GWAS-related meQTLs across different cancer types

We identified 2,214,458 meQTLs that overlap with GWAS linkage disequilibrium (LD) regions (r² ≥ 0.5).



e.g., "BLCA"
e.g., "rs10000012"
e.g., "CTBP1"
e.g., "cg02980000"
Cancer type
QTL type
tagSNP
LD
SNP ID
SNP position (hg19)
alleles
probe
Gene position (hg19)
Gene
Beta
t-stat
r
p-value
Traits
BLCA cis rs16973500 0.808 rs112121746 chr16:71874983 G/A cg00732059 chr16:71740210 PHLPP2 -0.5 -6.52 -0.32 2.25E-10 Response to anti-TNF therapy in rheumatoid arthritis;Attention deficit hyperactivity disorder and conduct disorder;
BLCA cis rs9937943 0.72 rs112685216 chr16:74609517 G/A cg01733217 chr16:74700730 RFWD3 0.55 6.46 0.31 3.24E-10 Neutrophil percentage of white cells;
BLCA cis rs9399135 0.684 rs1135205 chr6:135281795 C/T cg24558204 chr6:135376177 HBS1L 0.6 9.52 0.44 2.11E-19 Red blood cell count;
BLCA cis rs7582720 1 rs114123510 chr2:203831212 T/A cg15057621 chr2:203777863 WDR12;ALS2CR8 0.89 9.49 0.44 2.61E-19 Coronary artery disease or ischemic stroke;Coronary artery disease or large artery stroke;
BLCA cis rs6582630 0.502 rs11522899 chr12:38270637 T/C cg13010199 chr12:38710504 ALG10B 0.67 10.93 0.49 2.37E-24 Drug-induced liver injury (flucloxacillin);
BLCA cis rs6502050 0.723 rs11650635 chr17:80083816 T/C cg23985595 chr17:80112537 CCDC57 0.37 7.2 0.35 3.26E-12 Life satisfaction;
BLCA cis rs12950390 0.853 rs11655112 chr17:45856563 T/C cg03474202 chr17:45855739 NA -0.31 -6.69 -0.32 8.1E-11 IgG glycosylation;
BLCA cis rs6466055 0.72 rs1204058 chr7:104958129 T/G cg04380332 chr7:105027541 SRPK2 0.52 8.5 0.4 4.52E-16 Schizophrenia;
BLCA cis rs208520 0.69 rs12189780 chr6:66759619 G/A cg07460842 chr6:66804631 NA 0.94 16.21 0.64 2.6E-45 Exhaled nitric oxide output;
BLCA cis rs208520 0.69 rs12213581 chr6:66735818 T/C cg07460842 chr6:66804631 NA 0.93 15.74 0.63 2.4E-43 Exhaled nitric oxide output;
BLCA cis rs873946 0.564 rs12263364 chr10:134555548 G/T cg27297192 chr10:134578999 INPP5A 0.35 6.74 0.33 5.75E-11 Gestational age at birth in labor-initiated deliveries (child effect);Gestational age at birth (child effect);
BLCA cis rs4423214 1 rs12278461 chr11:71182185 C/T cg24826892 chr11:71159390 DHCR7 0.42 6.05 0.3 3.42E-9 Vitamin D levels;
BLCA cis rs6582630 0.519 rs12372510 chr12:38293074 T/C cg26384229 chr12:38710491 ALG10B 0.74 13.59 0.57 1.48E-34 Drug-induced liver injury (flucloxacillin);
BLCA cis rs3096299 0.685 rs12446145 chr16:89542695 C/T cg06640241 chr16:89574553 SPG7 0.81 14.81 0.6 1.7E-39 Multiple myeloma (IgH translocation);
BLCA cis rs769267 0.965 rs12460764 chr19:19431963 G/T cg20644253 chr19:19431407 KIAA0892;SF4 -0.54 -8.24 -0.39 2.81E-15 Tonsillectomy;