0.0007004| 0.0006544| 0.2922844|
| 56|chr6 | 33245804| -0.0044990| 0.0006645| 0.0000001|
| 57|chr6 | 33245893| -0.0064717| 0.0007401| 0.0000000|
| 57|chr6 | 33245895| -0.0049468| 0.0007351| 0.0000001|
| 57|chr6 | 33245990| -0.0027917| 0.0004471| 0.0000005|
| 57|chr6 | 33246008| -0.0048952| 0.0007035| 0.0000001|
| 57|chr6 | 33246043| -0.0033446| 0.0006808| 0.0000239|
| 57|chr6 | 33246091| -0.0039444| 0.0006273| 0.0000004|
| 57|chr6 | 33246094| -0.0049641| 0.0006145| 0.0000000|
| 58|chr6 | 41010111| 0.0044863| 0.0006439| 0.0000001|
| 58|chr6 | 41010217| 0.0032720| 0.0005836| 0.0000031|
| 58|chr6 | 41010223| 0.0039473| 0.0009742| 0.0003036|
| 58|chr6 | 41010316| 0.0041379| 0.0006334| 0.0000002|
| 58|chr6 | 41010375| 0.0023833| 0.0006209| 0.0005315|
| 58|chr6 | 41010654| 0.0019212| 0.0007352| 0.0134150|
| 59|chr6 | 53530503| 0.0027975| 0.0010874| 0.0147887|
| 59|chr6 | 53530538| 0.0037586| 0.0009116| 0.0002374|
| 59|chr6 | 53530570| 0.0038971| 0.0008697| 0.0000847|
| 59|chr6 | 53530600| 0.0032789| 0.0009137| 0.0010653|
| 59|chr6 | 53530624| 0.0028774| 0.0010029| 0.0071356|
| 59|chr6 | 53530628| 0.0052701| 0.0008981| 0.0000014|
| 60|chr6 | 149805995| -0.0097817| 0.0012361| 0.0000000|
| 60|chr6 | 149806077| -0.0176011| 0.0016213| 0.0000000|
| 60|chr6 | 149806081| -0.0210694| 0.0018994| 0.0000000|
| 60|chr6 | 149806131| -0.0159030| 0.0012826| 0.0000000|
| 60|chr6 | 149806235| -0.0180270| 0.0016008| 0.0000000|
| 60|chr6 | 149806273| -0.0119123| 0.0011342| 0.0000000|
| 60|chr6 | 149806331| -0.0164691| 0.0014486| 0.0000000|
| 60|chr6 | 149806339| -0.0206545| 0.0018827| 0.0000000|
| 60|chr6 | 149806502| -0.0045615| 0.0011026| 0.0002283|
| 60|chr6 | 149806635| -0.0024949| 0.0008287| 0.0049745|
| 60|chr6 | 149806732| -0.0050078| 0.0008231| 0.0000008|
| 61|chr6 | 152702330| 0.0026328| 0.0007299| 0.0010120|
| 61|chr6 | 152702365| 0.0018266| 0.0006656| 0.0097409|
| 61|chr6 | 152702387| 0.0025174| 0.0009955| 0.0164158|
| 61|chr6 | 152702444| 0.0018338| 0.0005983| 0.0043233|
| 61|chr6 | 152702463| 0.0060321| 0.0005759| 0.0000000|
| 62|chr6 | 170580947| -0.0057303| 0.0017864| 0.0029749|
| 62|chr6 | 170580966| -0.0061513| 0.0026272| 0.0254148|
| 62|chr6 | 170581039| -0.0039265| 0.0012441| 0.0034079|
| 62|chr6 | 170581085| -0.0002133| 0.0003829| 0.5812049|
| 62|chr6 | 170581248| -0.0008610| 0.0003069| 0.0083619|
| 62|chr6 | 170581355| -0.0006148| 0.0002833| 0.0373224|
| 62|chr6 | 170581502| -0.0061059| 0.0010420| 0.0000015|
| 62|chr6 | 170581690| -0.0027766| 0.0012361| 0.0315156|
best6 <- dmrs6[which.min(dmrs6$p.value),]
dmrff.plot(
best6$chr, best6$start, best6$end,
stats[[acc]]$estimate, stats[[acc]]$se, stats[[acc]]$chr, stats[[acc]]$pos)
Going back to full set of DMRs,
we can ask which regions are novel,
i.e. contain no CpG sites identified by Bohlin et al.
## consider only autosomal regions
dmrs <- dmrs[which(dmrs$chr %in% paste0("chr", 1:22)),]
## collect CpG sites in the regions
sites <- dmrff.sites(dmrs, meta$ewas$chr, meta$ewas$pos)
sites <- cbind(sites, meta$ewas[sites$site,c("cpg","estimate","se","p.value")])
## identify sites with associations according to Bohlin et al.
sites$bohlin <- sites$cpg %in% rownames(bohlin)
## novel regions do not contain any of the Bohlin sites
dmrs$novel <- !(1:nrow(dmrs) %in% sites$region[sites$bohlin])
Of 1713 DMRs identified,
29.54%
are novel.
They appear on the following chromosomes:
freq.novel <- table(dmrs$chr[dmrs$novel])
freq <- table(dmrs$chr)
prop <- 100*freq.novel/freq
prop <- as.data.frame(prop)
colnames(prop) <- c("chr","pct")
prop$novel <- freq.novel
prop$total <- freq
prop <- prop[order(prop$pct),]
kable(prop,row.names=F,digits=2)
|chr | pct| novel| total|
|:-----|-----:|-----:|-----:|
|chr22 | 8.70| 4| 46|
|chr19 | 22.89| 19| 83|
|chr9 | 23.08| 6| 26|
|chr14 | 25.00| 14| 56|
|chr10 | 26.14| 23| 88|
|chr11 | 26.47| 36| 136|
|chr7 | 26.97| 24| 89|
|chr18 | 27.27| 3| 11|
|chr17 | 27.40| 40| 146|
|chr21 | 28.57| 4| 14|
|chr12 | 28.75| 23| 80|
|chr2 | 30.30| 30| 99|
|chr13 | 30.43| 14| 46|
|chr6 | 30.46| 60| 197|
|chr16 | 32.97| 30| 91|
|chr5 | 33.33| 20| 60|
|chr1 | 33.70| 62| 184|
|chr4 | 34.09| 15| 44|
|chr8 | 34.43| 21| 61|
|chr15 | 36.59| 15| 41|
|chr3 | 37.18| 29| 78|
|chr20 | 37.84| 14| 37|
perishky/dmrff documentation built on Jan. 4, 2024, 10:23 p.m.
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title: "Meta-analysis using dmrff" output: pdf_document: default word_document: highlight: tango html_document: toc: true
Meta-analysis using dmrff
Download and prepare DNA methylation datasets
We'll use a couple of small cord blood DNA methylation datasets available on GEO: GSE79056, GSE62924.
Loading each dataset takes about 1 minute.
accessions <- c("GSE79056", "GSE62924")
library(geograbi) ## https://github.com/yousefi138
## Loading required package: XML
## Loading required package: data.table
samples <- sapply(accessions, geograbi.get.samples, simplify=F)
## Tue Dec 12 19:02:41 2023 reading
## Tue Dec 12 19:02:42 2023 reading
vars <- sapply(samples, geograbi.extract.characteristics, simplify=F)
system.time(methylation <- sapply(accessions, geograbi.get.data, simplify=F))
## Tue Dec 12 19:02:44 2023 reading
## Tue Dec 12 19:02:53 2023 reading
## user system elapsed
## 15.290 1.666 15.312
Remove non-CpG probes from the datasets.
for (acc in accessions)
methylation[[acc]] <- methylation[[acc]][grepl("^c", rownames(methylation[[acc]])),]
Extract the variable of interest from each dataset.
variable <- sapply(accessions, function(acc) {
idx <- grep("(ga weeks|gestational_age|gestational age)", colnames(vars[[acc]]))
stopifnot(length(idx) == 1)
as.numeric(vars[[acc]][,idx])
}, simplify=F)
Remove samples with incomplete data.
for (acc in accessions) {
idx <- which(!is.na(variable[[acc]]))
samples[[acc]] <- samples[[acc]][idx,]
vars[[acc]] <- vars[[acc]][idx,]
variable[[acc]] <- variable[[acc]][idx]
methylation[[acc]] <- methylation[[acc]][,idx]
}
Calculate surrogate variables to handle unknown confounding
SVA takes a few seconds for each dataset.
library(sva, quietly=T)
## This is mgcv 1.8-41. For overview type 'help("mgcv-package")'.
set.seed(20191029)
covariates <- sapply(accessions, function(acc) {
mod <- model.matrix(~ var, data.frame(var=variable[[acc]]))
mod0 <- mod[,1,drop=F]
random.idx <- sample(1:nrow(methylation[[acc]]), 5000)
meth.sva <- methylation[[acc]][random.idx,]
meth.mean <- rowMeans(meth.sva, na.rm=T)
idx <- which(is.na(meth.sva), arr.ind=T)
if (nrow(idx) > 0)
meth.sva[idx] <- meth.mean[idx[,1]]
sva(meth.sva, mod=mod, mod0=mod0)$sv
}, simplify=F)
## Number of significant surrogate variables is: 3
## Iteration (out of 5 ):1 2 3 4 5 Number of significant surrogate variables is: 2
## Iteration (out of 5 ):1 2 3 4 5
Test the associations with gestational age
Testing associations takes a few seconds for each dataset.
library(limma)
stats <- sapply(accessions, function(acc) {
mod <- model.matrix(~ ., data.frame(ga=variable[[acc]],
covariates[[acc]]))
fit <- lmFit(methylation[[acc]], mod)
fit <- eBayes(fit)
data.frame(estimate=fit$coefficients[,"ga"],
se=sqrt(fit$s2.post) * fit$stdev.unscaled[,"ga"],
p.value=fit$p.value[,"ga"])
},simplify=F)
Now we check the agreement between the datasets.
kable(sapply(stats, function(a) sapply(stats, function(b) {
sites <- intersect(rownames(a), rownames(b))
sites <- sites[order(a[sites,"p.value"])[1:100]]
cor(a[sites,"estimate"], b[sites,"estimate"])
})))
| | GSE79056| GSE62924| |:--------|---------:|---------:| |GSE79056 | 1.0000000| 0.5844022| |GSE62924 | 0.8681764| 1.0000000|
A previous study reported thousands of associations with gestational age:
Bohlin J, et al. Prediction of gestational age based on genome-wide differentially methylated regions. Genome Biol. 2016;17(1):207.
The effect estimates are strongly associated.
bohlin <- read.csv("bohlin.csv",stringsAsFactors=F,row.names=1)
kable(sapply(stats, function(stats) {
cor(bohlin$estimate, stats[rownames(bohlin),"estimate"], use="p")
}))
| | x| |:--------|---------:| |GSE79056 | 0.7631472| |GSE62924 | 0.5647381|
Annotate summary statistics with genomic locations
If your data was generated using one of the Illumina BeadChips, then it is possible to annotate your EWAS summary statistics using the appropriate Bioconductor annotation package.
For the Illumina 450K microaray, we use the
IlluminaHumanMethylation450kanno.ilmn12.hg19 package.
if (!require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly=T)) {
install.packages("BiocManager")
BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19")
}
##
## Attaching package: 'BiocGenerics'
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## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
## table, tapply, union, unique, unsplit, which.max, which.min
##
## Attaching package: 'S4Vectors'
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## The following objects are masked from 'package:genefilter':
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## Welcome to Bioconductor
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## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
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## locfit 1.5-9.6 2022-07-11
## Setting options('download.file.method.GEOquery'='auto')
## Setting options('GEOquery.inmemory.gpl'=FALSE)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
If we were using the more recent Illumina MethylationEPIC BeadChip,
then we would load the IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package instead.
We construct an annotation data frame as follows:
data(list="IlluminaHumanMethylation450kanno.ilmn12.hg19")
data(Locations)
data(Other)
annotation <- cbind(as.data.frame(Locations), as.data.frame(Other))
We then add the annotation to the stats object
(Warning: we assume that the row names of the stats object
are the Illumina CpG site identifiers, e.g. cg05775921).
stats <- sapply(stats, function(stats) {
annotation <- annotation[match(rownames(stats), rownames(annotation)),]
cbind(stats, annotation)
}, simplify=F)
Construct 'pre' objects for DMR meta-analysis
Takes about 2 minutes per dataset to calculate CpG site correlations.
library(dmrff)
pre <- sapply(accessions, function(acc) {
cat(date(), "pre", acc, "\n")
with(stats[[acc]], dmrff.pre(estimate, se, methylation[[acc]], chr, pos))
}, simplify=F)
## Tue Dec 12 19:04:18 2023 pre GSE79056
## Tue Dec 12 19:05:22 2023 pre GSE62924
Perform DMR meta-analysis
There are hundreds of DMRs for this phenotype, so the final meta-analysis takes about 15 minutes with a single processor.
options(mc.cores=20) ## if you have 20 processors available
meta <- dmrff.meta(pre)
## [dmrff.candidates] Tue Dec 12 19:06:45 2023 Found 92222 candidate regions.
The output contains a data frame of the meta-analysed regions and the EWAS meta-analysis on which it was based.
kable(meta$dmrs[1:2,])
|chr | start| end| n|B |S | estimate| se| z| p.value| p.adjust| |:----|--------:|--------:|--:|:--|:--|---------:|---------:|---------:|-------:|---------:| |chr6 | 32120203| 32121113| 18|NA |NA | 0.1363391| 0.0104200| 13.084374| 0e+00| 0.0000000| |chr6 | 32119874| 32119874| 1|NA |NA | 0.1136654| 0.0209026| 5.437861| 1e-07| 0.0368855|
kable(meta$ewas[1:2,])
| | estimate| se| z| p.value|chr | pos| |:----------|----------:|---------:|----------:|---------:|:----|-----:| |cg13869341 | 0.0196382| 0.0270016| 0.7272998| 0.4670423|chr1 | 15865| |cg14008030 | -0.0030598| 0.0201270| -0.1520225| 0.8791692|chr1 | 18827|
Here we add the CpG sites and gene names to the EWAS sites:
idx <- match(with(meta$ewas, paste(chr,pos)),
with(annotation, paste(chr,pos)))
meta$ewas$cpg <- rownames(annotation)[idx]
meta$ewas$gene <- annotation$UCSC_RefGene_Name[idx]
Meta-analyzed DMRs
dmrs <- meta$dmrs[which(meta$dmrs$p.adjust < 0.05 & meta$dmrs$n >= 2), ]
We've identified 1987 DMRs with Bonferroni adjusted p < 0.05.
For convenience, we'll just look at DMRs on chromosome 6 with at least 5 CpG sites.
dmrs6 <- meta$dmrs[which(meta$dmrs$p.adjust < 0.05
& meta$dmrs$n >= 5
& meta$dmrs$chr == "chr6"), ]
dmrs6 <- dmrs6[order(dmrs6$start),]
kable(dmrs6[,c("chr","start","end","n","estimate","se","p.value","p.adjust")])
| |chr | start| end| n| estimate| se| p.value| p.adjust| |:-----|:----|---------:|---------:|--:|----------:|---------:|-------:|---------:| |3259 |chr6 | 1635611| 1635847| 5| 0.1027082| 0.0078696| 0e+00| 0.0000000| |1218 |chr6 | 15504844| 15506085| 9| -0.1462422| 0.0121251| 0e+00| 0.0000000| |2159 |chr6 | 25652383| 25652602| 7| 0.0880595| 0.0162855| 1e-07| 0.0437835| |5135 |chr6 | 28543262| 28543670| 5| 0.0989848| 0.0152585| 0e+00| 0.0000598| |3266 |chr6 | 29520752| 29521046| 6| 0.1262316| 0.0185271| 0e+00| 0.0000065| |2164 |chr6 | 29571363| 29571693| 8| 0.0801718| 0.0070362| 0e+00| 0.0000000| |3272 |chr6 | 29576987| 29577348| 5| 0.0433758| 0.0042732| 0e+00| 0.0000000| |8281 |chr6 | 29577916| 29578423| 5| 0.0311143| 0.0056372| 0e+00| 0.0232597| |643 |chr6 | 29589573| 29589729| 5| 0.0352142| 0.0060229| 0e+00| 0.0034298| |88 |chr6 | 29599012| 29599836| 10| 0.1287574| 0.0118910| 0e+00| 0.0000000| |1219 |chr6 | 29911295| 29911550| 7| -0.1202450| 0.0151196| 0e+00| 0.0000000| |264 |chr6 | 30127760| 30128775| 15| 0.0328547| 0.0031879| 0e+00| 0.0000000| |66 |chr6 | 30458158| 30459317| 12| -0.1553172| 0.0110948| 0e+00| 0.0000000| |67 |chr6 | 30459540| 30460600| 9| -0.1038827| 0.0125606| 0e+00| 0.0000000| |3918 |chr6 | 30581820| 30582416| 6| -0.1515777| 0.0125543| 0e+00| 0.0000000| |221 |chr6 | 30652771| 30653530| 9| -0.1228585| 0.0147872| 0e+00| 0.0000000| |2221 |chr6 | 30850543| 30850977| 8| 0.0708181| 0.0120973| 0e+00| 0.0032814| |238 |chr6 | 30854161| 30854551| 5| 0.1272353| 0.0190420| 0e+00| 0.0000161| |3299 |chr6 | 30955992| 30956440| 5| 0.0511286| 0.0066766| 0e+00| 0.0000000| |14716 |chr6 | 31079110| 31079617| 5| 0.0936230| 0.0068468| 0e+00| 0.0000000| |249 |chr6 | 31127159| 31127863| 8| -0.0618254| 0.0094440| 0e+00| 0.0000403| |1820 |chr6 | 31549480| 31550090| 7| -0.1139919| 0.0093255| 0e+00| 0.0000000| |3320 |chr6 | 31646236| 31646625| 5| 0.0718148| 0.0110119| 0e+00| 0.0000476| |562 |chr6 | 31744391| 31744831| 10| -0.1243364| 0.0169747| 0e+00| 0.0000002| |5186 |chr6 | 31846797| 31846970| 6| 0.0662870| 0.0122338| 1e-07| 0.0411449| |52 |chr6 | 31867945| 31868470| 14| -0.0694588| 0.0065306| 0e+00| 0.0000000| |170 |chr6 | 31937758| 31938533| 12| -0.0721526| 0.0126389| 0e+00| 0.0077834| |169 |chr6 | 31939059| 31939319| 8| -0.0813310| 0.0137086| 0e+00| 0.0020366| |179 |chr6 | 32013699| 32014739| 19| 0.0724101| 0.0047237| 0e+00| 0.0000000| |3326 |chr6 | 32020425| 32020750| 8| 0.0575820| 0.0073172| 0e+00| 0.0000000| |2223 |chr6 | 32022898| 32023650| 13| 0.0625395| 0.0097437| 0e+00| 0.0000942| |21 |chr6 | 32037018| 32037800| 17| 0.0666399| 0.0083409| 0e+00| 0.0000000| |85 |chr6 | 32042200| 32044254| 20| 0.0597093| 0.0043667| 0e+00| 0.0000000| |86 |chr6 | 32044384| 32045323| 6| 0.0389959| 0.0069651| 0e+00| 0.0147658| |187 |chr6 | 32048449| 32049845| 20| 0.0559469| 0.0060904| 0e+00| 0.0000000| |1518 |chr6 | 32060791| 32061478| 7| 0.1054549| 0.0066597| 0e+00| 0.0000000| |1024 |chr6 | 32086755| 32086893| 8| 0.0979195| 0.0167033| 0e+00| 0.0031226| |1 |chr6 | 32120203| 32121113| 18| 0.1363391| 0.0104200| 0e+00| 0.0000000| |10 |chr6 | 32121143| 32121475| 14| 0.0993614| 0.0096535| 0e+00| 0.0000000| |1824 |chr6 | 32122736| 32122864| 5| -0.1028521| 0.0164666| 0e+00| 0.0002878| |1520 |chr6 | 32135241| 32135803| 13| 0.0629867| 0.0044176| 0e+00| 0.0000000| |14783 |chr6 | 32150404| 32150716| 5| 0.0442438| 0.0077106| 0e+00| 0.0065511| |566 |chr6 | 32154416| 32154715| 6| -0.0954617| 0.0109209| 0e+00| 0.0000000| |824 |chr6 | 32158927| 32160074| 8| -0.1059600| 0.0100092| 0e+00| 0.0000000| |8386 |chr6 | 32171796| 32172124| 6| 0.0435022| 0.0072622| 0e+00| 0.0014331| |1258 |chr6 | 32805398| 32805684| 5| -0.1578966| 0.0142437| 0e+00| 0.0000000| |351 |chr6 | 32812933| 32813448| 9| -0.1547065| 0.0088548| 0e+00| 0.0000000| |70 |chr6 | 32820355| 32820577| 6| -0.1703108| 0.0153020| 0e+00| 0.0000000| |675 |chr6 | 32825701| 32826197| 5| 0.0464334| 0.0067413| 0e+00| 0.0000039| |236 |chr6 | 32908567| 32909523| 13| -0.1486117| 0.0100272| 0e+00| 0.0000000| |573 |chr6 | 32942063| 32943025| 11| -0.1361098| 0.0150253| 0e+00| 0.0000000| |1829 |chr6 | 33043841| 33044510| 7| -0.1374565| 0.0212478| 0e+00| 0.0000674| |213 |chr6 | 33132163| 33132318| 5| 0.0876268| 0.0147821| 0e+00| 0.0020991| |212 |chr6 | 33132650| 33134078| 19| 0.0319455| 0.0050725| 0e+00| 0.0002065| |42 |chr6 | 33245488| 33245553| 6| -0.1782523| 0.0143561| 0e+00| 0.0000000| |47 |chr6 | 33245706| 33245804| 7| -0.0949201| 0.0136651| 0e+00| 0.0000026| |44 |chr6 | 33245893| 33246094| 7| -0.1385954| 0.0148995| 0e+00| 0.0000000| |3338 |chr6 | 41010111| 41010654| 6| 0.0394107| 0.0045998| 0e+00| 0.0000000| |3339 |chr6 | 53530503| 53530628| 6| 0.1001493| 0.0159807| 0e+00| 0.0002519| |585 |chr6 | 149805995| 149806732| 11| -0.1157892| 0.0081252| 0e+00| 0.0000000| |5317 |chr6 | 152702330| 152702463| 5| 0.1032869| 0.0074051| 0e+00| 0.0000000| |2651 |chr6 | 170580947| 170581690| 8| -0.0842003| 0.0128133| 0e+00| 0.0000341|
Below we use the dmrff.sites function to show the CpG sites in each DMR and their
meta-analysed summary statistics.
sites <- dmrff.sites(dmrs6, meta$ewas$chr, meta$ewas$pos)
sites <- cbind(sites[,c("region","chr","pos")],
meta$ewas[sites$site,c("cpg", "estimate","se","p.value")])
kable(sites,row.names=F)
| region|chr | pos|cpg | estimate| se| p.value| |------:|:----|---------:|:----------|----------:|---------:|---------:| | 1|chr6 | 1635611|cg07714812 | 0.1325816| 0.0161031| 0.0000000| | 1|chr6 | 1635640|cg19295314 | 0.0976020| 0.0125669| 0.0000000| | 1|chr6 | 1635808|cg13394216 | 0.1330165| 0.0128689| 0.0000000| | 1|chr6 | 1635818|cg26908825 | 0.1246750| 0.0161058| 0.0000000| | 1|chr6 | 1635847|cg10707788 | 0.1219806| 0.0111667| 0.0000000| | 2|chr6 | 15504844|cg10975897 | -0.1515391| 0.0129587| 0.0000000| | 2|chr6 | 15504872|cg13027183 | -0.1431798| 0.0135442| 0.0000000| | 2|chr6 | 15504923|cg20052079 | -0.1618406| 0.0143556| 0.0000000| | 2|chr6 | 15505094|cg18188328 | -0.1427320| 0.0129587| 0.0000000| | 2|chr6 | 15505345|cg03173502 | -0.0992715| 0.0246547| 0.0000566| | 2|chr6 | 15505452|cg23850913 | -0.1082715| 0.0246992| 0.0000117| | 2|chr6 | 15505460|cg13500852 | -0.1251692| 0.0209455| 0.0000000| | 2|chr6 | 15505949|cg14058851 | -0.1135978| 0.0231285| 0.0000009| | 2|chr6 | 15506085|cg24408769 | -0.1431592| 0.0186050| 0.0000000| | 3|chr6 | 25652383|cg13586599 | 0.0985821| 0.0177986| 0.0000000| | 3|chr6 | 25652390|cg04200224 | 0.0835931| 0.0270537| 0.0020023| | 3|chr6 | 25652395|cg15562220 | 0.0598369| 0.0258873| 0.0208088| | 3|chr6 | 25652405|cg10721149 | 0.0658864| 0.0264927| 0.0128838| | 3|chr6 | 25652407|cg13834623 | 0.0347019| 0.0297161| 0.2428950| | 3|chr6 | 25652531|cg26718511 | 0.0564228| 0.0307144| 0.0662074| | 3|chr6 | 25652602|cg06493994 | 0.0758429| 0.0288685| 0.0086093| | 4|chr6 | 28543262|cg18214570 | 0.0273951| 0.0281027| 0.3296477| | 4|chr6 | 28543508|cg04113450 | 0.0414187| 0.0259925| 0.1110509| | 4|chr6 | 28543514|cg06280322 | 0.0746264| 0.0210831| 0.0004007| | 4|chr6 | 28543667|cg01254034 | 0.0971941| 0.0163355| 0.0000000| | 4|chr6 | 28543670|cg07031070 | 0.1028115| 0.0159255| 0.0000000| | 5|chr6 | 29520752|cg11935738 | 0.0855872| 0.0254399| 0.0007674| | 5|chr6 | 29520774|cg08065408 | 0.1288810| 0.0200188| 0.0000000| | 5|chr6 | 29520965|cg09641376 | 0.1043260| 0.0248782| 0.0000275| | 5|chr6 | 29521013|cg12749246 | 0.1097796| 0.0202969| 0.0000001| | 5|chr6 | 29521023|cg06343355 | 0.0930443| 0.0212854| 0.0000124| | 5|chr6 | 29521046|cg18342026 | 0.0876552| 0.0276076| 0.0014982| | 6|chr6 | 29571363|cg18656132 | 0.0540814| 0.0090586| 0.0000000| | 6|chr6 | 29571419|cg07169712 | 0.0471520| 0.0235234| 0.0450191| | 6|chr6 | 29571429|cg12166917 | -0.0049779| 0.0160092| 0.7558444| | 6|chr6 | 29571432|cg00806253 | 0.0258679| 0.0207753| 0.2130837| | 6|chr6 | 29571438|cg12083232 | 0.0053564| 0.0254470| 0.8332830| | 6|chr6 | 29571468|cg15136600 | 0.0224261| 0.0160977| 0.1635830| | 6|chr6 | 29571483|cg21652192 | -0.0188971| 0.0180588| 0.2953669| | 6|chr6 | 29571693|cg20067272 | 0.0028609| 0.0148239| 0.8469628| | 7|chr6 | 29576987|cg15154411 | 0.0351587| 0.0064316| 0.0000000| | 7|chr6 | 29577006|cg04960880 | -0.0031858| 0.0129476| 0.8056420| | 7|chr6 | 29577082|cg20642417 | 0.0208238| 0.0086763| 0.0163920| | 7|chr6 | 29577223|cg03258475 | 0.0243484| 0.0111411| 0.0288550| | 7|chr6 | 29577348|cg05972518 | 0.0356577| 0.0148130| 0.0160761| | 8|chr6 | 29577916|cg24962941 | 0.0387238| 0.0192038| 0.0437511| | 8|chr6 | 29578124|cg23801674 | -0.0098085| 0.0278039| 0.7242565| | 8|chr6 | 29578144|cg22783999 | 0.0522605| 0.0240929| 0.0300734| | 8|chr6 | 29578313|cg26569800 | 0.0371461| 0.0108821| 0.0006413| | 8|chr6 | 29578423|cg21552290 | 0.0303105| 0.0073074| 0.0000336| | 9|chr6 | 29589573|cg13730341 | -0.0073799| 0.0220999| 0.7384307| | 9|chr6 | 29589631|cg01373089 | 0.0042720| 0.0172564| 0.8044751| | 9|chr6 | 29589707|cg06266853 | 0.0259628| 0.0071999| 0.0003110| | 9|chr6 | 29589714|cg24430207 | 0.0093660| 0.0121189| 0.4396148| | 9|chr6 | 29589729|cg18004110 | 0.0044864| 0.0134167| 0.7380879| | 10|chr6 | 29599012|cg23306453 | 0.1207457| 0.0158933| 0.0000000| | 10|chr6 | 29599160|cg01765653 | 0.1269653| 0.0140006| 0.0000000| | 10|chr6 | 29599178|cg20139800 | 0.1414558| 0.0182363| 0.0000000| | 10|chr6 | 29599226|cg06519422 | 0.1285017| 0.0133170| 0.0000000| | 10|chr6 | 29599250|cg03127104 | 0.1345549| 0.0164055| 0.0000000| | 10|chr6 | 29599259|cg12991385 | 0.1442089| 0.0154134| 0.0000000| | 10|chr6 | 29599319|cg17806418 | 0.1430834| 0.0165113| 0.0000000| | 10|chr6 | 29599331|cg22679406 | 0.1331319| 0.0175590| 0.0000000| | 10|chr6 | 29599390|cg06512249 | 0.1434446| 0.0172208| 0.0000000| | 10|chr6 | 29599836|cg07839627 | 0.0542492| 0.0231074| 0.0188901| | 11|chr6 | 29911295|cg09535358 | -0.0890083| 0.0265383| 0.0007967| | 11|chr6 | 29911334|cg08039587 | -0.1139279| 0.0221143| 0.0000003| | 11|chr6 | 29911339|cg00082981 | -0.0998774| 0.0249472| 0.0000624| | 11|chr6 | 29911366|cg16742075 | -0.1416403| 0.0179065| 0.0000000| | 11|chr6 | 29911494|cg20408505 | -0.0587967| 0.0294647| 0.0459885| | 11|chr6 | 29911542|cg25637655 | -0.1136482| 0.0224943| 0.0000004| | 11|chr6 | 29911550|cg17608381 | -0.1207630| 0.0222267| 0.0000001| | 12|chr6 | 30127760|cg04560098 | 0.0401264| 0.0113225| 0.0003942| | 12|chr6 | 30127997|cg03189075 | 0.0327587| 0.0067979| 0.0000014| | 12|chr6 | 30128219|cg24449136 | 0.0491391| 0.0171271| 0.0041165| | 12|chr6 | 30128238|cg15118780 | 0.0478123| 0.0173236| 0.0057811| | 12|chr6 | 30128254|cg18765127 | 0.0356384| 0.0176748| 0.0437645| | 12|chr6 | 30128385|cg17232861 | 0.0250335| 0.0092835| 0.0070060| | 12|chr6 | 30128404|cg24679043 | 0.0402768| 0.0088223| 0.0000050| | 12|chr6 | 30128427|cg15109860 | 0.0272555| 0.0117868| 0.0207577| | 12|chr6 | 30128511|cg10391909 | 0.0253172| 0.0091443| 0.0056292| | 12|chr6 | 30128526|cg22733580 | 0.0153087| 0.0082243| 0.0626860| | 12|chr6 | 30128542|cg03266377 | 0.0062717| 0.0116496| 0.5903261| | 12|chr6 | 30128548|cg20136460 | 0.0212401| 0.0083472| 0.0109408| | 12|chr6 | 30128558|cg07738839 | 0.0368983| 0.0096792| 0.0001378| | 12|chr6 | 30128686|cg11334822 | 0.0458124| 0.0154149| 0.0029591| | 12|chr6 | 30128775|cg21126020 | 0.0351664| 0.0067421| 0.0000002| | 13|chr6 | 30458158|cg21176130 | -0.1187951| 0.0247921| 0.0000017| | 13|chr6 | 30458161|cg09326440 | -0.1279226| 0.0225586| 0.0000000| | 13|chr6 | 30458237|cg12700271 | -0.1475024| 0.0199043| 0.0000000| | 13|chr6 | 30458519|cg13007871 | -0.1490487| 0.0154139| 0.0000000| | 13|chr6 | 30458586|cg00340855 | -0.1577606| 0.0130459| 0.0000000| | 13|chr6 | 30458601|cg11594821 | -0.1466365| 0.0142721| 0.0000000| | 13|chr6 | 30458730|cg21758773 | -0.1130846| 0.0145080| 0.0000000| | 13|chr6 | 30458998|cg25786265 | -0.0724191| 0.0262484| 0.0057980| | 13|chr6 | 30459139|cg05201185 | -0.1186304| 0.0168037| 0.0000000| | 13|chr6 | 30459255|cg02188225 | -0.0937755| 0.0211501| 0.0000093| | 13|chr6 | 30459295|cg20652371 | -0.0980952| 0.0194738| 0.0000005| | 13|chr6 | 30459317|cg04907849 | -0.0678662| 0.0263028| 0.0098747| | 14|chr6 | 30459540|cg23235965 | -0.1008510| 0.0291446| 0.0005394| | 14|chr6 | 30459595|cg27486585 | -0.0878102| 0.0169830| 0.0000002| | 14|chr6 | 30459867|cg17615629 | -0.0841319| 0.0186010| 0.0000061| | 14|chr6 | 30460244|cg20105257 | -0.0966510| 0.0214485| 0.0000066| | 14|chr6 | 30460322|cg02678305 | -0.0790670| 0.0188239| 0.0000267| | 14|chr6 | 30460484|cg19109457 | -0.0108955| 0.0262903| 0.6785587| | 14|chr6 | 30460548|cg09569347 | -0.0922902| 0.0194441| 0.0000021| | 14|chr6 | 30460576|cg13036546 | -0.1021893| 0.0134941| 0.0000000| | 14|chr6 | 30460600|cg16535080 | -0.0767010| 0.0173629| 0.0000100| | 15|chr6 | 30581820|cg13522406 | -0.1540336| 0.0134155| 0.0000000| | 15|chr6 | 30582174|cg05235540 | -0.1331640| 0.0204797| 0.0000000| | 15|chr6 | 30582241|cg08677140 | -0.1462982| 0.0200799| 0.0000000| | 15|chr6 | 30582333|cg23583454 | -0.1278021| 0.0197341| 0.0000000| | 15|chr6 | 30582352|cg04694022 | -0.1133670| 0.0184513| 0.0000000| | 15|chr6 | 30582416|cg10977734 | -0.1577487| 0.0164834| 0.0000000| | 16|chr6 | 30652771|cg11414821 | -0.1226349| 0.0206328| 0.0000000| | 16|chr6 | 30652829|cg00278359 | -0.1349316| 0.0165676| 0.0000000| | 16|chr6 | 30652907|cg12036303 | -0.1437066| 0.0176865| 0.0000000| | 16|chr6 | 30653167|cg00010853 | -0.1255908| 0.0164041| 0.0000000| | 16|chr6 | 30653191|cg11554650 | -0.0818081| 0.0211529| 0.0001100| | 16|chr6 | 30653242|cg08253704 | -0.1141914| 0.0180993| 0.0000000| | 16|chr6 | 30653407|cg12105190 | -0.1148872| 0.0208874| 0.0000000| | 16|chr6 | 30653512|cg25980484 | -0.1206877| 0.0210263| 0.0000000| | 16|chr6 | 30653530|cg03052182 | -0.1253747| 0.0227586| 0.0000000| | 17|chr6 | 30850543|cg08951271 | 0.1071200| 0.0184280| 0.0000000| | 17|chr6 | 30850581|cg19178509 | -0.0092858| 0.0318039| 0.7703079| | 17|chr6 | 30850718|cg13396738 | 0.0621029| 0.0220589| 0.0048729| | 17|chr6 | 30850829|cg17604312 | 0.1115154| 0.0207763| 0.0000001| | 17|chr6 | 30850868|cg24727290 | 0.1061909| 0.0213050| 0.0000006| | 17|chr6 | 30850876|cg13329862 | 0.0696142| 0.0192965| 0.0003090| | 17|chr6 | 30850913|cg19215110 | 0.0400965| 0.0238290| 0.0924369| | 17|chr6 | 30850977|cg02696067 | 0.0938655| 0.0169445| 0.0000000| | 18|chr6 | 30854161|cg07187855 | 0.1007622| 0.0254437| 0.0000749| | 18|chr6 | 30854164|cg24566261 | 0.1226748| 0.0218724| 0.0000000| | 18|chr6 | 30854186|cg09965419 | 0.0852155| 0.0242037| 0.0004303| | 18|chr6 | 30854233|cg17091577 | 0.0834024| 0.0257151| 0.0011815| | 18|chr6 | 30854551|cg15656686 | 0.1179877| 0.0191640| 0.0000000| | 19|chr6 | 30955992|cg05123447 | 0.0459193| 0.0185740| 0.0134271| | 19|chr6 | 30956214|cg26556020 | 0.0469319| 0.0285778| 0.1005376| | 19|chr6 | 30956221|cg07491399 | 0.0337318| 0.0220895| 0.1267479| | 19|chr6 | 30956397|cg24067150 | 0.0465228| 0.0078675| 0.0000000| | 19|chr6 | 30956440|cg25159149 | 0.0458519| 0.0100622| 0.0000052| | 20|chr6 | 31079110|cg17323974 | 0.0534675| 0.0107817| 0.0000007| | 20|chr6 | 31079152|cg08951273 | 0.0715681| 0.0087428| 0.0000000| | 20|chr6 | 31079306|cg15993401 | 0.0217831| 0.0176159| 0.2162510| | 20|chr6 | 31079555|cg10185489 | 0.0228372| 0.0132467| 0.0847102| | 20|chr6 | 31079617|cg17784811 | 0.0393704| 0.0181017| 0.0296334| | 21|chr6 | 31127159|cg23679615 | -0.0885155| 0.0228118| 0.0001043| | 21|chr6 | 31127173|cg21863888 | -0.0874801| 0.0238761| 0.0002484| | 21|chr6 | 31127178|cg09045681 | -0.0785239| 0.0248822| 0.0016005| | 21|chr6 | 31127271|cg10094358 | -0.1115438| 0.0258876| 0.0000164| | 21|chr6 | 31127357|cg09329266 | -0.0940475| 0.0283812| 0.0009206| | 21|chr6 | 31127379|cg21799473 | -0.0915739| 0.0256380| 0.0003545| | 21|chr6 | 31127527|cg23654219 | -0.0594847| 0.0149943| 0.0000727| | 21|chr6 | 31127863|cg16095155 | -0.0687672| 0.0146127| 0.0000025| | 22|chr6 | 31549480|cg22934035 | -0.0926485| 0.0225478| 0.0000397| | 22|chr6 | 31549563|cg26311932 | -0.0991315| 0.0140378| 0.0000000| | 22|chr6 | 31549625|cg24479522 | -0.0720174| 0.0298864| 0.0159654| | 22|chr6 | 31549631|cg21055528 | -0.1077615| 0.0108198| 0.0000000| | 22|chr6 | 31549853|cg26724726 | -0.1432887| 0.0152955| 0.0000000| | 22|chr6 | 31549929|cg06526741 | -0.0943205| 0.0119944| 0.0000000| | 22|chr6 | 31550090|cg19279042 | -0.0865161| 0.0154381| 0.0000000| | 23|chr6 | 31646236|cg00621943 | 0.0748559| 0.0122366| 0.0000000| | 23|chr6 | 31646262|cg15039036 | 0.0573391| 0.0120663| 0.0000020| | 23|chr6 | 31646366|cg27334499 | 0.0028921| 0.0159384| 0.8560097| | 23|chr6 | 31646377|cg17187990 | 0.0170122| 0.0174635| 0.3299779| | 23|chr6 | 31646625|cg12632549 | 0.0731516| 0.0231392| 0.0015703| | 24|chr6 | 31744391|cg16672203 | -0.1329963| 0.0180809| 0.0000000| | 24|chr6 | 31744398|cg15369633 | -0.0949400| 0.0252150| 0.0001664| | 24|chr6 | 31744524|cg12988118 | -0.1012584| 0.0272224| 0.0001995| | 24|chr6 | 31744545|cg23916646 | -0.1270805| 0.0231574| 0.0000000| | 24|chr6 | 31744612|cg12383352 | -0.1185445| 0.0248924| 0.0000019| | 24|chr6 | 31744628|cg27143082 | -0.0902251| 0.0275646| 0.0010633| | 24|chr6 | 31744636|cg27574980 | -0.1179906| 0.0245011| 0.0000015| | 24|chr6 | 31744735|cg24065328 | -0.1385544| 0.0221587| 0.0000000| | 24|chr6 | 31744816|cg19868593 | -0.0939086| 0.0258975| 0.0002877| | 24|chr6 | 31744831|cg05447916 | -0.1131832| 0.0254600| 0.0000088| | 25|chr6 | 31846797|cg07357081 | 0.0596000| 0.0138991| 0.0000180| | 25|chr6 | 31846813|cg23431175 | 0.0243320| 0.0245092| 0.3208223| | 25|chr6 | 31846899|cg21236501 | 0.0739955| 0.0172653| 0.0000182| | 25|chr6 | 31846924|cg24529722 | 0.0849608| 0.0199092| 0.0000198| | 25|chr6 | 31846956|cg04567302 | 0.0477799| 0.0190684| 0.0122206| | 25|chr6 | 31846970|cg03045620 | 0.0418653| 0.0183732| 0.0226909| | 26|chr6 | 31867945|cg17243044 | -0.0755680| 0.0181911| 0.0000327| | 26|chr6 | 31867956|cg00058449 | -0.0991778| 0.0127343| 0.0000000| | 26|chr6 | 31867995|cg07249939 | -0.1080695| 0.0136897| 0.0000000| | 26|chr6 | 31868021|cg12484688 | -0.0930608| 0.0153543| 0.0000000| | 26|chr6 | 31868025|cg25110523 | -0.1148973| 0.0147600| 0.0000000| | 26|chr6 | 31868133|cg00889295 | -0.0723599| 0.0297440| 0.0149846| | 26|chr6 | 31868144|cg05680710 | -0.0238520| 0.0241229| 0.3227749| | 26|chr6 | 31868162|cg07910050 | -0.0404111| 0.0219174| 0.0652134| | 26|chr6 | 31868169|cg17766150 | -0.0571946| 0.0272606| 0.0358991| | 26|chr6 | 31868207|cg06169557 | -0.0652424| 0.0258276| 0.0115346| | 26|chr6 | 31868368|cg12229403 | -0.0439614| 0.0197288| 0.0258615| | 26|chr6 | 31868418|cg03537740 | -0.0597538| 0.0244753| 0.0146307| | 26|chr6 | 31868452|cg13464142 | -0.0625777| 0.0287193| 0.0293356| | 26|chr6 | 31868470|cg20159839 | -0.0538207| 0.0252013| 0.0327092| | 27|chr6 | 31937758|cg14666908 | -0.0923688| 0.0246890| 0.0001831| | 27|chr6 | 31937906|cg22283528 | -0.0674884| 0.0140519| 0.0000016| | 27|chr6 | 31937968|cg08721491 | -0.0400322| 0.0261884| 0.1263581| | 27|chr6 | 31937973|cg15010006 | -0.0854724| 0.0235559| 0.0002851| | 27|chr6 | 31938090|cg04654261 | -0.0545310| 0.0234533| 0.0200670| | 27|chr6 | 31938176|cg00620476 | -0.0272449| 0.0191201| 0.1541751| | 27|chr6 | 31938187|cg17587998 | -0.0152135| 0.0271285| 0.5749374| | 27|chr6 | 31938207|cg20510378 | -0.0373073| 0.0202105| 0.0649021| | 27|chr6 | 31938358|cg09346993 | -0.0091692| 0.0246650| 0.7100784| | 27|chr6 | 31938372|cg01449563 | -0.0622017| 0.0206789| 0.0026299| | 27|chr6 | 31938527|cg10201402 | -0.0632100| 0.0184577| 0.0006158| | 27|chr6 | 31938533|cg23514417 | -0.0364712| 0.0225217| 0.1053658| | 28|chr6 | 31939059|cg12776033 | -0.0875861| 0.0152930| 0.0000000| | 28|chr6 | 31939085|cg26029547 | -0.0245157| 0.0271835| 0.3671311| | 28|chr6 | 31939106|cg16190718 | -0.0414330| 0.0279153| 0.1377455| | 28|chr6 | 31939112|cg23906067 | -0.0843669| 0.0240844| 0.0004601| | 28|chr6 | 31939181|cg04142955 | -0.0669547| 0.0267664| 0.0123689| | 28|chr6 | 31939224|cg10914467 | -0.0732949| 0.0274490| 0.0075801| | 28|chr6 | 31939280|cg20194050 | -0.0922175| 0.0232613| 0.0000736| | 28|chr6 | 31939319|cg04149916 | -0.0669540| 0.0280619| 0.0170354| | 29|chr6 | 32013699|cg10967176 | 0.0578634| 0.0082523| 0.0000000| | 29|chr6 | 32013710|cg14070039 | 0.0627561| 0.0075186| 0.0000000| | 29|chr6 | 32013845|cg20621471 | 0.0550659| 0.0169361| 0.0011484| | 29|chr6 | 32013974|cg13739666 | 0.0311762| 0.0218473| 0.1535798| | 29|chr6 | 32014003|cg03819671 | 0.0141546| 0.0206556| 0.4931753| | 29|chr6 | 32014059|cg26537323 | 0.0073518| 0.0258693| 0.7762629| | 29|chr6 | 32014096|cg25522795 | 0.0174326| 0.0227670| 0.4438562| | 29|chr6 | 32014100|cg18178844 | 0.0307302| 0.0224183| 0.1704485| | 29|chr6 | 32014148|cg06824720 | 0.0509557| 0.0287177| 0.0760027| | 29|chr6 | 32014189|cg16385684 | 0.0752194| 0.0182385| 0.0000372| | 29|chr6 | 32014300|cg04182226 | 0.0188578| 0.0243463| 0.4385966| | 29|chr6 | 32014381|cg22616343 | 0.0063350| 0.0161042| 0.6940419| | 29|chr6 | 32014476|cg13409674 | 0.0175369| 0.0304824| 0.5650800| | 29|chr6 | 32014484|cg14630748 | 0.0252643| 0.0285488| 0.3761814| | 29|chr6 | 32014510|cg07481886 | 0.0348800| 0.0292591| 0.2332197| | 29|chr6 | 32014605|cg09115485 | 0.0190211| 0.0158274| 0.2294474| | 29|chr6 | 32014663|cg09423875 | 0.0466589| 0.0206613| 0.0239289| | 29|chr6 | 32014674|cg08972588 | 0.0254215| 0.0186169| 0.1720938| | 29|chr6 | 32014739|cg25375757 | 0.0723296| 0.0169683| 0.0000202| | 30|chr6 | 32020425|cg07122553 | 0.0414882| 0.0096718| 0.0000179| | 30|chr6 | 32020477|cg22800959 | 0.0652162| 0.0163215| 0.0000645| | 30|chr6 | 32020479|cg00705156 | 0.0542607| 0.0108547| 0.0000006| | 30|chr6 | 32020489|cg21554399 | 0.0502569| 0.0151791| 0.0009299| | 30|chr6 | 32020498|cg01630940 | 0.0033497| 0.0179897| 0.8522878| | 30|chr6 | 32020572|cg23285599 | 0.0384311| 0.0164462| 0.0194509| | 30|chr6 | 32020587|cg05499272 | 0.0216049| 0.0169106| 0.2013937| | 30|chr6 | 32020750|cg22259126 | 0.0561279| 0.0174840| 0.0013262| | 31|chr6 | 32022898|cg25270367 | 0.0521446| 0.0125787| 0.0000339| | 31|chr6 | 32022929|cg05598103 | 0.0595188| 0.0119202| 0.0000006| | 31|chr6 | 32023102|cg11223361 | 0.0348962| 0.0140642| 0.0130939| | 31|chr6 | 32023142|cg01054725 | 0.0268959| 0.0161439| 0.0957121| | 31|chr6 | 32023246|cg14200543 | 0.0274669| 0.0168365| 0.1028078| | 31|chr6 | 32023249|cg07910408 | 0.0432637| 0.0225178| 0.0546919| | 31|chr6 | 32023251|cg09102573 | 0.0304399| 0.0210556| 0.1482642| | 31|chr6 | 32023283|cg11815438 | 0.0646882| 0.0197018| 0.0010258| | 31|chr6 | 32023332|cg02600478 | 0.0076457| 0.0244752| 0.7547475| | 31|chr6 | 32023383|cg14011611 | 0.0040272| 0.0223974| 0.8573050| | 31|chr6 | 32023409|cg16651678 | 0.0690415| 0.0233394| 0.0030949| | 31|chr6 | 32023527|cg10750010 | 0.0299052| 0.0160993| 0.0632324| | 31|chr6 | 32023650|cg06418131 | 0.0565061| 0.0125174| 0.0000064| | 32|chr6 | 32037018|cg13069985 | 0.0568268| 0.0101261| 0.0000000| | 32|chr6 | 32037097|cg15846590 | -0.0203538| 0.0293228| 0.4876016| | 32|chr6 | 32037148|cg19644336 | 0.0301327| 0.0246112| 0.2208210| | 32|chr6 | 32037290|cg05227556 | 0.0544538| 0.0142427| 0.0001317| | 32|chr6 | 32037339|cg07139946 | 0.0585110| 0.0162122| 0.0003073| | 32|chr6 | 32037342|cg01886385 | 0.0651169| 0.0149918| 0.0000140| | 32|chr6 | 32037421|cg23858197 | 0.0250787| 0.0155224| 0.1061706| | 32|chr6 | 32037426|cg08277291 | 0.0380627| 0.0191002| 0.0462847| | 32|chr6 | 32037453|cg09381582 | 0.0452096| 0.0154411| 0.0034129| | 32|chr6 | 32037474|cg21386904 | 0.0180316| 0.0142395| 0.2054043| | 32|chr6 | 32037587|cg02571560 | 0.0410477| 0.0178117| 0.0211927| | 32|chr6 | 32037602|cg02969214 | 0.0154629| 0.0160582| 0.3355837| | 32|chr6 | 32037632|cg14698808 | 0.0116169| 0.0141993| 0.4132799| | 32|chr6 | 32037653|cg21830122 | 0.0387630| 0.0152443| 0.0109969| | 32|chr6 | 32037735|cg16416464 | 0.0665907| 0.0252700| 0.0084096| | 32|chr6 | 32037751|cg24506088 | 0.0205561| 0.0189513| 0.2780633| | 32|chr6 | 32037800|cg05596841 | 0.0042574| 0.0205186| 0.8356263| | 33|chr6 | 32042200|cg03144708 | 0.0353414| 0.0124635| 0.0045741| | 33|chr6 | 32042344|cg13308063 | 0.0387898| 0.0213276| 0.0689480| | 33|chr6 | 32042351|cg13205613 | 0.0631600| 0.0182999| 0.0005577| | 33|chr6 | 32042430|cg02927981 | 0.0052016| 0.0154604| 0.7365348| | 33|chr6 | 32042518|cg03169843 | -0.0293359| 0.0264765| 0.2678632| | 33|chr6 | 32042526|cg26950876 | 0.0301300| 0.0338511| 0.3734258| | 33|chr6 | 32042534|cg07460894 | 0.0017347| 0.0280651| 0.9507137| | 33|chr6 | 32042658|cg00013543 | -0.0244076| 0.0246059| 0.3212247| | 33|chr6 | 32042797|cg23623681 | 0.0424775| 0.0129319| 0.0010209| | 33|chr6 | 32042947|cg20170809 | 0.0548336| 0.0094096| 0.0000000| | 33|chr6 | 32043029|cg14173662 | 0.0553816| 0.0193324| 0.0041739| | 33|chr6 | 32043191|cg06878311 | 0.0198667| 0.0098425| 0.0435443| | 33|chr6 | 32043561|cg22825871 | 0.0513585| 0.0083843| 0.0000000| | 33|chr6 | 32043676|cg25962829 | 0.0451832| 0.0153327| 0.0032104| | 33|chr6 | 32043739|cg04492496 | 0.0728570| 0.0091460| 0.0000000| | 33|chr6 | 32044104|cg15318957 | 0.0224676| 0.0138420| 0.1045586| | 33|chr6 | 32044163|cg08660959 | 0.0425730| 0.0205270| 0.0380790| | 33|chr6 | 32044179|cg07485305 | 0.0707318| 0.0180229| 0.0000869| | 33|chr6 | 32044203|cg20407792 | 0.0041450| 0.0145242| 0.7753506| | 33|chr6 | 32044254|cg05423418 | 0.0464549| 0.0130002| 0.0003524| | 34|chr6 | 32044384|cg05569328 | 0.0632515| 0.0168732| 0.0001778| | 34|chr6 | 32044404|cg22851080 | 0.0918711| 0.0199763| 0.0000042| | 34|chr6 | 32044496|cg27428104 | 0.0651064| 0.0215196| 0.0024827| | 34|chr6 | 32044869|cg23164535 | 0.0510180| 0.0166487| 0.0021812| | 34|chr6 | 32044959|cg02133510 | 0.0158587| 0.0143360| 0.2686349| | 34|chr6 | 32045323|cg04076535 | 0.0423971| 0.0116441| 0.0002715| | 35|chr6 | 32048449|cg18431489 | 0.0604830| 0.0128694| 0.0000026| | 35|chr6 | 32048463|cg15212833 | 0.0654139| 0.0213765| 0.0022127| | 35|chr6 | 32048632|cg06696874 | 0.0377689| 0.0135462| 0.0053009| | 35|chr6 | 32048679|cg02550722 | 0.0601228| 0.0147345| 0.0000450| | 35|chr6 | 32049053|cg27624229 | 0.0571857| 0.0230224| 0.0129948| | 35|chr6 | 32049177|cg00661399 | 0.0490283| 0.0264692| 0.0639859| | 35|chr6 | 32049196|cg13199127 | 0.0713010| 0.0281338| 0.0112656| | 35|chr6 | 32049235|cg17031787 | 0.0769871| 0.0219826| 0.0004615| | 35|chr6 | 32049263|cg15712520 | 0.0174487| 0.0216647| 0.4205907| | 35|chr6 | 32049322|cg09975576 | 0.0585593| 0.0116761| 0.0000005| | 35|chr6 | 32049354|cg07306331 | 0.0238488| 0.0207991| 0.2515368| | 35|chr6 | 32049373|cg15048806 | 0.0213092| 0.0192680| 0.2687527| | 35|chr6 | 32049376|cg14218053 | 0.0364012| 0.0204221| 0.0746769| | 35|chr6 | 32049513|cg17295739 | 0.0579886| 0.0284546| 0.0415565| | 35|chr6 | 32049516|cg10303653 | 0.0409066| 0.0235653| 0.0825851| | 35|chr6 | 32049622|cg08753391 | 0.0958057| 0.0218816| 0.0000120| | 35|chr6 | 32049699|cg04872123 | 0.0663145| 0.0182384| 0.0002769| | 35|chr6 | 32049825|cg20116929 | 0.0344560| 0.0164789| 0.0365355| | 35|chr6 | 32049829|cg11289677 | 0.0601781| 0.0218992| 0.0059967| | 35|chr6 | 32049845|cg05471725 | 0.0014822| 0.0220097| 0.9463090| | 36|chr6 | 32060791|cg02151997 | 0.0942577| 0.0241650| 0.0000960| | 36|chr6 | 32060794|cg04757901 | 0.0726107| 0.0237271| 0.0022115| | 36|chr6 | 32060816|cg23145336 | 0.1308970| 0.0166251| 0.0000000| | 36|chr6 | 32061084|cg15642307 | 0.1245957| 0.0218110| 0.0000000| | 36|chr6 | 32061160|cg07148038 | 0.0606021| 0.0144964| 0.0000291| | 36|chr6 | 32061318|cg23641899 | 0.0681344| 0.0094939| 0.0000000| | 36|chr6 | 32061478|cg24504289 | 0.0982410| 0.0078538| 0.0000000| | 37|chr6 | 32086755|cg25065981 | 0.0880026| 0.0257344| 0.0006270| | 37|chr6 | 32086758|cg27001603 | 0.1049990| 0.0284150| 0.0002197| | 37|chr6 | 32086779|cg04962282 | 0.0473999| 0.0276648| 0.0866461| | 37|chr6 | 32086782|cg06111526 | 0.0822598| 0.0249918| 0.0009966| | 37|chr6 | 32086818|cg10089357 | 0.0959562| 0.0261365| 0.0002413| | 37|chr6 | 32086857|cg07986385 | 0.0919125| 0.0255865| 0.0003279| | 37|chr6 | 32086878|cg17396404 | 0.0867368| 0.0233334| 0.0002014| | 37|chr6 | 32086893|cg19004565 | 0.1020329| 0.0178593| 0.0000000| | 38|chr6 | 32120203|cg04749507 | 0.1198729| 0.0210175| 0.0000000| | 38|chr6 | 32120324|cg19048176 | 0.1256765| 0.0152671| 0.0000000| | 38|chr6 | 32120584|cg06814287 | 0.1260252| 0.0212687| 0.0000000| | 38|chr6 | 32120623|cg18235088 | 0.1353823| 0.0194376| 0.0000000| | 38|chr6 | 32120625|cg08045906 | 0.1523929| 0.0174620| 0.0000000| | 38|chr6 | 32120773|cg12883279 | 0.1521650| 0.0182417| 0.0000000| | 38|chr6 | 32120783|cg12626589 | 0.1453301| 0.0180123| 0.0000000| | 38|chr6 | 32120826|cg25426302 | 0.1421975| 0.0178451| 0.0000000| | 38|chr6 | 32120863|cg06025456 | 0.1338643| 0.0165478| 0.0000000| | 38|chr6 | 32120878|cg13934406 | 0.1395729| 0.0138750| 0.0000000| | 38|chr6 | 32120895|cg17113856 | 0.1269924| 0.0174787| 0.0000000| | 38|chr6 | 32120899|cg06108383 | 0.1275164| 0.0150833| 0.0000000| | 38|chr6 | 32120901|cg02956248 | 0.1351876| 0.0166930| 0.0000000| | 38|chr6 | 32120907|cg23359665 | 0.1316898| 0.0176902| 0.0000000| | 38|chr6 | 32120933|cg10551329 | 0.1316254| 0.0155450| 0.0000000| | 38|chr6 | 32120955|cg16481280 | 0.1206437| 0.0145211| 0.0000000| | 38|chr6 | 32121055|cg01111041 | 0.1320252| 0.0150413| 0.0000000| | 38|chr6 | 32121113|cg20328456 | 0.1215476| 0.0141210| 0.0000000| | 39|chr6 | 32121143|cg03570994 | 0.1095963| 0.0112578| 0.0000000| | 39|chr6 | 32121156|cg11386011 | 0.1113099| 0.0121279| 0.0000000| | 39|chr6 | 32121204|cg12738718 | 0.1161463| 0.0188377| 0.0000000| | 39|chr6 | 32121225|cg14130039 | 0.1262075| 0.0179329| 0.0000000| | 39|chr6 | 32121249|cg05133205 | 0.1261820| 0.0165417| 0.0000000| | 39|chr6 | 32121259|cg17329164 | 0.1225339| 0.0163152| 0.0000000| | 39|chr6 | 32121261|cg18049167 | 0.1125958| 0.0185609| 0.0000000| | 39|chr6 | 32121355|cg04105091 | 0.1160281| 0.0188530| 0.0000000| | 39|chr6 | 32121368|cg12585943 | 0.1145624| 0.0151163| 0.0000000| | 39|chr6 | 32121393|cg13102294 | 0.1197061| 0.0157364| 0.0000000| | 39|chr6 | 32121420|cg00552704 | 0.1117626| 0.0194779| 0.0000000| | 39|chr6 | 32121433|cg06264679 | 0.1134183| 0.0173969| 0.0000000| | 39|chr6 | 32121471|cg00933538 | 0.0603220| 0.0228462| 0.0082819| | 39|chr6 | 32121475|cg23470939 | 0.0752624| 0.0282451| 0.0077076| | 40|chr6 | 32122736|cg21241317 | -0.0940792| 0.0272468| 0.0005547| | 40|chr6 | 32122738|cg04877280 | -0.0913755| 0.0275097| 0.0008951| | 40|chr6 | 32122753|cg06832687 | -0.1184888| 0.0195084| 0.0000000| | 40|chr6 | 32122779|cg27070869 | -0.0633859| 0.0275227| 0.0212767| | 40|chr6 | 32122864|cg03995156 | -0.1012236| 0.0166360| 0.0000000| | 41|chr6 | 32135241|cg16681436 | 0.0380111| 0.0129310| 0.0032871| | 41|chr6 | 32135285|cg12508392 | 0.0139004| 0.0204100| 0.4958368| | 41|chr6 | 32135321|cg00359087 | 0.0078081| 0.0196024| 0.6903941| | 41|chr6 | 32135326|cg26687830 | 0.0019283| 0.0262969| 0.9415444| | 41|chr6 | 32135370|cg10262770 | 0.0209381| 0.0190779| 0.2724211| | 41|chr6 | 32135379|cg07754347 | -0.0052812| 0.0200649| 0.7923923| | 41|chr6 | 32135384|cg16006963 | 0.0104801| 0.0214948| 0.6258590| | 41|chr6 | 32135396|cg06024540 | 0.0017704| 0.0278038| 0.9492295| | 41|chr6 | 32135715|cg12305588 | 0.0487057| 0.0073939| 0.0000000| | 41|chr6 | 32135718|cg08759957 | 0.0567178| 0.0077728| 0.0000000| | 41|chr6 | 32135728|cg12827283 | 0.0674969| 0.0115235| 0.0000000| | 41|chr6 | 32135776|cg11356887 | 0.0455947| 0.0100301| 0.0000055| | 41|chr6 | 32135803|cg26785234 | 0.0590164| 0.0091618| 0.0000000| | 42|chr6 | 32150404|cg08321684 | 0.0317791| 0.0084644| 0.0001737| | 42|chr6 | 32150577|cg23177883 | 0.0082737| 0.0115063| 0.4721083| | 42|chr6 | 32150585|cg11105830 | 0.0124544| 0.0103557| 0.2291065| | 42|chr6 | 32150656|cg26505596 | 0.0243330| 0.0324130| 0.4528236| | 42|chr6 | 32150716|cg26653489 | -0.0166842| 0.0177231| 0.3465108| | 43|chr6 | 32154416|cg18057469 | -0.0650918| 0.0205330| 0.0015238| | 43|chr6 | 32154447|cg14635654 | -0.1158400| 0.0209838| 0.0000000| | 43|chr6 | 32154454|cg18809947 | -0.0651060| 0.0261868| 0.0129111| | 43|chr6 | 32154568|cg03422527 | -0.0994093| 0.0213716| 0.0000033| | 43|chr6 | 32154613|cg01940915 | -0.0724621| 0.0223119| 0.0011634| | 43|chr6 | 32154715|cg20765522 | -0.1057901| 0.0139633| 0.0000000| | 44|chr6 | 32158927|cg17851795 | -0.0634730| 0.0262394| 0.0155636| | 44|chr6 | 32158953|cg03280235 | -0.0645184| 0.0223107| 0.0038302| | 44|chr6 | 32159036|cg16609995 | -0.0991986| 0.0183662| 0.0000001| | 44|chr6 | 32159527|cg21386484 | -0.1405397| 0.0184502| 0.0000000| | 44|chr6 | 32159604|cg19555708 | -0.1147191| 0.0228179| 0.0000005| | 44|chr6 | 32159607|cg06194738 | -0.1290303| 0.0224632| 0.0000000| | 44|chr6 | 32159933|cg19321684 | -0.1487378| 0.0157545| 0.0000000| | 44|chr6 | 32160074|cg00442389 | -0.1422843| 0.0151954| 0.0000000| | 45|chr6 | 32171796|cg14996490 | 0.0336560| 0.0134619| 0.0124162| | 45|chr6 | 32171823|cg05380127 | 0.0257353| 0.0088432| 0.0036123| | 45|chr6 | 32172007|cg13336485 | 0.0045858| 0.0122188| 0.7074334| | 45|chr6 | 32172013|cg27597473 | -0.0067288| 0.0176515| 0.7030529| | 45|chr6 | 32172027|cg16642360 | -0.0018143| 0.0158587| 0.9089182| | 45|chr6 | 32172124|cg22022067 | 0.0401365| 0.0099830| 0.0000581| | 46|chr6 | 32805398|cg12854186 | -0.1513757| 0.0150578| 0.0000000| | 46|chr6 | 32805548|cg03438552 | -0.1426522| 0.0177625| 0.0000000| | 46|chr6 | 32805554|cg22940798 | -0.1581847| 0.0164751| 0.0000000| | 46|chr6 | 32805570|cg08998192 | -0.1475779| 0.0188510| 0.0000000| | 46|chr6 | 32805684|cg13563634 | -0.1146810| 0.0221911| 0.0000002| | 47|chr6 | 32812933|cg05697726 | -0.1267054| 0.0124278| 0.0000000| | 47|chr6 | 32812953|cg16483840 | -0.1160184| 0.0193411| 0.0000000| | 47|chr6 | 32812965|cg02657012 | -0.1461522| 0.0140874| 0.0000000| | 47|chr6 | 32813084|cg16890093 | -0.1692340| 0.0112045| 0.0000000| | 47|chr6 | 32813154|cg11706729 | -0.0774957| 0.0156555| 0.0000007| | 47|chr6 | 32813211|cg07218288 | -0.0535592| 0.0329116| 0.1036598| | 47|chr6 | 32813337|cg19136673 | -0.1617629| 0.0137228| 0.0000000| | 47|chr6 | 32813441|cg05693489 | 0.0110656| 0.0259386| 0.6696656| | 47|chr6 | 32813448|cg12253437 | -0.0440842| 0.0214105| 0.0394945| | 48|chr6 | 32820355|cg08818207 | -0.1206501| 0.0223959| 0.0000001| | 48|chr6 | 32820410|cg04773990 | -0.1622381| 0.0159072| 0.0000000| | 48|chr6 | 32820421|cg24154161 | -0.1310339| 0.0231500| 0.0000000| | 48|chr6 | 32820546|cg23880953 | -0.1491729| 0.0203307| 0.0000000| | 48|chr6 | 32820553|cg26700949 | -0.1247669| 0.0267352| 0.0000031| | 48|chr6 | 32820577|cg15926590 | -0.1422087| 0.0182045| 0.0000000| | 49|chr6 | 32825701|cg02878284 | 0.0431232| 0.0083064| 0.0000002| | 49|chr6 | 32825852|cg19994157 | 0.0095956| 0.0095798| 0.3165110| | 49|chr6 | 32825897|cg00045690 | 0.0322623| 0.0123032| 0.0087349| | 49|chr6 | 32826171|cg04913118 | 0.0424573| 0.0083450| 0.0000004| | 49|chr6 | 32826197|cg06043617 | 0.0262839| 0.0109621| 0.0164979| | 50|chr6 | 32908567|cg10310595 | -0.1324225| 0.0227564| 0.0000000| | 50|chr6 | 32908605|cg16236263 | -0.1433555| 0.0215182| 0.0000000| | 50|chr6 | 32908642|cg00575744 | -0.1351980| 0.0219912| 0.0000000| | 50|chr6 | 32908718|cg12840248 | -0.1329792| 0.0227719| 0.0000000| | 50|chr6 | 32908794|cg25247351 | -0.1312033| 0.0237725| 0.0000000| | 50|chr6 | 32908901|cg10714284 | -0.1429521| 0.0224331| 0.0000000| | 50|chr6 | 32908980|cg16300030 | -0.1676273| 0.0150704| 0.0000000| | 50|chr6 | 32909003|cg20392842 | -0.1598784| 0.0169428| 0.0000000| | 50|chr6 | 32909282|cg20600379 | -0.1404678| 0.0202167| 0.0000000| | 50|chr6 | 32909397|cg00862588 | -0.1205997| 0.0173209| 0.0000000| | 50|chr6 | 32909440|cg10518264 | -0.1094457| 0.0163014| 0.0000000| | 50|chr6 | 32909493|cg21470947 | -0.1094288| 0.0137516| 0.0000000| | 50|chr6 | 32909523|cg07623567 | -0.1350158| 0.0190329| 0.0000000| | 51|chr6 | 32942063|cg11439393 | -0.1165383| 0.0234906| 0.0000007| | 51|chr6 | 32942205|cg18918417 | -0.1316404| 0.0227900| 0.0000000| | 51|chr6 | 32942358|cg16416715 | -0.1340703| 0.0224418| 0.0000000| | 51|chr6 | 32942400|cg26264318 | -0.1063840| 0.0258753| 0.0000393| | 51|chr6 | 32942429|cg25158622 | -0.1444292| 0.0186863| 0.0000000| | 51|chr6 | 32942494|cg26953232 | -0.1526354| 0.0190591| 0.0000000| | 51|chr6 | 32942541|cg24275356 | -0.1114375| 0.0251043| 0.0000090| | 51|chr6 | 32942710|cg27395200 | -0.1336472| 0.0157469| 0.0000000| | 51|chr6 | 32942714|cg07275218 | -0.1278996| 0.0183328| 0.0000000| | 51|chr6 | 32942808|cg17451586 | -0.1454581| 0.0210295| 0.0000000| | 51|chr6 | 32943025|cg02471378 | -0.1317711| 0.0201084| 0.0000000| | 52|chr6 | 33043841|cg02286081 | -0.1337190| 0.0230865| 0.0000000| | 52|chr6 | 33043849|cg22483030 | -0.1296716| 0.0229438| 0.0000000| | 52|chr6 | 33043868|cg26350754 | -0.1189423| 0.0252242| 0.0000024| | 52|chr6 | 33043976|cg12365667 | -0.0930881| 0.0274477| 0.0006952| | 52|chr6 | 33044012|cg12939283 | -0.1348687| 0.0220010| 0.0000000| | 52|chr6 | 33044345|cg14356799 | -0.1094301| 0.0256268| 0.0000195| | 52|chr6 | 33044510|cg00750366 | -0.0952827| 0.0279658| 0.0006565| | 53|chr6 | 33132163|cg04820679 | 0.0800563| 0.0160236| 0.0000006| | 53|chr6 | 33132181|cg07570257 | 0.0624801| 0.0221740| 0.0048367| | 53|chr6 | 33132192|cg14147420 | 0.0474335| 0.0179623| 0.0082726| | 53|chr6 | 33132241|cg12945707 | 0.0890059| 0.0151261| 0.0000000| | 53|chr6 | 33132318|cg10537192 | 0.0416781| 0.0206160| 0.0432140| | 54|chr6 | 33132650|cg13478289 | 0.0623967| 0.0190634| 0.0010637| | 54|chr6 | 33132693|cg19887293 | 0.0368220| 0.0175806| 0.0362184| | 54|chr6 | 33132705|cg01828813 | 0.0621322| 0.0226616| 0.0061115| | 54|chr6 | 33132727|cg17578548 | 0.0095940| 0.0253775| 0.7053936| | 54|chr6 | 33132943|cg20506659 | 0.0302774| 0.0192878| 0.1164694| | 54|chr6 | 33132996|cg15047502 | 0.0203154| 0.0133922| 0.1292778| | 54|chr6 | 33133039|cg26144659 | 0.0151949| 0.0100293| 0.1297575| | 54|chr6 | 33133083|cg17790159 | 0.0308606| 0.0080224| 0.0001197| | 54|chr6 | 33133329|cg24483785 | 0.0186437| 0.0114476| 0.1033937| | 54|chr6 | 33133370|cg23332813 | 0.0141153| 0.0146426| 0.3350509| | 54|chr6 | 33133485|cg06049932 | 0.0595455| 0.0171565| 0.0005190| | 54|chr6 | 33133517|cg02667414 | 0.0254879| 0.0180811| 0.1586442| | 54|chr6 | 33133531|cg00324223 | 0.0250070| 0.0161946| 0.1225495| | 54|chr6 | 33133535|cg24213189 | 0.0049175| 0.0214155| 0.8183834| | 54|chr6 | 33133538|cg22370716 | 0.0126669| 0.0180955| 0.4839249| | 54|chr6 | 33133675|cg01701055 | 0.0448536| 0.0101642| 0.0000102| | 54|chr6 | 33133752|cg15081128 | 0.0278885| 0.0105656| 0.0083013| | 54|chr6 | 33134045|cg06924878 | 0.0309625| 0.0157284| 0.0490022| | 54|chr6 | 33134078|cg23945333 | 0.0349533| 0.0139671| 0.0123307| | 55|chr6 | 33245488|cg06753439 | -0.1322913| 0.0199100| 0.0000000| | 55|chr6 | 33245490|cg03108070 | -0.1468223| 0.0187034| 0.0000000| | 55|chr6 | 33245516|cg19241689 | -0.1433868| 0.0209017| 0.0000000| | 55|chr6 | 33245537|cg16396284 | -0.1578083| 0.0176820| 0.0000000| | 55|chr6 | 33245541|cg17416730 | -0.1662809| 0.0145976| 0.0000000| | 55|chr6 | 33245553|cg26270195 | -0.1255039| 0.0246871| 0.0000004| | 56|chr6 | 33245706|cg03721978 | -0.0999077| 0.0175918| 0.0000000| | 56|chr6 | 33245717|cg09349343 | -0.1014203| 0.0205029| 0.0000008| | 56|chr6 | 33245721|cg17103217 | -0.1046379| 0.0202272| 0.0000002| | 56|chr6 | 33245739|cg23950233 | -0.0855352| 0.0231036| 0.0002137| | 56|chr6 | 33245770|cg21618521 | -0.0915700| 0.0176115| 0.0000002| | 56|chr6 | 33245779|cg19882268 | -0.0246106| 0.0283363| 0.3851114| | 56|chr6 | 33245804|cg00052772 | -0.1124515| 0.0163070| 0.0000000| | 57|chr6 | 33245893|cg06362282 | -0.1471256| 0.0167391| 0.0000000| | 57|chr6 | 33245895|cg24605046 | -0.1352626| 0.0197275| 0.0000000| | 57|chr6 | 33245990|cg26055446 | -0.1388379| 0.0213931| 0.0000000| | 57|chr6 | 33246008|cg03169472 | -0.1472251| 0.0203723| 0.0000000| | 57|chr6 | 33246043|cg16090881 | -0.1000398| 0.0189134| 0.0000001| | 57|chr6 | 33246091|cg16226644 | -0.1307261| 0.0200605| 0.0000000| | 57|chr6 | 33246094|cg13882090 | -0.1377345| 0.0168440| 0.0000000| | 58|chr6 | 41010111|cg25533211 | 0.0474561| 0.0066796| 0.0000000| | 58|chr6 | 41010217|cg20377447 | 0.0401030| 0.0070032| 0.0000000| | 58|chr6 | 41010223|cg13983640 | 0.0524027| 0.0123288| 0.0000213| | 58|chr6 | 41010316|cg22801217 | 0.0390960| 0.0059316| 0.0000000| | 58|chr6 | 41010375|cg22815409 | 0.0316286| 0.0080956| 0.0000935| | 58|chr6 | 41010654|cg04904815 | 0.0536667| 0.0193641| 0.0055808| | 59|chr6 | 53530503|cg00536792 | 0.0575961| 0.0249095| 0.0207659| | 59|chr6 | 53530538|cg15658676 | 0.0764135| 0.0187394| 0.0000455| | 59|chr6 | 53530570|cg19801120 | 0.0816580| 0.0191154| 0.0000194| | 59|chr6 | 53530600|cg06485521 | 0.0743545| 0.0231992| 0.0013504| | 59|chr6 | 53530624|cg26980034 | 0.0661843| 0.0233828| 0.0046481| | 59|chr6 | 53530628|cg13840445 | 0.0994877| 0.0172199| 0.0000000| | 60|chr6 | 149805995|cg15132169 | -0.1421403| 0.0180800| 0.0000000| | 60|chr6 | 149806077|cg18951352 | -0.1573447| 0.0143688| 0.0000000| | 60|chr6 | 149806081|cg09678939 | -0.1582970| 0.0141131| 0.0000000| | 60|chr6 | 149806131|cg13136655 | -0.1593556| 0.0127474| 0.0000000| | 60|chr6 | 149806235|cg02464487 | -0.1654364| 0.0146566| 0.0000000| | 60|chr6 | 149806273|cg04275695 | -0.1607989| 0.0149558| 0.0000000| | 60|chr6 | 149806331|cg17501395 | -0.1619124| 0.0139751| 0.0000000| | 60|chr6 | 149806339|cg18082788 | -0.1565043| 0.0142206| 0.0000000| | 60|chr6 | 149806502|cg00073460 | -0.0965617| 0.0247094| 0.0000931| | 60|chr6 | 149806635|cg06762457 | -0.0436767| 0.0158661| 0.0059081| | 60|chr6 | 149806732|cg14030904 | -0.0843969| 0.0139906| 0.0000000| | 61|chr6 | 152702330|cg00041666 | 0.0477057| 0.0136213| 0.0004613| | 61|chr6 | 152702365|cg07604117 | 0.0420085| 0.0163071| 0.0099925| | 61|chr6 | 152702387|cg19827346 | 0.0435096| 0.0198885| 0.0286934| | 61|chr6 | 152702444|cg20187047 | 0.0427556| 0.0134452| 0.0014728| | 61|chr6 | 152702463|cg13806292 | 0.0875492| 0.0082688| 0.0000000| | 62|chr6 | 170580947|cg24039042 | -0.0921876| 0.0250976| 0.0002396| | 62|chr6 | 170580966|cg01766850 | -0.0748875| 0.0274486| 0.0063665| | 62|chr6 | 170581039|cg05973084 | -0.0874901| 0.0273323| 0.0013696| | 62|chr6 | 170581085|cg09344348 | -0.0212537| 0.0316357| 0.5016956| | 62|chr6 | 170581248|cg18555277 | -0.0576516| 0.0198330| 0.0036508| | 62|chr6 | 170581355|cg01209642 | -0.0589026| 0.0255071| 0.0209289| | 62|chr6 | 170581502|cg21138542 | -0.1174579| 0.0191805| 0.0000000| | 62|chr6 | 170581690|cg03899510 | -0.0532274| 0.0254434| 0.0364393|
best6 <- dmrs6[which.min(dmrs6$p.value),]
dmrff.plot(
best6$chr, best6$start, best6$end,
meta$ewas$estimate, meta$ewas$se, meta$ewas$chr, meta$ewas$pos)
## Loading required package: ggplot2
We can use the same function to show the summary statistics for these sites from one of the original studies.
acc <- "GSE79056"
sites <- dmrff.sites(dmrs6, stats[[acc]]$chr, stats[[acc]]$pos)
sites <- cbind(sites[,c("region","chr","pos")],
stats[[acc]][sites$site,c("estimate","se","p.value")])
kable(sites,row.names=F)
| region|chr | pos| estimate| se| p.value| |------:|:----|---------:|----------:|---------:|---------:| | 1|chr6 | 1635611| 0.0053363| 0.0006958| 0.0000000| | 1|chr6 | 1635640| 0.0063335| 0.0008181| 0.0000000| | 1|chr6 | 1635808| 0.0073781| 0.0007358| 0.0000000| | 1|chr6 | 1635818| 0.0064351| 0.0008352| 0.0000000| | 1|chr6 | 1635847| 0.0083883| 0.0007770| 0.0000000| | 2|chr6 | 15504844| -0.0113105| 0.0009718| 0.0000000| | 2|chr6 | 15504872| -0.0100702| 0.0009470| 0.0000000| | 2|chr6 | 15504923| -0.0109958| 0.0009858| 0.0000000| | 2|chr6 | 15505094| -0.0184816| 0.0016960| 0.0000000| | 2|chr6 | 15505345| -0.0023223| 0.0005873| 0.0003840| | 2|chr6 | 15505452| -0.0017037| 0.0004356| 0.0004337| | 2|chr6 | 15505460| -0.0038243| 0.0006648| 0.0000020| | 2|chr6 | 15505949| -0.0049969| 0.0009589| 0.0000099| | 2|chr6 | 15506085| -0.0111326| 0.0014722| 0.0000000| | 3|chr6 | 25652383| 0.0029570| 0.0004757| 0.0000005| | 3|chr6 | 25652390| 0.0020246| 0.0005783| 0.0013540| | 3|chr6 | 25652395| 0.0011633| 0.0005708| 0.0496633| | 3|chr6 | 25652405| 0.0014082| 0.0005784| 0.0204916| | 3|chr6 | 25652407| 0.0005231| 0.0004102| 0.2111513| | 3|chr6 | 25652531| 0.0008247| 0.0003650| 0.0305841| | 3|chr6 | 25652602| 0.0010391| 0.0003115| 0.0021187| | 4|chr6 | 28543262| 0.0007349| 0.0006114| 0.2379327| | 4|chr6 | 28543508| 0.0010910| 0.0006956| 0.1266460| | 4|chr6 | 28543514| 0.0021095| 0.0005610| 0.0006616| | 4|chr6 | 28543667| 0.0083357| 0.0014310| 0.0000016| | 4|chr6 | 28543670| 0.0083497| 0.0013315| 0.0000004| | 5|chr6 | 29520752| 0.0051044| 0.0016067| 0.0032272| | 5|chr6 | 29520774| 0.0120810| 0.0019128| 0.0000004| | 5|chr6 | 29520965| 0.0038275| 0.0009041| 0.0001729| | 5|chr6 | 29521013| 0.0045393| 0.0008581| 0.0000086| | 5|chr6 | 29521023| 0.0039910| 0.0009063| 0.0001060| | 5|chr6 | 29521046| 0.0030241| 0.0011091| 0.0104404| | 6|chr6 | 29571363| 0.0027398| 0.0004724| 0.0000017| | 6|chr6 | 29571419| 0.0006992| 0.0006111| 0.2607553| | 6|chr6 | 29571429| -0.0001876| 0.0005052| 0.7127723| | 6|chr6 | 29571432| 0.0008405| 0.0006006| 0.1710513| | 6|chr6 | 29571438| 0.0001579| 0.0005151| 0.7611272| | 6|chr6 | 29571468| 0.0005212| 0.0003924| 0.1932056| | 6|chr6 | 29571483| -0.0008368| 0.0007880| 0.2960132| | 6|chr6 | 29571693| 0.0000680| 0.0004994| 0.8925189| | 7|chr6 | 29576987| 0.0021864| 0.0004052| 0.0000058| | 7|chr6 | 29577006| -0.0000740| 0.0004983| 0.8828218| | 7|chr6 | 29577082| 0.0009482| 0.0004277| 0.0336305| | 7|chr6 | 29577223| 0.0015588| 0.0007135| 0.0361197| | 7|chr6 | 29577348| 0.0019153| 0.0007907| 0.0210915| | 8|chr6 | 29577916| 0.0011126| 0.0007108| 0.1270934| | 8|chr6 | 29578124| -0.0001449| 0.0009887| 0.8844037| | 8|chr6 | 29578144| 0.0015863| 0.0007730| 0.0481615| | 8|chr6 | 29578313| 0.0025291| 0.0007500| 0.0019188| | 8|chr6 | 29578423| 0.0019701| 0.0004786| 0.0002421| | 9|chr6 | 29589573| -0.0001670| 0.0005581| 0.7666850| | 9|chr6 | 29589631| 0.0001497| 0.0005547| 0.7888916| | 9|chr6 | 29589707| 0.0012088| 0.0003386| 0.0011217| | 9|chr6 | 29589714| 0.0003982| 0.0004516| 0.3842728| | 9|chr6 | 29589729| 0.0004549| 0.0007802| 0.5638605| | 10|chr6 | 29599012| 0.0046057| 0.0006266| 0.0000000| | 10|chr6 | 29599160| 0.0090858| 0.0010374| 0.0000000| | 10|chr6 | 29599178| 0.0090018| 0.0012280| 0.0000000| | 10|chr6 | 29599226| 0.0108933| 0.0011754| 0.0000000| | 10|chr6 | 29599250| 0.0109745| 0.0013997| 0.0000000| | 10|chr6 | 29599259| 0.0102835| 0.0011497| 0.0000000| | 10|chr6 | 29599319| 0.0140782| 0.0016932| 0.0000000| | 10|chr6 | 29599331| 0.0099653| 0.0013887| 0.0000000| | 10|chr6 | 29599390| 0.0113110| 0.0014083| 0.0000000| | 10|chr6 | 29599836| 0.0016739| 0.0007429| 0.0310341| | 11|chr6 | 29911295| -0.0046014| 0.0013833| 0.0021706| | 11|chr6 | 29911334| -0.0055718| 0.0010543| 0.0000080| | 11|chr6 | 29911339| -0.0038322| 0.0010044| 0.0005674| | 11|chr6 | 29911366| -0.0087870| 0.0010933| 0.0000000| | 11|chr6 | 29911494| -0.0028189| 0.0016230| 0.0917497| | 11|chr6 | 29911542| -0.0082911| 0.0015855| 0.0000094| | 11|chr6 | 29911550| -0.0055508| 0.0010538| 0.0000084| | 12|chr6 | 30127760| 0.0034895| 0.0009843| 0.0012340| | 12|chr6 | 30127997| 0.0029891| 0.0006232| 0.0000337| | 12|chr6 | 30128219| 0.0018831| 0.0006779| 0.0089632| | 12|chr6 | 30128238| 0.0021771| 0.0007528| 0.0067290| | 12|chr6 | 30128254| 0.0012274| 0.0006494| 0.0675670| | 12|chr6 | 30128385| 0.0014351| 0.0005207| 0.0094515| | 12|chr6 | 30128404| 0.0028702| 0.0006394| 0.0000827| | 12|chr6 | 30128427| 0.0014605| 0.0007050| 0.0461996| | 12|chr6 | 30128511| 0.0020327| 0.0007291| 0.0087386| | 12|chr6 | 30128526| 0.0009337| 0.0005204| 0.0819474| | 12|chr6 | 30128542| 0.0003235| 0.0006045| 0.5961825| | 12|chr6 | 30128548| 0.0012666| 0.0004980| 0.0158615| | 12|chr6 | 30128558| 0.0020794| 0.0005404| 0.0005179| | 12|chr6 | 30128686| 0.0033997| 0.0011544| 0.0058861| | 12|chr6 | 30128775| 0.0037394| 0.0007283| 0.0000125| | 13|chr6 | 30458158| -0.0010364| 0.0002062| 0.0000171| | 13|chr6 | 30458161| -0.0052931| 0.0009179| 0.0000019| | 13|chr6 | 30458237| -0.0063287| 0.0009044| 0.0000001| | 13|chr6 | 30458519| -0.0087248| 0.0009109| 0.0000000| | 13|chr6 | 30458586| -0.0078358| 0.0006527| 0.0000000| | 13|chr6 | 30458601| -0.0108134| 0.0010658| 0.0000000| | 13|chr6 | 30458730| -0.0055093| 0.0007080| 0.0000000| | 13|chr6 | 30458998| -0.0034406| 0.0013169| 0.0134299| | 13|chr6 | 30459139| -0.0067699| 0.0009491| 0.0000000| | 13|chr6 | 30459255| -0.0034567| 0.0007771| 0.0000930| | 13|chr6 | 30459295| -0.0048622| 0.0009776| 0.0000200| | 13|chr6 | 30459317| -0.0022834| 0.0008987| 0.0159493| | 14|chr6 | 30459540| -0.0055945| 0.0018240| 0.0044619| | 14|chr6 | 30459595| -0.0065842| 0.0012847| 0.0000128| | 14|chr6 | 30459867| -0.0053297| 0.0012047| 0.0000998| | 14|chr6 | 30460244| -0.0031765| 0.0007381| 0.0001414| | 14|chr6 | 30460322| -0.0034656| 0.0008761| 0.0003823| | 14|chr6 | 30460484| -0.0007314| 0.0023526| 0.7578311| | 14|chr6 | 30460548| -0.0056734| 0.0012089| 0.0000456| | 14|chr6 | 30460576| -0.0071095| 0.0009408| 0.0000000| | 14|chr6 | 30460600| -0.0052924| 0.0011727| 0.0000771| | 15|chr6 | 30581820| -0.0072376| 0.0006511| 0.0000000| | 15|chr6 | 30582174| -0.0046628| 0.0007254| 0.0000003| | 15|chr6 | 30582241| -0.0087080| 0.0012550| 0.0000001| | 15|chr6 | 30582333| -0.0079857| 0.0012664| 0.0000004| | 15|chr6 | 30582352| -0.0046817| 0.0007966| 0.0000014| | 15|chr6 | 30582416| -0.0050133| 0.0005547| 0.0000000| | 16|chr6 | 30652771| -0.0036735| 0.0006103| 0.0000009| | 16|chr6 | 30652829| -0.0082523| 0.0010218| 0.0000000| | 16|chr6 | 30652907| -0.0067420| 0.0008282| 0.0000000| | 16|chr6 | 30653167| -0.0091442| 0.0012343| 0.0000000| | 16|chr6 | 30653191| -0.0039108| 0.0010121| 0.0004953| | 16|chr6 | 30653242| -0.0026327| 0.0004126| 0.0000003| | 16|chr6 | 30653407| -0.0062780| 0.0011103| 0.0000027| | 16|chr6 | 30653512| -0.0050652| 0.0008696| 0.0000016| | 16|chr6 | 30653530| -0.0059723| 0.0010842| 0.0000041| | 17|chr6 | 30850543| 0.0080152| 0.0013483| 0.0000011| | 17|chr6 | 30850581| -0.0031452| 0.0053412| 0.5599735| | 17|chr6 | 30850718| 0.0023579| 0.0007733| 0.0045015| | 17|chr6 | 30850829| 0.0048777| 0.0009207| 0.0000077| | 17|chr6 | 30850868| 0.0070721| 0.0014112| 0.0000179| | 17|chr6 | 30850876| 0.0027450| 0.0007419| 0.0007826| | 17|chr6 | 30850913| 0.0015332| 0.0008513| 0.0808466| | 17|chr6 | 30850977| 0.0081431| 0.0014615| 0.0000034| | 18|chr6 | 30854161| 0.0071258| 0.0017536| 0.0002815| | 18|chr6 | 30854164| 0.0051399| 0.0009032| 0.0000024| | 18|chr6 | 30854186| 0.0059085| 0.0016669| 0.0012016| | 18|chr6 | 30854233| 0.0049327| 0.0014393| 0.0016544| | 18|chr6 | 30854551| 0.0074110| 0.0011912| 0.0000005| | 19|chr6 | 30955992| 0.0013819| 0.0005706| 0.0211023| | 19|chr6 | 30956214| 0.0017557| 0.0011167| 0.1254763| | 19|chr6 | 30956221| 0.0009545| 0.0006868| 0.1739330| | 19|chr6 | 30956397| 0.0046973| 0.0007931| 0.0000012| | 19|chr6 | 30956440| 0.0046062| 0.0010511| 0.0001128| | 20|chr6 | 31079110| 0.0021681| 0.0004168| 0.0000102| | 20|chr6 | 31079152| 0.0034412| 0.0004245| 0.0000000| | 20|chr6 | 31079306| 0.0006828| 0.0005854| 0.2518531| | 20|chr6 | 31079555| 0.0009611| 0.0005674| 0.0997232| | 20|chr6 | 31079617| 0.0012210| 0.0005581| 0.0358930| | 21|chr6 | 31127159| -0.0031986| 0.0008677| 0.0008135| | 21|chr6 | 31127173| -0.0028072| 0.0007980| 0.0012939| | 21|chr6 | 31127178| -0.0027491| 0.0009275| 0.0056065| | 21|chr6 | 31127271| -0.0029349| 0.0007459| 0.0004054| | 21|chr6 | 31127357| -0.0023601| 0.0008021| 0.0059212| | 21|chr6 | 31127379| -0.0028426| 0.0008402| 0.0018635| | 21|chr6 | 31127527| -0.0015685| 0.0004125| 0.0005893| | 21|chr6 | 31127863| -0.0021863| 0.0004672| 0.0000475| | 22|chr6 | 31549480| -0.0015810| 0.0003835| 0.0002382| | 22|chr6 | 31549563| -0.0043659| 0.0006342| 0.0000001| | 22|chr6 | 31549625| -0.0021442| 0.0009244| 0.0267130| | 22|chr6 | 31549631| -0.0058549| 0.0005927| 0.0000000| | 22|chr6 | 31549853| -0.0058183| 0.0006280| 0.0000000| | 22|chr6 | 31549929| -0.0047272| 0.0006038| 0.0000000| | 22|chr6 | 31550090| -0.0049884| 0.0009083| 0.0000048| | 23|chr6 | 31646236| 0.0043452| 0.0007266| 0.0000010| | 23|chr6 | 31646262| 0.0025956| 0.0005409| 0.0000335| | 23|chr6 | 31646366| 0.0000296| 0.0004468| 0.9475834| | 23|chr6 | 31646377| 0.0004806| 0.0004894| 0.3332814| | 23|chr6 | 31646625| 0.0025643| 0.0007651| 0.0020295| | 24|chr6 | 31744391| -0.0050457| 0.0006990| 0.0000000| | 24|chr6 | 31744398| -0.0018473| 0.0005261| 0.0013156| | 24|chr6 | 31744524| -0.0030812| 0.0008451| 0.0009093| | 24|chr6 | 31744545| -0.0046108| 0.0008439| 0.0000047| | 24|chr6 | 31744612| -0.0044627| 0.0009478| 0.0000436| | 24|chr6 | 31744628| -0.0034480| 0.0010534| 0.0025021| | 24|chr6 | 31744636| -0.0053844| 0.0011241| 0.0000343| | 24|chr6 | 31744735| -0.0065323| 0.0010509| 0.0000005| | 24|chr6 | 31744816| -0.0033457| 0.0009076| 0.0008133| | 24|chr6 | 31744831| -0.0031882| 0.0007461| 0.0001543| | 25|chr6 | 31846797| 0.0027906| 0.0006335| 0.0001055| | 25|chr6 | 31846813| 0.0011288| 0.0008538| 0.1955051| | 25|chr6 | 31846899| 0.0038241| 0.0008466| 0.0000762| | 25|chr6 | 31846924| 0.0040218| 0.0009684| 0.0002181| | 25|chr6 | 31846956| 0.0045979| 0.0017440| 0.0126826| | 25|chr6 | 31846970| 0.0018120| 0.0007503| 0.0214568| | 26|chr6 | 31867945| -0.0021363| 0.0005188| 0.0002410| | 26|chr6 | 31867956| -0.0092438| 0.0011713| 0.0000000| | 26|chr6 | 31867995| -0.0076270| 0.0009856| 0.0000000| | 26|chr6 | 31868021| -0.0041524| 0.0006997| 0.0000012| | 26|chr6 | 31868025| -0.0077718| 0.0010175| 0.0000000| | 26|chr6 | 31868133| -0.0023261| 0.0010224| 0.0295304| | 26|chr6 | 31868144| -0.0007071| 0.0007210| 0.3338497| | 26|chr6 | 31868162| -0.0008090| 0.0004455| 0.0785049| | 26|chr6 | 31868169| -0.0012835| 0.0005928| 0.0377116| | 26|chr6 | 31868207| -0.0011950| 0.0004271| 0.0085196| | 26|chr6 | 31868368| -0.0008705| 0.0004044| 0.0387621| | 26|chr6 | 31868418| -0.0010511| 0.0004663| 0.0309463| | 26|chr6 | 31868452| -0.0009970| 0.0003899| 0.0153497| | 26|chr6 | 31868470| -0.0011890| 0.0004890| 0.0206447| | 27|chr6 | 31937758| -0.0024101| 0.0006967| 0.0015157| | 27|chr6 | 31937906| -0.0023675| 0.0005143| 0.0000593| | 27|chr6 | 31937968| -0.0007674| 0.0005002| 0.1345344| | 27|chr6 | 31937973| -0.0018000| 0.0005101| 0.0012542| | 27|chr6 | 31938090| -0.0009554| 0.0005194| 0.0748506| | 27|chr6 | 31938176| -0.0007199| 0.0004237| 0.0987293| | 27|chr6 | 31938187| -0.0003214| 0.0005346| 0.5517659| | 27|chr6 | 31938207| -0.0010164| 0.0005838| 0.0912894| | 27|chr6 | 31938358| -0.0003664| 0.0005078| 0.4756917| | 27|chr6 | 31938372| -0.0015409| 0.0005593| 0.0094789| | 27|chr6 | 31938527| -0.0015529| 0.0004554| 0.0017341| | 27|chr6 | 31938533| -0.0010392| 0.0006738| 0.1325230| | 28|chr6 | 31939059| -0.0027433| 0.0004824| 0.0000024| | 28|chr6 | 31939085| -0.0008313| 0.0008125| 0.3137230| | 28|chr6 | 31939106| -0.0020200| 0.0010173| 0.0554381| | 28|chr6 | 31939112| -0.0039003| 0.0010390| 0.0006968| | 28|chr6 | 31939181| -0.0031801| 0.0010732| 0.0056176| | 28|chr6 | 31939224| -0.0030100| 0.0010536| 0.0073586| | 28|chr6 | 31939280| -0.0044583| 0.0010547| 0.0001763| | 28|chr6 | 31939319| -0.0033072| 0.0011398| 0.0065710| | 29|chr6 | 32013699| 0.0059543| 0.0008817| 0.0000001| | 29|chr6 | 32013710| 0.0066619| 0.0008109| 0.0000000| | 29|chr6 | 32013845| 0.0018667| 0.0006313| 0.0057110| | 29|chr6 | 32013974| 0.0006072| 0.0004168| 0.1546392| | 29|chr6 | 32014003| 0.0003136| 0.0006145| 0.6131548| | 29|chr6 | 32014059| 0.0001794| 0.0006347| 0.7791855| | 29|chr6 | 32014096| 0.0002089| 0.0003722| 0.5784243| | 29|chr6 | 32014100| 0.0004546| 0.0004554| 0.3254209| | 29|chr6 | 32014148| 0.0013972| 0.0008293| 0.1014986| | 29|chr6 | 32014189| 0.0025051| 0.0006349| 0.0003933| | 29|chr6 | 32014300| 0.0005311| 0.0006692| 0.4330893| | 29|chr6 | 32014381| 0.0001677| 0.0006949| 0.8108247| | 29|chr6 | 32014476| 0.0011984| 0.0018292| 0.5169125| | 29|chr6 | 32014484| 0.0010834| 0.0011520| 0.3538185| | 29|chr6 | 32014510| 0.0014252| 0.0010947| 0.2019818| | 29|chr6 | 32014605| 0.0006342| 0.0005843| 0.2856641| | 29|chr6 | 32014663| 0.0018555| 0.0008157| 0.0295622| | 29|chr6 | 32014674| 0.0011431| 0.0008564| 0.1911191| | 29|chr6 | 32014739| 0.0029281| 0.0007009| 0.0002030| | 30|chr6 | 32020425| 0.0020827| 0.0005039| 0.0002306| | 30|chr6 | 32020477| 0.0015273| 0.0004015| 0.0005851| | 30|chr6 | 32020479| 0.0021571| 0.0004397| 0.0000244| | 30|chr6 | 32020489| 0.0015262| 0.0004735| 0.0028541| | 30|chr6 | 32020498| -0.0000017| 0.0005183| 0.9973686| | 30|chr6 | 32020572| 0.0009896| 0.0004088| 0.0211588| | 30|chr6 | 32020587| 0.0006498| 0.0004170| 0.1287077| | 30|chr6 | 32020750| 0.0024541| 0.0008160| 0.0050132| | 31|chr6 | 32022898| 0.0022802| 0.0005643| 0.0003002| | 31|chr6 | 32022929| 0.0022027| 0.0004470| 0.0000229| | 31|chr6 | 32023102| 0.0016554| 0.0006389| 0.0141459| | 31|chr6 | 32023142| 0.0008489| 0.0005198| 0.1119170| | 31|chr6 | 32023246| 0.0008791| 0.0005057| 0.0914957| | 31|chr6 | 32023249| 0.0012437| 0.0006695| 0.0721889| | 31|chr6 | 32023251| 0.0005900| 0.0004299| 0.1791401| | 31|chr6 | 32023283| 0.0017482| 0.0005553| 0.0034788| | 31|chr6 | 32023332| 0.0002324| 0.0007577| 0.7610253| | 31|chr6 | 32023383| 0.0003477| 0.0007625| 0.6513856| | 31|chr6 | 32023409| 0.0022897| 0.0007285| 0.0035287| | 31|chr6 | 32023527| 0.0014054| 0.0007570| 0.0723335| | 31|chr6 | 32023650| 0.0017740| 0.0003961| 0.0000851| | 32|chr6 | 32037018| 0.0026723| 0.0004962| 0.0000059| | 32|chr6 | 32037097| -0.0013256| 0.0025792| 0.6107074| | 32|chr6 | 32037148| 0.0010102| 0.0006431| 0.1257408| | 32|chr6 | 32037290| 0.0020436| 0.0005277| 0.0004836| | 32|chr6 | 32037339| 0.0012885| 0.0004185| 0.0041670| | 32|chr6 | 32037342| 0.0018824| 0.0004367| 0.0001458| | 32|chr6 | 32037421| 0.0007300| 0.0004808| 0.1384573| | 32|chr6 | 32037426| 0.0011939| 0.0006062| 0.0573444| | 32|chr6 | 32037453| 0.0013684| 0.0004575| 0.0052290| | 32|chr6 | 32037474| 0.0005452| 0.0005051| 0.2884926| | 32|chr6 | 32037587| 0.0011717| 0.0005700| 0.0480694| | 32|chr6 | 32037602| 0.0007434| 0.0006194| 0.2386053| | 32|chr6 | 32037632| 0.0003933| 0.0005328| 0.4656375| | 32|chr6 | 32037653| 0.0012443| 0.0005433| 0.0285275| | 32|chr6 | 32037735| 0.0016637| 0.0006331| 0.0129396| | 32|chr6 | 32037751| 0.0005364| 0.0005487| 0.3354639| | 32|chr6 | 32037800| 0.0000891| 0.0010872| 0.9352074| | 33|chr6 | 32042200| 0.0014293| 0.0004842| 0.0057855| | 33|chr6 | 32042344| 0.0011513| 0.0006680| 0.0941661| | 33|chr6 | 32042351| 0.0026276| 0.0007252| 0.0009681| | 33|chr6 | 32042430| 0.0000574| 0.0005808| 0.9219081| | 33|chr6 | 32042518| -0.0007150| 0.0005161| 0.1752731| | 33|chr6 | 32042526| 0.0001437| 0.0002279| 0.5325884| | 33|chr6 | 32042534| 0.0002357| 0.0003114| 0.4544765| | 33|chr6 | 32042658| -0.0005557| 0.0004400| 0.2154079| | 33|chr6 | 32042797| 0.0016001| 0.0005211| 0.0043381| | 33|chr6 | 32042947| 0.0028341| 0.0004951| 0.0000022| | 33|chr6 | 32043029| 0.0022139| 0.0008258| 0.0113761| | 33|chr6 | 32043191| 0.0010731| 0.0005525| 0.0607045| | 33|chr6 | 32043561| 0.0025143| 0.0004325| 0.0000017| | 33|chr6 | 32043676| 0.0017213| 0.0005664| 0.0046229| | 33|chr6 | 32043739| 0.0036167| 0.0004596| 0.0000000| | 33|chr6 | 32044104| 0.0010326| 0.0005928| 0.0908754| | 33|chr6 | 32044163| 0.0012238| 0.0005234| 0.0256076| | 33|chr6 | 32044179| 0.0023767| 0.0006243| 0.0005812| | 33|chr6 | 32044203| 0.0000922| 0.0003763| 0.8079619| | 33|chr6 | 32044254| 0.0021710| 0.0006306| 0.0015861| | 34|chr6 | 32044384| 0.0024851| 0.0006693| 0.0007805| | 34|chr6 | 32044404| 0.0020356| 0.0004539| 0.0000836| | 34|chr6 | 32044496| 0.0027983| 0.0009480| 0.0057832| | 34|chr6 | 32044869| 0.0021456| 0.0007448| 0.0069241| | 34|chr6 | 32044959| 0.0005330| 0.0004470| 0.2415568| | 34|chr6 | 32045323| 0.0016298| 0.0004460| 0.0008879| | 35|chr6 | 32048449| 0.0024789| 0.0005231| 0.0000399| | 35|chr6 | 32048463| 0.0013852| 0.0004396| 0.0034536| | 35|chr6 | 32048632| 0.0014067| 0.0005307| 0.0122437| | 35|chr6 | 32048679| 0.0023866| 0.0005699| 0.0001975| | 35|chr6 | 32049053| 0.0019867| 0.0008200| 0.0210623| | 35|chr6 | 32049177| 0.0015486| 0.0010356| 0.1446383| | 35|chr6 | 32049196| 0.0020956| 0.0009048| 0.0269247| | 35|chr6 | 32049235| 0.0022859| 0.0007026| 0.0026370| | 35|chr6 | 32049263| 0.0002777| 0.0007076| 0.6972357| | 35|chr6 | 32049322| 0.0022113| 0.0004534| 0.0000265| | 35|chr6 | 32049354| 0.0007787| 0.0006394| 0.2319110| | 35|chr6 | 32049373| 0.0004675| 0.0006475| 0.4753871| | 35|chr6 | 32049376| 0.0007720| 0.0004805| 0.1176681| | 35|chr6 | 32049513| 0.0044872| 0.0019918| 0.0310568| | 35|chr6 | 32049516| 0.0018892| 0.0009905| 0.0652198| | 35|chr6 | 32049622| 0.0054246| 0.0013535| 0.0003297| | 35|chr6 | 32049699| 0.0020965| 0.0005851| 0.0010812| | 35|chr6 | 32049825| 0.0009969| 0.0005786| 0.0942450| | 35|chr6 | 32049829| 0.0015914| 0.0006348| 0.0172882| | 35|chr6 | 32049845| -0.0000463| 0.0004556| 0.9196930| | 36|chr6 | 32060791| 0.0018855| 0.0005010| 0.0006560| | 36|chr6 | 32060794| 0.0020018| 0.0006337| 0.0033841| | 36|chr6 | 32060816| 0.0058113| 0.0007286| 0.0000000| | 36|chr6 | 32061084| 0.0055124| 0.0010282| 0.0000064| | 36|chr6 | 32061160| 0.0016416| 0.0004351| 0.0006386| | 36|chr6 | 32061318| 0.0034423| 0.0004940| 0.0000001| | 36|chr6 | 32061478| 0.0067209| 0.0005456| 0.0000000| | 37|chr6 | 32086755| 0.0015567| 0.0004910| 0.0032805| | 37|chr6 | 32086758| 0.0013796| 0.0004483| 0.0041843| | 37|chr6 | 32086779| 0.0004479| 0.0003126| 0.1613656| | 37|chr6 | 32086782| 0.0012962| 0.0004033| 0.0029276| | 37|chr6 | 32086818| 0.0017141| 0.0004723| 0.0009513| | 37|chr6 | 32086857| 0.0034127| 0.0009315| 0.0008933| | 37|chr6 | 32086878| 0.0027513| 0.0007137| 0.0005076| | 37|chr6 | 32086893| 0.0026092| 0.0004671| 0.0000033| | 38|chr6 | 32120203| 0.0047441| 0.0008483| 0.0000032| | 38|chr6 | 32120324| 0.0070977| 0.0009075| 0.0000000| | 38|chr6 | 32120584| 0.0123171| 0.0021697| 0.0000025| | 38|chr6 | 32120623| 0.0071143| 0.0010378| 0.0000001| | 38|chr6 | 32120625| 0.0129119| 0.0015077| 0.0000000| | 38|chr6 | 32120773| 0.0164555| 0.0020453| 0.0000000| | 38|chr6 | 32120783| 0.0143953| 0.0018676| 0.0000000| | 38|chr6 | 32120826| 0.0141621| 0.0018371| 0.0000000| | 38|chr6 | 32120863| 0.0214823| 0.0027928| 0.0000000| | 38|chr6 | 32120878| 0.0205448| 0.0020839| 0.0000000| | 38|chr6 | 32120895| 0.0083636| 0.0011945| 0.0000001| | 38|chr6 | 32120899| 0.0103226| 0.0012918| 0.0000000| | 38|chr6 | 32120901| 0.0196434| 0.0025588| 0.0000000| | 38|chr6 | 32120907| 0.0166847| 0.0023794| 0.0000001| | 38|chr6 | 32120933| 0.0170291| 0.0021530| 0.0000000| | 38|chr6 | 32120955| 0.0127698| 0.0015906| 0.0000000| | 38|chr6 | 32121055| 0.0094295| 0.0011082| 0.0000000| | 38|chr6 | 32121113| 0.0097364| 0.0011803| 0.0000000| | 39|chr6 | 32121143| 0.0109729| 0.0011602| 0.0000000| | 39|chr6 | 32121156| 0.0099459| 0.0011021| 0.0000000| | 39|chr6 | 32121204| 0.0032973| 0.0005583| 0.0000013| | 39|chr6 | 32121225| 0.0053628| 0.0008030| 0.0000001| | 39|chr6 | 32121249| 0.0099222| 0.0013729| 0.0000000| | 39|chr6 | 32121259| 0.0070243| 0.0010034| 0.0000001| | 39|chr6 | 32121261| 0.0043735| 0.0007757| 0.0000028| | 39|chr6 | 32121355| 0.0046116| 0.0007507| 0.0000006| | 39|chr6 | 32121368| 0.0046871| 0.0006328| 0.0000000| | 39|chr6 | 32121393| 0.0057123| 0.0007757| 0.0000000| | 39|chr6 | 32121420| 0.0038576| 0.0007068| 0.0000048| | 39|chr6 | 32121433| 0.0057492| 0.0009363| 0.0000006| | 39|chr6 | 32121471| 0.0016624| 0.0006661| 0.0177519| | 39|chr6 | 32121475| 0.0009150| 0.0003760| 0.0205303| | 40|chr6 | 32122736| -0.0019809| 0.0005945| 0.0021386| | 40|chr6 | 32122738| -0.0017221| 0.0005213| 0.0023083| | 40|chr6 | 32122753| -0.0054938| 0.0009396| 0.0000015| | 40|chr6 | 32122779| -0.0021445| 0.0008217| 0.0135258| | 40|chr6 | 32122864| -0.0042917| 0.0007076| 0.0000008| | 41|chr6 | 32135241| 0.0025645| 0.0009279| 0.0092807| | 41|chr6 | 32135285| 0.0004048| 0.0006879| 0.5602335| | 41|chr6 | 32135321| 0.0001307| 0.0005663| 0.8189223| | 41|chr6 | 32135326| 0.0002122| 0.0004804| 0.6616047| | 41|chr6 | 32135370| 0.0005473| 0.0004846| 0.2668586| | 41|chr6 | 32135379| -0.0000150| 0.0003912| 0.9696503| | 41|chr6 | 32135384| 0.0003727| 0.0004929| 0.4550117| | 41|chr6 | 32135396| 0.0001756| 0.0008316| 0.8340676| | 41|chr6 | 32135715| 0.0046879| 0.0007164| 0.0000002| | 41|chr6 | 32135718| 0.0046263| 0.0006358| 0.0000000| | 41|chr6 | 32135728| 0.0057995| 0.0010419| 0.0000035| | 41|chr6 | 32135776| 0.0041579| 0.0009441| 0.0001057| | 41|chr6 | 32135803| 0.0050413| 0.0007966| 0.0000004| | 42|chr6 | 32150404| 0.0025165| 0.0006867| 0.0008637| | 42|chr6 | 32150577| 0.0003203| 0.0005143| 0.5376663| | 42|chr6 | 32150585| 0.0004927| 0.0003992| 0.2257965| | 42|chr6 | 32150656| 0.0002132| 0.0003881| 0.5865275| | 42|chr6 | 32150716| -0.0003987| 0.0004324| 0.3632602| | 43|chr6 | 32154416| -0.0016134| 0.0004878| 0.0022828| | 43|chr6 | 32154447| -0.0037112| 0.0006244| 0.0000011| | 43|chr6 | 32154454| -0.0025579| 0.0008551| 0.0052262| | 43|chr6 | 32154568| -0.0023963| 0.0004999| 0.0000340| | 43|chr6 | 32154613| -0.0018532| 0.0005691| 0.0026145| | 43|chr6 | 32154715| -0.0061503| 0.0007977| 0.0000000| | 44|chr6 | 32158927| -0.0023200| 0.0008853| 0.0131813| | 44|chr6 | 32158953| -0.0025423| 0.0008705| 0.0062623| | 44|chr6 | 32159036| -0.0059181| 0.0010988| 0.0000059| | 44|chr6 | 32159527| -0.0086710| 0.0011671| 0.0000000| | 44|chr6 | 32159604| -0.0049000| 0.0009847| 0.0000199| | 44|chr6 | 32159607| -0.0065540| 0.0011702| 0.0000031| | 44|chr6 | 32159933| -0.0137602| 0.0014807| 0.0000000| | 44|chr6 | 32160074| -0.0089959| 0.0009821| 0.0000000| | 45|chr6 | 32171796| 0.0014813| 0.0006109| 0.0209610| | 45|chr6 | 32171823| 0.0018818| 0.0006666| 0.0080082| | 45|chr6 | 32172007| 0.0000657| 0.0004591| 0.8870551| | 45|chr6 | 32172013| -0.0001783| 0.0005026| 0.7250002| | 45|chr6 | 32172027| -0.0000996| 0.0004899| 0.8401518| | 45|chr6 | 32172124| 0.0020267| 0.0005030| 0.0003105| | 46|chr6 | 32805398| -0.0052602| 0.0005470| 0.0000000| | 46|chr6 | 32805548| -0.0056497| 0.0007112| 0.0000000| | 46|chr6 | 32805554| -0.0064121| 0.0006925| 0.0000000| | 46|chr6 | 32805570| -0.0052904| 0.0007072| 0.0000000| | 46|chr6 | 32805684| -0.0032412| 0.0006549| 0.0000215| | 47|chr6 | 32812933| -0.0062452| 0.0006269| 0.0000000| | 47|chr6 | 32812953| -0.0026982| 0.0004877| 0.0000039| | 47|chr6 | 32812965| -0.0081845| 0.0008237| 0.0000000| | 47|chr6 | 32813084| -0.0149186| 0.0010165| 0.0000000| | 47|chr6 | 32813154| -0.0029333| 0.0006178| 0.0000388| | 47|chr6 | 32813211| -0.0002499| 0.0002206| 0.2653142| | 47|chr6 | 32813337| -0.0136689| 0.0011875| 0.0000000| | 47|chr6 | 32813441| 0.0001788| 0.0003417| 0.6043078| | 47|chr6 | 32813448| -0.0007677| 0.0003414| 0.0313178| | 48|chr6 | 32820355| -0.0056831| 0.0010883| 0.0000096| | 48|chr6 | 32820410| -0.0087937| 0.0008914| 0.0000000| | 48|chr6 | 32820421| -0.0056739| 0.0011000| 0.0000116| | 48|chr6 | 32820546| -0.0064499| 0.0009647| 0.0000001| | 48|chr6 | 32820553| -0.0028039| 0.0007199| 0.0004542| | 48|chr6 | 32820577| -0.0044637| 0.0005969| 0.0000000| | 49|chr6 | 32825701| 0.0036795| 0.0007241| 0.0000146| | 49|chr6 | 32825852| 0.0006878| 0.0007489| 0.3652902| | 49|chr6 | 32825897| 0.0028278| 0.0010861| 0.0137263| | 49|chr6 | 32826171| 0.0024772| 0.0004859| 0.0000139| | 49|chr6 | 32826197| 0.0012497| 0.0005665| 0.0344650| | 50|chr6 | 32908567| -0.0077758| 0.0014040| 0.0000038| | 50|chr6 | 32908605| -0.0089481| 0.0013805| 0.0000003| | 50|chr6 | 32908642| -0.0079963| 0.0013258| 0.0000009| | 50|chr6 | 32908718| -0.0059827| 0.0010752| 0.0000035| | 50|chr6 | 32908794| -0.0028700| 0.0005460| 0.0000087| | 50|chr6 | 32908901| -0.0049536| 0.0008100| 0.0000007| | 50|chr6 | 32908980| -0.0111032| 0.0010072| 0.0000000| | 50|chr6 | 32909003| -0.0151386| 0.0016320| 0.0000000| | 50|chr6 | 32909282| -0.0096443| 0.0014176| 0.0000001| | 50|chr6 | 32909397| -0.0029869| 0.0004300| 0.0000001| | 50|chr6 | 32909440| -0.0040748| 0.0006100| 0.0000001| | 50|chr6 | 32909493| -0.0075823| 0.0009612| 0.0000000| | 50|chr6 | 32909523| -0.0081156| 0.0011620| 0.0000001| | 51|chr6 | 32942063| -0.0040017| 0.0008592| 0.0000506| | 51|chr6 | 32942205| -0.0029352| 0.0005267| 0.0000038| | 51|chr6 | 32942358| -0.0044676| 0.0008093| 0.0000040| | 51|chr6 | 32942400| -0.0026140| 0.0008169| 0.0030381| | 51|chr6 | 32942429| -0.0054339| 0.0007539| 0.0000000| | 51|chr6 | 32942494| -0.0076144| 0.0010191| 0.0000000| | 51|chr6 | 32942541| -0.0026536| 0.0007427| 0.0011115| | 51|chr6 | 32942710| -0.0062878| 0.0007592| 0.0000000| | 51|chr6 | 32942714| -0.0052184| 0.0007741| 0.0000001| | 51|chr6 | 32942808| -0.0051455| 0.0008107| 0.0000004| | 51|chr6 | 32943025| -0.0068885| 0.0011701| 0.0000014| | 52|chr6 | 33043841| -0.0089592| 0.0016461| 0.0000050| | 52|chr6 | 33043849| -0.0049225| 0.0008960| 0.0000043| | 52|chr6 | 33043868| -0.0048543| 0.0011048| 0.0001090| | 52|chr6 | 33043976| -0.0040812| 0.0013144| 0.0038955| | 52|chr6 | 33044012| -0.0075230| 0.0012858| 0.0000015| | 52|chr6 | 33044345| -0.0076685| 0.0019056| 0.0003148| | 52|chr6 | 33044510| -0.0090305| 0.0029214| 0.0040381| | 53|chr6 | 33132163| 0.0044894| 0.0009285| 0.0000301| | 53|chr6 | 33132181| 0.0026369| 0.0009792| 0.0113280| | 53|chr6 | 33132192| 0.0023092| 0.0007936| 0.0064369| | 53|chr6 | 33132241| 0.0039578| 0.0007188| 0.0000042| | 53|chr6 | 33132318| 0.0016570| 0.0007374| 0.0314602| | 54|chr6 | 33132650| 0.0029044| 0.0008988| 0.0027934| | 54|chr6 | 33132693| 0.0014578| 0.0007445| 0.0587333| | 54|chr6 | 33132705| 0.0018258| 0.0006080| 0.0050709| | 54|chr6 | 33132727| 0.0005718| 0.0010938| 0.6046186| | 54|chr6 | 33132943| 0.0013510| 0.0009483| 0.1636810| | 54|chr6 | 33132996| 0.0010484| 0.0006467| 0.1145411| | 54|chr6 | 33133039| 0.0008051| 0.0005092| 0.1233940| | 54|chr6 | 33133083| 0.0022452| 0.0005955| 0.0006438| | 54|chr6 | 33133329| 0.0009322| 0.0005292| 0.0874075| | 54|chr6 | 33133370| 0.0005597| 0.0006001| 0.3578041| | 54|chr6 | 33133485| 0.0013197| 0.0003820| 0.0015343| | 54|chr6 | 33133517| 0.0006703| 0.0006335| 0.2984729| | 54|chr6 | 33133531| 0.0006133| 0.0004131| 0.1471008| | 54|chr6 | 33133535| 0.0001841| 0.0007781| 0.8144606| | 54|chr6 | 33133538| 0.0004572| 0.0006730| 0.5016341| | 54|chr6 | 33133675| 0.0018501| 0.0004255| 0.0001246| | 54|chr6 | 33133752| 0.0013819| 0.0005242| 0.0126865| | 54|chr6 | 33134045| 0.0014330| 0.0008152| 0.0880898| | 54|chr6 | 33134078| 0.0013833| 0.0005912| 0.0254883| | 55|chr6 | 33245488| -0.0063308| 0.0009790| 0.0000002| | 55|chr6 | 33245490| -0.0072472| 0.0009477| 0.0000000| | 55|chr6 | 33245516| -0.0027005| 0.0004193| 0.0000003| | 55|chr6 | 33245537| -0.0059599| 0.0006817| 0.0000000| | 55|chr6 | 33245541| -0.0066055| 0.0005880| 0.0000000| | 55|chr6 | 33245553| -0.0020256| 0.0004237| 0.0000353| | 56|chr6 | 33245706| -0.0034841| 0.0006308| 0.0000040| | 56|chr6 | 33245717| -0.0031527| 0.0006644| 0.0000392| | 56|chr6 | 33245721| -0.0040674| 0.0008277| 0.0000239| | 56|chr6 | 33245739| -0.0061758| 0.0016666| 0.0007708| | 56|chr6 | 33245770| -0.0033426| 0.0006525| 0.0000129| | 56|chr6 | 33245779| -0.0007004| 0.0006544| 0.2922844| | 56|chr6 | 33245804| -0.0044990| 0.0006645| 0.0000001| | 57|chr6 | 33245893| -0.0064717| 0.0007401| 0.0000000| | 57|chr6 | 33245895| -0.0049468| 0.0007351| 0.0000001| | 57|chr6 | 33245990| -0.0027917| 0.0004471| 0.0000005| | 57|chr6 | 33246008| -0.0048952| 0.0007035| 0.0000001| | 57|chr6 | 33246043| -0.0033446| 0.0006808| 0.0000239| | 57|chr6 | 33246091| -0.0039444| 0.0006273| 0.0000004| | 57|chr6 | 33246094| -0.0049641| 0.0006145| 0.0000000| | 58|chr6 | 41010111| 0.0044863| 0.0006439| 0.0000001| | 58|chr6 | 41010217| 0.0032720| 0.0005836| 0.0000031| | 58|chr6 | 41010223| 0.0039473| 0.0009742| 0.0003036| | 58|chr6 | 41010316| 0.0041379| 0.0006334| 0.0000002| | 58|chr6 | 41010375| 0.0023833| 0.0006209| 0.0005315| | 58|chr6 | 41010654| 0.0019212| 0.0007352| 0.0134150| | 59|chr6 | 53530503| 0.0027975| 0.0010874| 0.0147887| | 59|chr6 | 53530538| 0.0037586| 0.0009116| 0.0002374| | 59|chr6 | 53530570| 0.0038971| 0.0008697| 0.0000847| | 59|chr6 | 53530600| 0.0032789| 0.0009137| 0.0010653| | 59|chr6 | 53530624| 0.0028774| 0.0010029| 0.0071356| | 59|chr6 | 53530628| 0.0052701| 0.0008981| 0.0000014| | 60|chr6 | 149805995| -0.0097817| 0.0012361| 0.0000000| | 60|chr6 | 149806077| -0.0176011| 0.0016213| 0.0000000| | 60|chr6 | 149806081| -0.0210694| 0.0018994| 0.0000000| | 60|chr6 | 149806131| -0.0159030| 0.0012826| 0.0000000| | 60|chr6 | 149806235| -0.0180270| 0.0016008| 0.0000000| | 60|chr6 | 149806273| -0.0119123| 0.0011342| 0.0000000| | 60|chr6 | 149806331| -0.0164691| 0.0014486| 0.0000000| | 60|chr6 | 149806339| -0.0206545| 0.0018827| 0.0000000| | 60|chr6 | 149806502| -0.0045615| 0.0011026| 0.0002283| | 60|chr6 | 149806635| -0.0024949| 0.0008287| 0.0049745| | 60|chr6 | 149806732| -0.0050078| 0.0008231| 0.0000008| | 61|chr6 | 152702330| 0.0026328| 0.0007299| 0.0010120| | 61|chr6 | 152702365| 0.0018266| 0.0006656| 0.0097409| | 61|chr6 | 152702387| 0.0025174| 0.0009955| 0.0164158| | 61|chr6 | 152702444| 0.0018338| 0.0005983| 0.0043233| | 61|chr6 | 152702463| 0.0060321| 0.0005759| 0.0000000| | 62|chr6 | 170580947| -0.0057303| 0.0017864| 0.0029749| | 62|chr6 | 170580966| -0.0061513| 0.0026272| 0.0254148| | 62|chr6 | 170581039| -0.0039265| 0.0012441| 0.0034079| | 62|chr6 | 170581085| -0.0002133| 0.0003829| 0.5812049| | 62|chr6 | 170581248| -0.0008610| 0.0003069| 0.0083619| | 62|chr6 | 170581355| -0.0006148| 0.0002833| 0.0373224| | 62|chr6 | 170581502| -0.0061059| 0.0010420| 0.0000015| | 62|chr6 | 170581690| -0.0027766| 0.0012361| 0.0315156|
best6 <- dmrs6[which.min(dmrs6$p.value),]
dmrff.plot(
best6$chr, best6$start, best6$end,
stats[[acc]]$estimate, stats[[acc]]$se, stats[[acc]]$chr, stats[[acc]]$pos)
Going back to full set of DMRs, we can ask which regions are novel, i.e. contain no CpG sites identified by Bohlin et al.
## consider only autosomal regions
dmrs <- dmrs[which(dmrs$chr %in% paste0("chr", 1:22)),]
## collect CpG sites in the regions
sites <- dmrff.sites(dmrs, meta$ewas$chr, meta$ewas$pos)
sites <- cbind(sites, meta$ewas[sites$site,c("cpg","estimate","se","p.value")])
## identify sites with associations according to Bohlin et al.
sites$bohlin <- sites$cpg %in% rownames(bohlin)
## novel regions do not contain any of the Bohlin sites
dmrs$novel <- !(1:nrow(dmrs) %in% sites$region[sites$bohlin])
Of 1713 DMRs identified, 29.54% are novel.
They appear on the following chromosomes:
freq.novel <- table(dmrs$chr[dmrs$novel])
freq <- table(dmrs$chr)
prop <- 100*freq.novel/freq
prop <- as.data.frame(prop)
colnames(prop) <- c("chr","pct")
prop$novel <- freq.novel
prop$total <- freq
prop <- prop[order(prop$pct),]
kable(prop,row.names=F,digits=2)
|chr | pct| novel| total| |:-----|-----:|-----:|-----:| |chr22 | 8.70| 4| 46| |chr19 | 22.89| 19| 83| |chr9 | 23.08| 6| 26| |chr14 | 25.00| 14| 56| |chr10 | 26.14| 23| 88| |chr11 | 26.47| 36| 136| |chr7 | 26.97| 24| 89| |chr18 | 27.27| 3| 11| |chr17 | 27.40| 40| 146| |chr21 | 28.57| 4| 14| |chr12 | 28.75| 23| 80| |chr2 | 30.30| 30| 99| |chr13 | 30.43| 14| 46| |chr6 | 30.46| 60| 197| |chr16 | 32.97| 30| 91| |chr5 | 33.33| 20| 60| |chr1 | 33.70| 62| 184| |chr4 | 34.09| 15| 44| |chr8 | 34.43| 21| 61| |chr15 | 36.59| 15| 41| |chr3 | 37.18| 29| 78| |chr20 | 37.84| 14| 37|
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