Noi/NOTES/2012-4-26

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mQTL analysis on UCLA-SZ data set (no CpG-SNP)

  • 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


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

  • 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 3,202 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

  • 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
  • 85kb 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
  • 91kb CpG-SNP distance
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