Noi/NOTES/2012-4-26: Difference between revisions
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| '''Total in 2Mb'''||'''742'''|| | | '''Total in 2Mb'''||'''742'''|| | ||
|}<br> | |}<br> | ||
* | * Within 150kb there are 696 association (account for 77.3% of total noSNP mQTL) | ||
* Within 100kb there are 666 association (account for 74.0% of total noSNP mQTL) | |||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Associated CpG-SNP distance''' | | align="center" style="background:#f0f0f0;"|'''Associated CpG-SNP distance''' | ||
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| align="center" style="background:#f0f0f0;"|'''% of no CpG-SNP to all significant associations''' | | align="center" style="background:#f0f0f0;"|'''% of no CpG-SNP to all significant associations''' | ||
|- | |- | ||
| # of association (10%FDR)||742|| | | # of association (10%FDR)||742||2,788||23.17% | ||
|- | |- | ||
| significant p-value||1.636E-04||5.448E-04|| | | significant p-value||1.636E-04||5.448E-04|| | ||
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Total single CpG: 236+134 = 370<br> | Total single CpG: 236+134 = 370<br> | ||
* Print out the list of unique CpGs and SNPs and duplicated CpGs and SNPs | * Print out the list of unique CpGs and SNPs and duplicated CpGs and SNPs | ||
== Association of SNP to adjacent CpGs == | == Association of SNP to adjacent CpGs == | ||
* I could observe a strong association of SNPs to many CpGs on the same region and also observe an adjacent SNPs consistently associate to the same adjacent CpGs | * I could observe a strong association of SNPs to many CpGs on the same region and also observe an adjacent SNPs consistently associate to the same adjacent CpGs |
Latest revision as of 10:52, 30 April 2012
- Link to calendar: [[1]]
- Previous analysis of mQTL on UCLA data set: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-11
- Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-21
mQTL analysis on UCLA-SZ data set (no CpG-SNP)[edit]
- Details will be filled later
- Filter out SNP from methylMatrix (Note: the sample IDs were modified to be compatible with tfam file and plink)
./remove_snps.pl ./UCLA-4batches_methyl_min76_minSTD0.1-edit /t4T/GenomeDB/HsGenome/snp134_snv.txt > UCLA-4batches_methyl-noSNP_min76_minSTD0.1
61664 UCLA-4batches_methyl-noSNP_min76_minSTD0.1
- Split the methylMatrix in to 10,000 CpG sites each
split -10000 UCLA-4batches_methyl-noSNP_min76_minSTD0.1 UCLA_noSNP_ 10000 UCLA_noSNP_aa 10001 UCLA_noSNP_ab 10001 UCLA_noSNP_ac 10001 UCLA_noSNP_ad 10001 UCLA_noSNP_ae 10001 UCLA_noSNP_af 1666 UCLA_noSNP_ag
- Run mQTL (no CpG-SNP)
nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_aa > 2MB_noNSP_aa nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_ab > 2MB_noNSP_ab nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_ac > 2MB_noNSP_ac nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_ad > 2MB_noNSP_ad nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_ae > 2MB_noNSP_ae nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_af > 2MB_noNSP_af nohup ../mQTL_2MB_plink_allP.pl ../UCLA.hg19SNP ../UCLA_noSNP_ag > 2MB_noNSP_ag
- Concatenate the out put files to the same file
cat mQTL_noSNP_a*/2MB_noNSP_a* > 2MB_mQTL-noSNP_rawoutput awk '{if ($1 ~ /chr/) print $0}' 2MB_mQTL-noSNP_rawoutput > 2MB_mQTL-noSNP_output
- Number of test
433,947 2MB_mQTL-noSNP_output
- Sort out adj. p-val and count the number of significant associated CpG-SNP roughly at different p-value
sort column7 (adj p_val) sort -g -k7 2MB_mQTL-noSNP_output | awk '{if ($7<=0.05) print $0}' | wc -l --> 6,418 sort -g -k7 2MB_mQTL-noSNP_output | awk '{if ($7<=0.01) print $0}' | wc -l --> 2,292 sort -g -k7 2MB_mQTL-noSNP_output | awk '{if ($7<=0.001) print $0}' | wc -l --> 1,026 sort -g -k7 2MB_mQTL-noSNP_output | awk '{if ($7<=0.0001) print $0}' | wc -l --> 698 sort -g -k7 2MB_mQTL-noSNP_output | awk '{if ($7<=0.00001) print $0}' | wc -l --> 526
- Print out the site at min p-value 0.05 before multiple test correction
sort -g -k7 2MB_mQTL-noSNP_output | awk '{if ($7<=0.05) print $0}' > sorted_2MB_mQTL-noSNP_minPVal0.05.txt 6418 sorted_2MB_mQTL-noSNP_minPVal0.05.txt
- Concatenate QVal to the mQTL file
paste -d"\t" sorted_2MB_mQTL-noSNP_minPVal0.05.txt sorted_2MB_mQTL-noSNP_QVal.txt.txt > sorted_2MB_mQTL-noSNP_minPVal0.05_QVal.txt.txt awk '{if ($8 <=0.1) print $0}' sorted_2MB_mQTL-noSNP_minPVal0.05_QVal.txt.txt > 10%FDR_2MB_mQTL-noSNP 741 10%FDR_2MB_mQTL-noSNP p-value cut off: 0.0001636 or 1.636E-4
- Look at # of associated CpG
awk '{print $1}' 10%FDR_2MB_mQTL-noSNP | sort | uniq -u | wc -l 295 awk '{print $1}' 10%FDR_2MB_mQTL-noSNP | sort | uniq -d | wc -l 121 295+121X = 741 --> X ~ (741-295)/121 ~3.69 this show >1 SNPs associated with the same CpG Total single CpG: 295+121 = 416
- Look at # of associated SNP
awk '{print $2}' 10%FDR_2MB_mQTL-noSNP | sort | uniq -u | wc -l --> 195 awk '{print $2}' 10%FDR_2MB_mQTL-noSNP | sort | uniq -d | wc -l --> 109 195+109Y = 741 --> Y ~ (741-195)/109 ~ 5 this also suggest >1 CpGs associated with the same SNP Total single SNP 195+109 = 304
- Separate the CpG-SNP association based on the distance between CpG and SNP
- Note: Dr. Zhang suggested to break down the CpG-SNP distance with equal length
sed s'/:/\t/g' 10%FDR_2MB_mQTL-noSNP > 10%FDR_2MB_mQTL-noSNP_split_pos Run sh print_distance.sh
- Note again: P-value of 10%FDR is p <= 1.636E−4
Associated CpG-SNP distance | Number of assiciated CpG-SNP | % |
10%FDR_10kb | 378 | 50.94% |
10%FDR_10-20kb | 27 | 3.64% |
10%FDR_20-30kb | 21 | 2.83% |
10%FDR_30-40kb | 36 | 4.85% |
10%FDR_40-50kb | 2 | 0.27% |
10%FDR_50kb-2Mb | 278 | 37.47% |
Total in 2Mb | 742 |
- Within 150kb there are 696 association (account for 77.3% of total noSNP mQTL)
- Within 100kb there are 666 association (account for 74.0% of total noSNP mQTL)
Associated CpG-SNP distance | Number of assiciated CpG-SNP | % |
minpval0.05_10kb | 862 | 13.43% |
minpval0.05_10-20kb | 124 | 1.93% |
minpval0.05_20-30kb | 133 | 2.07% |
minpval0.05_30-40kb | 108 | 1.68% |
minpval0.05_40-50kb | 75 | 1.17% |
minpval0.05_50kb-2Mb | 5,116 | 79.71% |
Total in 2Mb | 6,418 |
- Get sequences for manhattan plots
Run get_manht_seq.sh
Comparing no CpG-SNP mQTL to the whole CpG and SNP mQTL result[edit]
- Analyzing the association of CpG and SNP with 10%FDR derived from each analysis
' | no CpG-SNP | SNP-free CpG and CpG-SNP | % of no CpG-SNP to all significant associations |
# of association (10%FDR) | 742 | 2,788 | 23.17% |
significant p-value | 1.636E-04 | 5.448E-04 |
- From the table above, I could see the different of significant p-value from each test. The reason is that the number of tests were different between the test of the whole methylation matrix and the whose SNPs have been filtered out. Therefore the BH correction which deals with the number of test in calculation provide the q-value with at the different significant p-value. It turned out that the significant p-value of no SNP analysis was lower than the whole CpG. This implied that there might be more no CpG-SNP between 1.636E-04 to 5.448E-04 p-value of the 2MB_UCLA_mQTL_3202_10%FDR.txt file (Total significant CpG-SNP association 3,202 sites, 10%FDR)
- I then checked the number of CpG-SNP association with the significant p-value 5.448E-04 in no SNP-CpG file and got total 900 sites (but have ~27.4% FDR by the test with out CpG-SNP.
- Note: I can count the # of sites based on p-value because this value was not changed, and just used it as the reference. This account for ~28% of the association I got from all association.
- Then, I printed out another files of CpG-SNP association with no CpG-SNP significant p-value 0.0005613
awk '{if ($7<=0.0005613) print $0}' sorted_2MB_mQTL-noSNP_minPVal0.05_QVal.txt.txt > sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt
- I also checked if those sites exit in the 10%FDR mQTL result derived from the previous analysis (on the whole mathylMatrix)
./get_overlapping_CpG_SNP.pl ./2MB_UCLA_mQTL_3202_10%FDR.txt <./sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt > test_mQTL
- I checked the overlapped sites on both files again, and there were consistent. This helped to confirm that the analysis of this time and the previous time were likely to be correct.
head sorted_2MB_mQTL-noSNP_minPVal chr8:17533620 rs17125083 8 17533468 0.8961 1.331e-40 2.262e-39 chr8:17533620 rs2301541 8 17533568 0.9029 3.106e-40 2.64e-39 chr8:17533604 rs17125083 8 17533468 0.8839 1.099e-38 1.867e-37 chr19:58791188 rs260500 19 58791213 0.889 5.069e-38 6.083e-37 chr8:17533604 rs2301541 8 17533568 0.8859 1.473e-37 1.252e-36 chr19:58791159 rs260500 19 58791213 0.8844 2.421e-37 2.906e-36
head sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt chr8:17533620 rs17125083 8 17533468 0.8961 1.331e-40 2.262e-39 5.9861604e-34 chr8:17533620 rs2301541 8 17533568 0.9029 3.106e-40 2.64e-39 5.9861604e-34 chr8:17533604 rs17125083 8 17533468 0.8839 1.099e-38 1.867e-37 2.82226299666667e-32 chr19:58791188 rs260500 19 58791213 0.889 5.069e-38 6.083e-37 6.8965556275e-32 chr8:17533604 rs2301541 8 17533568 0.8859 1.473e-37 1.252e-36 1.135556488e-31 chr19:58791159 rs260500 19 58791213 0.8844 2.421e-37 2.906e-36 2.19643713666667e-31
- Also break down CpG-SNP distance not only at equal length, but also at a very short distance like within 2kb and 5kb. The table below implied the cis regulation of genetic factor on methylation status especially within 2kb since the number of association not largely increase from 2-5kb (393-327 = 66 association) or 2-10kb (426-327 = 99 association)
CpG-SNP distance | number of association | % |
2kb-noSNP | 327 | 36.33% |
5kb-noSNP | 393 | 43.67% |
10kb-noSNP | 426 | 47.33% |
10-20kb-noSNP | 34 | 3.78% |
20-30kb-noSNP | 24 | 2.67% |
30-40kb-noSNP | 41 | 4.56% |
40-50kb-noSNP | 4 | 0.44% |
50kb-2Mb-noSNP | 371 | 41.22% |
- Look at # of associated CpG
900 sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt awk '{print $1}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -u | wc -l --> 361 awk '{print $1}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -d | wc -l --> 155 361+155X = 900 --> X ~ (900-361)/155 ~ 3.5 this shows that >1 SNPs associated with the same CpG (155 of individual CpGs associated with more than one SNPs)
Total single CpG: 361+155 = 516
- Look at # of associated CpG
awk '{print $2}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -u | wc -l --> 236 awk '{print $2}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -d | wc -l --> 134 236+134Y = 900 --> Y ~ (900-236)/134 ~ 5 this suggests that > 1 CpGs associated with the same SNP (134 of individual SNPs associated with more than one CpGs)
Total single CpG: 236+134 = 370
- Print out the list of unique CpGs and SNPs and duplicated CpGs and SNPs
Association of SNP to adjacent CpGs[edit]
- I could observe a strong association of SNPs to many CpGs on the same region and also observe an adjacent SNPs consistently associate to the same adjacent CpGs
- Ex. 2-10kb
- 2kb
chr10:60271627 rs7091440 10 60271372 0.2668 9.34E-07 4.55E-07 0.000536756 chr10:60271631 rs7091440 10 60271372 0.2279 7.56E-06 5.45E-07 0.000639583 chr10:60271648 rs7091440 10 60271372 0.3081 9.12E-08 4.05E-07 0.000479902 chr10:60271650 rs7091440 10 60271372 0.3196 4.67E-08 3.95E-07 0.000469923 chr10:60271812 rs7091440 10 60271372 0.3834 1.94E-09 3.46E-07 0.000416711 chr10:60271830 rs7091440 10 60271372 0.4331 7.82E-11 3.24E-07 0.000392263 chr10:60272193 rs7091440 10 60271372 0.2507 2.24E-06 4.79E-07 0.000564103 chr10:60271627 rs7095501 10 60271940 0.2959 1.84E-07 9.05E-07 0.001005233 chr10:60271631 rs7095501 10 60271940 0.2413 3.71E-06 1.07E-06 0.001181073 chr10:60271648 rs7095501 10 60271940 0.3216 4.14E-08 8.84E-07 0.000992305 chr10:60271650 rs7095501 10 60271940 0.3299 2.53E-08 7.83E-07 0.000892295 chr10:60271812 rs7095501 10 60271940 0.3876 1.49E-09 6.74E-07 0.000773815 chr10:60271830 rs7095501 10 60271940 0.4569 1.53E-11 5.87E-07 0.000682804 chr10:60272193 rs7095501 10 60271940 0.2695 8.07E-07 9.05E-07 0.001005233 chr10:60271627 rs79792017 10 60271846 0.2406 9.14E-06 1.94E-06 0.002036537 chr10:60271631 rs79792017 10 60271846 0.1929 9.07E-05 2.12E-06 0.002192416 chr10:60271648 rs79792017 10 60271846 0.2596 3.55E-06 1.91E-06 0.002005488 chr10:60271650 rs79792017 10 60271846 0.2842 1.01E-06 1.70E-06 0.001792846 chr10:60271812 rs79792017 10 60271846 0.3352 9.97E-08 1.56E-06 0.001671061 chr10:60271830 rs79792017 10 60271846 0.4346 3.04E-10 1.51E-06 0.001621171 chr10:60272193 rs79792017 10 60271846 0.2602 3.44E-06 1.70E-06 0.001792846
chr6:2952811 rs2580109 6 2952892 0.3668 3.51E-08 2.46E-07 0.00030611 chr6:2952839 rs2580109 6 2952892 0.4152 2.31E-09 1.62E-08 2.53E-05 chr6:2952902 rs2580109 6 2952892 0.5847 2.37E-16 1.66E-15 1.24E-11 chr6:2952920 rs2580109 6 2952892 0.6349 1.60E-18 1.12E-17 1.04E-13 chr6:2952937 rs2580109 6 2952892 0.6169 1.04E-17 7.25E-17 6.21E-13 chr6:2952939 rs2580109 6 2952892 0.4959 4.48E-13 3.14E-12 1.05E-08 chr6:2952945 rs2580109 6 2952892 0.6665 4.83E-20 3.38E-19 4.38E-15 chr6:2952960 rs2580109 6 2952892 0.4364 4.67E-11 3.27E-10 7.50E-07 chr6:2952963 rs2580109 6 2952892 0.5566 1.58E-14 1.11E-13 5.12E-10 chr6:2953027 rs2580109 6 2952892 0.4807 1.42E-12 9.96E-12 2.93E-08 chr6:2953042 rs2580109 6 2952892 0.4885 7.92E-13 5.54E-12 1.79E-08
chr6:27486295 rs4478400 6 27486303 0.2428 1.44E-06 1.44E-05 0.012059661 chr6:27486295 rs7774613 6 27486633 0.2177 3.18E-05 9.93E-05 0.064608683 chr6:27486306 rs4478400 6 27486303 0.2915 8.11E-08 4.05E-07 0.000479902 chr6:27486306 rs7774613 6 27486633 0.2722 2.21E-06 7.35E-06 0.006671848 chr6:27486314 rs4478400 6 27486303 0.277 1.94E-07 1.94E-06 0.002036537 chr6:27486314 rs7774613 6 27486633 0.2529 5.78E-06 1.93E-05 0.015494481 chr6:27486318 rs4478400 6 27486303 0.2198 5.28E-06 2.64E-05 0.020299756 chr6:27486318 rs7774613 6 27486633 0.2166 3.34E-05 8.35E-05 0.055926831 chr6:27486350 rs4478400 6 27486303 0.253 8.00E-07 8.00E-06 0.007153982 chr6:27486350 rs7774613 6 27486633 0.2511 6.33E-06 2.17E-05 0.017180559
chr1:204599347 rs7531829 1 204599325 0.2238 1.22E-05 9.14E-05 0.060085066 chr1:204599553 rs7531829 1 204599325 0.2849 4.85E-07 6.21E-06 0.005709647 chr1:204599592 rs7531829 1 204599325 0.2078 2.74E-05 0.0003644 0.199277047 chr1:204599653 rs7531829 1 204599325 0.2712 1.02E-06 7.65E-06 0.006900728 chr1:204599656 rs7531829 1 204599325 0.357 7.67E-09 1.15E-07 0.000152624 chr1:204599658 rs7531829 1 204599325 0.3363 2.63E-08 3.95E-07 0.000469923 chr1:204599682 rs7531829 1 204599325 0.3126 1.04E-07 1.56E-06 0.001671061 chr1:204599716 rs7531829 1 204599325 0.251 2.99E-06 4.49E-05 0.032729068 chr1:204599347 rs7546057 1 204599692 0.229 8.18E-06 9.14E-05 0.060085066 chr1:204599553 rs7546057 1 204599692 0.272 8.28E-07 6.21E-06 0.005709647 chr1:204599592 rs7546057 1 204599692 0.194 4.86E-05 0.0003644 0.199277047 chr1:204599653 rs7546057 1 204599692 0.2668 9.36E-07 7.65E-06 0.006900728 chr1:204599656 rs7546057 1 204599692 0.3252 3.35E-08 2.51E-07 0.000311981 chr1:204599658 rs7546057 1 204599692 0.3107 7.83E-08 5.87E-07 0.000682804 chr1:204599682 rs7546057 1 204599692 0.278 5.04E-07 3.78E-06 0.003634702 chr1:204599716 rs7546057 1 204599692 0.184 7.18E-05 0.0005385 0.272249871
chr1:247619148 rs4372298 1 247616446 0.1849 2.34E-05 0.0002031 0.120873019 chr1:247616203 rs4372298 1 247616446 0.4787 1.61E-14 1.23E-13 5.58E-10 chr1:247619148 rs4333884 1 247616723 0.1704 9.54E-05 0.0003135 0.176391203 chr1:247616203 rs4333884 1 247616723 0.4781 1.23E-13 5.64E-13 2.26E-09 chr1:247619148 rs4518943 1 247616766 0.1704 9.54E-05 0.0003135 0.176391203 chr1:247616203 rs4518943 1 247616766 0.4781 1.23E-13 5.64E-13 2.26E-09 chr1:247616203 rs12745508 1 247617979 0.4505 1.13E-12 3.71E-12 1.23E-08 chr1:247619148 rs9700400 1 247618743 0.1754 4.41E-05 0.0002031 0.120873019 chr1:247616203 rs9700400 1 247618743 0.492 6.85E-15 7.88E-14 3.93E-10 chr1:247619148 rs10925038 1 247619018 0.1871 3.20E-05 0.0002031 0.120873019 chr1:247616203 rs10925038 1 247619018 0.387 7.67E-11 1.96E-10 4.68E-07 chr1:247619148 rs9988617 1 247619046 0.1871 3.20E-05 0.0002031 0.120873019 chr1:247616203 rs9988617 1 247619046 0.387 7.67E-11 1.96E-10 4.68E-07 chr1:247619148 rs9988620 1 247619191 0.1758 3.89E-05 0.0002031 0.120873019 chr1:247616203 rs9988620 1 247619191 0.498 5.66E-15 7.88E-14 3.93E-10
- Ex. 50kb-2Mb
chr1:205819406 rs1772153 1 205745782 0.1932 5.06E-05 0.0003792 0.205210098 chr1:205819423 rs1772153 1 205745782 0.1899 5.96E-05 0.0004468 0.235607511 chr1:205819463 rs1772153 1 205745782 0.2354 5.86E-06 4.40E-05 0.032213672 chr1:205819492 rs1772153 1 205745782 0.2048 2.83E-05 0.0002119 0.124638151 chr1:205819571 rs1772153 1 205745782 0.2265 9.30E-06 6.98E-05 0.04794013
chr1:205819406 rs1775151 1 205745684 0.1695 9.97E-05 0.0004986 0.256228373 chr1:205819423 rs1775151 1 205745684 0.1692 0.0001013 0.0005066 0.258717996 chr1:205819463 rs1775151 1 205745684 0.1892 3.55E-05 0.0001774 0.107267157 chr1:205819492 rs1775151 1 205745684 0.175 7.48E-05 0.0003742 0.203475512 chr1:205819571 rs1775151 1 205745684 0.1895 3.50E-05 0.0001749 0.106180221
- 85-92kb CpG-SNP distance
chr10:124234817 rs2277229 10 124331944 0.2488 1.59E-06 8.59E-06 0.007530506 chr10:124235096 rs2277229 10 124331944 0.3377 6.83E-09 2.31E-08 3.43E-05 chr10:124235103 rs2277229 10 124331944 0.2145 1.34E-05 4.52E-05 0.032834927 chr10:124235253 rs2277229 10 124331944 0.5503 6.88E-16 4.19E-15 2.67E-11 chr10:124235281 rs2277229 10 124331944 0.3764 5.49E-10 2.13E-09 4.04E-06 chr10:124235284 rs2277229 10 124331944 0.5064 3.27E-14 2.34E-13 9.90E-10 chr10:124235399 rs2277229 10 124331944 0.4443 4.47E-12 1.51E-11 4.22E-08 chr10:124234817 rs2277230 10 124331957 0.2497 1.30E-06 8.59E-06 0.007530506 chr10:124235096 rs2277230 10 124331957 0.3351 6.51E-09 2.31E-08 3.43E-05 chr10:124235103 rs2277230 10 124331957 0.214 1.21E-05 4.52E-05 0.032834927 chr10:124235253 rs2277230 10 124331957 0.5478 5.81E-16 4.19E-15 2.67E-11 chr10:124235281 rs2277230 10 124331957 0.3726 5.57E-10 2.13E-09 4.04E-06 chr10:124235284 rs2277230 10 124331957 0.5113 1.51E-14 2.34E-13 9.90E-10 chr10:124235399 rs2277230 10 124331957 0.4382 5.28E-12 1.59E-11 4.38E-08
chr10:124234817 rs2981798 10 124331429 0.234 5.49E-06 1.48E-05 0.012385563 chr10:124235096 rs2981798 10 124331429 0.3504 4.72E-09 2.31E-08 3.43E-05 chr10:124235103 rs2981798 10 124331429 0.3306 2.43E-08 6.56E-07 0.000755521 chr10:124235253 rs2981798 10 124331429 0.5087 5.57E-14 1.50E-13 6.75E-10 chr10:124235281 rs2981798 10 124331429 0.4177 5.47E-11 7.38E-10 1.54E-06 chr10:124235284 rs2981798 10 124331429 0.4452 7.66E-12 2.30E-11 6.32E-08 chr10:124235399 rs2981798 10 124331429 0.4996 1.16E-13 3.14E-12 1.05E-08 chr10:124235096 rs2981800 10 124331645 0.3084 3.40E-07 8.35E-07 0.000939515 chr10:124235253 rs2981800 10 124331645 0.4409 1.52E-10 3.74E-10 8.43E-07 chr10:124235281 rs2981800 10 124331645 0.3015 4.89E-07 1.20E-06 0.001308164 chr10:124235284 rs2981800 10 124331645 0.3511 3.35E-08 8.22E-08 0.000112962 chr10:124235399 rs2981800 10 124331645 0.4476 9.85E-11 2.64E-10 6.17E-07 chr10:124234817 rs2981801 10 124331722 0.2805 1.45E-06 8.59E-06 0.007530506 chr10:124235096 rs2981801 10 124331722 0.3573 1.88E-08 5.08E-08 7.15E-05 chr10:124235103 rs2981801 10 124331722 0.2507 7.51E-06 3.38E-05 0.025259858 chr10:124235253 rs2981801 10 124331722 0.5553 2.67E-14 8.01E-14 3.95E-10 chr10:124235281 rs2981801 10 124331722 0.414 6.30E-10 2.13E-09 4.04E-06 chr10:124235284 rs2981801 10 124331722 0.4529 5.11E-11 1.38E-10 3.36E-07 chr10:124235399 rs2981801 10 124331722 0.4903 3.85E-12 1.48E-11 4.18E-08 chr10:124234817 rs3013231 10 124320726 0.2236 3.28E-06 1.11E-05 0.009534624 chr10:124235096 rs3013231 10 124320726 0.3311 2.99E-09 2.31E-08 3.43E-05 chr10:124235103 rs3013231 10 124320726 0.2231 3.85E-06 2.27E-05 0.017626487 chr10:124235253 rs3013231 10 124320726 0.5238 7.75E-16 4.19E-15 2.67E-11 chr10:124235281 rs3013231 10 124320726 0.3974 2.78E-11 7.38E-10 1.54E-06 chr10:124235284 rs3013231 10 124320726 0.4663 1.23E-13 5.54E-13 2.26E-09 chr10:124235399 rs3013231 10 124320726 0.4499 4.72E-13 6.38E-12 2.04E-08 chr10:124234817 rs3019492 10 124320881 0.2411 2.44E-06 9.96E-06 0.008618167 chr10:124235096 rs3019492 10 124320881 0.329 1.18E-08 3.53E-08 5.09E-05 chr10:124235103 rs3019492 10 124320881 0.2364 4.20E-06 2.27E-05 0.017626487 chr10:124235253 rs3019492 10 124320881 0.5303 4.20E-15 1.42E-14 8.13E-11 chr10:124235281 rs3019492 10 124320881 0.3351 8.02E-09 2.17E-08 3.32E-05 chr10:124235284 rs3019492 10 124320881 0.4663 8.34E-13 2.82E-12 9.60E-09 chr10:124235399 rs3019492 10 124320881 0.4003 1.08E-10 2.64E-10 6.17E-07
chr10:124234817 rs3019515 10 124325409 0.2326 2.58E-06 9.96E-06 0.008618167 chr10:124235096 rs3019515 10 124325409 0.3303 4.74E-09 2.31E-08 3.43E-05 chr10:124235103 rs3019515 10 124325409 0.1998 1.80E-05 4.85E-05 0.034706111 chr10:124235253 rs3019515 10 124325409 0.5225 1.84E-15 8.29E-15 5.08E-11 chr10:124235281 rs3019515 10 124325409 0.3668 4.07E-10 2.13E-09 4.04E-06 chr10:124235284 rs3019515 10 124325409 0.4683 1.99E-13 7.66E-13 2.97E-09 chr10:124235399 rs3019515 10 124325409 0.4491 9.31E-13 8.38E-12 2.58E-08 chr10:124234817 rs3019523 10 124326737 0.2209 4.37E-06 1.31E-05 0.011142099 chr10:124235096 rs3019523 10 124326737 0.3221 6.64E-09 2.31E-08 3.43E-05 chr10:124235103 rs3019523 10 124326737 0.1997 1.61E-05 4.83E-05 0.034574669 chr10:124235253 rs3019523 10 124326737 0.5136 2.84E-15 1.10E-14 6.38E-11 chr10:124235281 rs3019523 10 124326737 0.3529 8.46E-10 2.54E-09 4.72E-06 chr10:124235284 rs3019523 10 124326737 0.4852 3.46E-14 2.34E-13 9.90E-10 chr10:124235399 rs3019523 10 124326737 0.44 1.41E-12 9.49E-12 2.84E-08 chr10:124234817 rs3019524 10 124326793 0.2383 1.40E-06 8.59E-06 0.007530506 chr10:124234834 rs3019524 10 124326793 0.1824 3.33E-05 0.0004493 0.236102204 chr10:124235096 rs3019524 10 124326793 0.3311 2.98E-09 2.31E-08 3.43E-05 chr10:124235103 rs3019524 10 124326793 0.226 3.28E-06 2.27E-05 0.017626487 chr10:124235253 rs3019524 10 124326793 0.5259 6.36E-16 4.19E-15 2.67E-11 chr10:124235281 rs3019524 10 124326793 0.3659 2.71E-10 1.83E-09 3.54E-06 chr10:124235284 rs3019524 10 124326793 0.4787 4.33E-14 2.34E-13 9.90E-10 chr10:124235399 rs3019524 10 124326793 0.4261 3.14E-12 1.41E-11 4.01E-08 chr10:124234817 rs3019525 10 124326838 0.2383 1.40E-06 8.59E-06 0.007530506 chr10:124234834 rs3019525 10 124326838 0.1824 3.33E-05 0.0004493 0.236102204 chr10:124235096 rs3019525 10 124326838 0.3311 2.98E-09 2.31E-08 3.43E-05 chr10:124235103 rs3019525 10 124326838 0.226 3.28E-06 2.27E-05 0.017626487 chr10:124235253 rs3019525 10 124326838 0.5259 6.36E-16 4.19E-15 2.67E-11 chr10:124235281 rs3019525 10 124326838 0.3659 2.71E-10 1.83E-09 3.54E-06 chr10:124235284 rs3019525 10 124326838 0.4787 4.33E-14 2.34E-13 9.90E-10 chr10:124235399 rs3019525 10 124326838 0.4261 3.14E-12 1.41E-11 4.01E-08
- 190kb CpG-SNP distance
chr22:49826476 rs135880 22 50018654 0.4064 1.20E-10 7.77E-10 1.62E-06 chr22:49826577 rs135880 22 50018654 0.2238 7.17E-06 4.66E-05 0.033590501 chr22:49826596 rs135880 22 50018654 0.1918 3.87E-05 0.000478 0.247456126 chr22:49842443 rs135880 22 50018654 0.2439 2.09E-06 1.41E-05 0.011880107 chr22:49881777 rs135880 22 50018654 0.2423 3.52E-06 1.69E-05 0.013849603 chr22:49881809 rs135880 22 50018654 0.221 9.50E-06 5.98E-05 0.041813961 chr22:49946027 rs135880 22 50018654 0.1786 7.63E-05 0.0003656 0.199277047 chr22:49826476 rs4524218 22 50018639 0.4355 2.87E-10 1.25E-09 2.51E-06 chr22:49826577 rs4524218 22 50018639 0.2038 6.89E-05 0.0002987 0.169961799 chr22:49842443 rs4524218 22 50018639 0.2135 3.88E-05 0.000168 0.102265095 chr22:49881777 rs4524218 22 50018639 0.3383 1.29E-07 1.68E-06 0.001789503 chr22:49881809 rs4524218 22 50018639 0.241 1.38E-05 5.98E-05 0.041813961 chr22:49881820 rs4524218 22 50018639 0.2456 1.11E-05 0.0001445 0.090014171 chr22:49946027 rs4524218 22 50018639 0.2319 1.61E-05 0.0002096 0.12376689
chr22:49826476 rs4524218 22 50018639 0.4355 2.87E-10 1.25E-09 2.51E-06 chr22:49826577 rs4524218 22 50018639 0.2038 6.89E-05 0.0002987 0.169961799 chr22:49842443 rs4524218 22 50018639 0.2135 3.88E-05 0.000168 0.102265095 chr22:49881777 rs4524218 22 50018639 0.3383 1.29E-07 1.68E-06 0.001789503 chr22:49881809 rs4524218 22 50018639 0.241 1.38E-05 5.98E-05 0.041813961 chr22:49881820 rs4524218 22 50018639 0.2456 1.11E-05 0.0001445 0.090014171 chr22:49946027 rs4524218 22 50018639 0.2319 1.61E-05 0.0002096 0.12376689 chr22:49826476 rs135880 22 50018654 0.4064 1.20E-10 7.77E-10 1.62E-06 chr22:49826577 rs135880 22 50018654 0.2238 7.17E-06 4.66E-05 0.033590501 chr22:49826596 rs135880 22 50018654 0.1918 3.87E-05 0.000478 0.247456126 chr22:49842443 rs135880 22 50018654 0.2439 2.09E-06 1.41E-05 0.011880107 chr22:49881777 rs135880 22 50018654 0.2423 3.52E-06 1.69E-05 0.013849603 chr22:49881809 rs135880 22 50018654 0.221 9.50E-06 5.98E-05 0.041813961 chr22:49946027 rs135880 22 50018654 0.1786 7.63E-05 0.0003656 0.199277047 chr22:49826577 rs739240 22 50052607 0.225 6.74E-06 4.66E-05 0.033590501 chr22:49826596 rs739240 22 50052607 0.1794 7.35E-05 0.000478 0.247456126 chr22:49842443 rs739240 22 50052607 0.2432 2.17E-06 1.41E-05 0.011880107 chr22:49881777 rs739240 22 50052607 0.2404 3.90E-06 1.69E-05 0.013849603 chr22:49881809 rs739240 22 50052607 0.2158 1.25E-05 5.98E-05 0.041813961 chr22:49946027 rs739240 22 50052607 0.1767 8.44E-05 0.0003656 0.199277047 chr22:49826476 rs9616715 22 50058582 0.2611 5.29E-06 1.72E-05 0.013987574 chr22:49842443 rs9616715 22 50058582 0.1975 9.19E-05 0.0002986 0.169961799 chr22:49881777 rs9616715 22 50058582 0.2286 3.25E-05 0.0001057 0.06831484 chr22:49881809 rs9616715 22 50058582 0.225 3.35E-05 0.0001087 0.069922162
- 1.5Mb CpG-SNP association on X chromosome
chrX:150151410 rs3761504 23 152083947 0.5195 9.43E-13 9.43E-13 3.59E-09 chrX:150151419 rs3761504 23 152083947 0.4183 8.38E-10 8.38E-10 1.73E-06 chrX:150151421 rs3761504 23 152083947 0.3854 5.99E-09 5.99E-09 1.06E-05 chrX:150151426 rs3761504 23 152083947 0.3911 4.29E-09 4.29E-09 7.78E-06 chrX:150151445 rs3761504 23 152083947 0.3577 2.89E-08 2.89E-08 4.23E-05 chrX:150151450 rs3761504 23 152083947 0.4871 9.50E-12 9.50E-12 2.84E-08 chrX:150151473 rs3761504 23 152083947 0.4205 1.28E-09 1.28E-09 2.56E-06 chrX:150151527 rs3761504 23 152083947 0.3756 1.05E-08 1.05E-08 1.77E-05 chrX:150151546 rs3761504 23 152083947 0.4116 1.26E-09 1.26E-09 2.53E-06 chrX:150151567 rs3761504 23 152083947 0.2603 4.68E-06 4.68E-06 0.004431773 chrX:150151572 rs3761504 23 152083947 0.2893 1.10E-06 1.10E-06 0.001211155 chrX:150151580 rs3761504 23 152083947 0.4008 2.41E-09 2.41E-09 4.52E-06 chrX:150343016 rs3761504 23 152083947 0.3565 3.10E-08 3.10E-08 4.48E-05 chrX:150343097 rs3761504 23 152083947 0.3494 4.59E-08 4.59E-08 6.53E-05 chrX:150343148 rs3761504 23 152083947 0.4026 2.17E-09 2.17E-09 4.10E-06 chrX:150343150 rs3761504 23 152083947 0.4304 3.95E-10 3.95E-10 8.83E-07 chrX:150343154 rs3761504 23 152083947 0.3566 3.09E-08 3.09E-08 4.48E-05 chrX:150884503 rs3761504 23 152083947 0.175 0.0002549 0.0002549 0.147444369 chrX:151649158 rs3761504 23 152083947 0.205 0.000135 0.000135 0.084677863 chrX:151806016 rs3761504 23 152083947 0.4221 6.66E-10 6.66E-10 1.41E-06 chrX:151806054 rs3761504 23 152083947 0.2775 2.00E-06 2.00E-06 0.002087758 chrX:151807270 rs3761504 23 152083947 0.2413 4.35E-05 4.35E-05 0.031979991 chrX:151807272 rs3761504 23 152083947 0.2605 2.26E-05 2.26E-05 0.017626487 chrX:151807274 rs3761504 23 152083947 0.3277 9.48E-07 9.48E-07 0.001046353 chrX:151807316 rs3761504 23 152083947 0.3087 2.77E-06 2.77E-06 0.002744798 chrX:151998770 rs3761504 23 152083947 0.2009 0.0002297 0.0002297 0.13423745 chrX:152160951 rs3761504 23 152083947 0.1916 0.000237 0.000237 0.137970204 chrX:152712189 rs3761504 23 152083947 0.1822 0.0004366 0.0004366 0.231034761 chrX:152951690 rs3761504 23 152083947 0.2121 4.69E-05 4.69E-05 0.033753134 chrX:152951702 rs3761504 23 152083947 0.2101 5.14E-05 5.14E-05 0.036357583 chrX:152952364 rs3761504 23 152083947 0.2795 1.19E-05 1.19E-05 0.010190848 chrX:153046764 rs3761504 23 152083947 0.2257 7.29E-05 7.29E-05 0.04974146 chrX:153046767 rs3761504 23 152083947 0.2318 4.89E-05 4.89E-05 0.034841669 chrX:153058860 rs3761504 23 152083947 0.2091 0.0002401 0.0002401 0.139416939 chrX:153094895 rs3761504 23 152083947 0.3286 1.42E-07 1.42E-07 0.000185308 chrX:153094979 rs3761504 23 152083947 0.3439 6.22E-08 6.22E-08 8.67E-05 chrX:153094992 rs3761504 23 152083947 0.3469 5.25E-08 5.25E-08 7.38E-05 chrX:153095000 rs3761504 23 152083947 0.4404 2.12E-10 2.12E-10 5.02E-07 chrX:153095008 rs3761504 23 152083947 0.4109 1.32E-09 1.32E-09 2.62E-06 chrX:153095013 rs3761504 23 152083947 0.3564 3.11E-08 3.11E-08 4.49E-05 chrX:153095031 rs3761504 23 152083947 0.3584 2.78E-08 2.78E-08 4.08E-05 chrX:153095036 rs3761504 23 152083947 0.3973 2.98E-09 2.98E-09 5.43E-06 chrX:153095041 rs3761504 23 152083947 0.3482 7.61E-08 7.61E-08 0.000104952 chrX:153141052 rs3761504 23 152083947 0.1834 0.0001752 0.0001752 0.106220153 chrX:153145145 rs3761504 23 152083947 0.2541 6.35E-06 6.35E-06 0.005817588 chrX:153191067 rs3761504 23 152083947 0.2907 3.00E-06 3.00E-06 0.002959561 chrX:153191096 rs3761504 23 152083947 0.3562 1.23E-07 1.23E-07 0.000161607 chrX:153191197 rs3761504 23 152083947 0.3867 9.14E-09 9.14E-09 1.54E-05 chrX:153235365 rs3761504 23 152083947 0.222 3.84E-05 3.84E-05 0.028479018 chrX:153235411 rs3761504 23 152083947 0.3435 9.78E-08 9.78E-08 0.000131555 chrX:153235420 rs3761504 23 152083947 0.2717 3.72E-06 3.72E-06 0.003586486 chrX:153235423 rs3761504 23 152083947 0.1727 0.0003475 0.0003475 0.193362218 chrX:153284077 rs3761504 23 152083947 0.3401 9.45E-08 9.45E-08 0.000127506 chrX:153284096 rs3761504 23 152083947 0.17 0.0003524 0.0003524 0.194893101 chrX:153361902 rs3761504 23 152083947 0.2305 9.03E-05 9.03E-05 0.059547847 chrX:153534012 rs3761504 23 152083947 0.1744 0.0003219 0.0003219 0.180669164 chrX:153534026 rs3761504 23 152083947 0.2677 4.51E-06 4.51E-06 0.004283978 chrX:153534030 rs3761504 23 152083947 0.1967 0.0001206 0.0001206 0.07709449 chrX:153602056 rs3761504 23 152083947 0.3114 3.52E-07 3.52E-07 0.000423545 chrX:153602069 rs3761504 23 152083947 0.3452 5.78E-08 5.78E-08 8.09E-05 chrX:153602087 rs3761504 23 152083947 0.3584 2.78E-08 2.78E-08 4.08E-05 chrX:153602147 rs3761504 23 152083947 0.3133 3.20E-07 3.20E-07 0.000388938 chrX:153602173 rs3761504 23 152083947 0.333 1.12E-07 1.12E-07 0.000148949 chrX:153602182 rs3761504 23 152083947 0.4238 5.96E-10 5.96E-10 1.29E-06 chrX:153627683 rs3761504 23 152083947 0.35 4.44E-08 4.44E-08 6.33E-05 chrX:153627702 rs3761504 23 152083947 0.3736 1.18E-08 1.18E-08 1.95E-05 chrX:153627775 rs3761504 23 152083947 0.3094 3.91E-07 3.91E-07 0.000466267 chrX:153627782 rs3761504 23 152083947 0.3098 3.84E-07 3.84E-07 0.00045924 chrX:153627784 rs3761504 23 152083947 0.3504 4.35E-08 4.35E-08 6.22E-05 chrX:153627788 rs3761504 23 152083947 0.3665 1.76E-08 1.76E-08 2.73E-05 chrX:153628595 rs3761504 23 152083947 0.3167 2.67E-07 2.67E-07 0.000330954 chrX:153713942 rs3761504 23 152083947 0.2541 6.35E-06 6.35E-06 0.005817588 chrX:153713946 rs3761504 23 152083947 0.2968 7.52E-07 7.52E-07 0.000858446 chrX:153713952 rs3761504 23 152083947 0.2331 1.74E-05 1.74E-05 0.014140345 chrX:153713959 rs3761504 23 152083947 0.1691 0.0003321 0.0003321 0.185475805 chrX:153713966 rs3761504 23 152083947 0.235 1.60E-05 1.60E-05 0.013256066 chrX:153713982 rs3761504 23 152083947 0.2404 1.23E-05 1.23E-05 0.010530354 chrX:153978033 rs3761504 23 152083947 0.2877 1.19E-06 1.19E-06 0.001303667 chrX:153978288 rs3761504 23 152083947 0.2058 0.0002131 0.0002131 0.12518162 chrX:153978521 rs3761504 23 152083947 0.3729 1.23E-08 1.23E-08 2.01E-05 chrX:153978540 rs3761504 23 152083947 0.3639 2.04E-08 2.04E-08 3.14E-05 chrX:153978552 rs3761504 23 152083947 0.4089 1.48E-09 1.48E-09 2.94E-06 chrX:154003098 rs3761504 23 152083947 0.2748 2.29E-06 2.29E-06 0.002324299 chrX:154032859 rs3761504 23 152083947 0.1611 0.0004751 0.0004751 0.246800028 chrX:154033288 rs3761504 23 152083947 0.3881 1.09E-08 1.09E-08 1.81E-05 chrX:154033302 rs3761504 23 152083947 0.3755 2.19E-08 2.19E-08 3.34E-05 chrX:154035783 rs3761504 23 152083947 0.224 2.69E-05 2.69E-05 0.020533549 chrX:154035825 rs3761504 23 152083947 0.2813 1.65E-06 1.65E-06 0.001763837