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 rs9309473 1 rs1881245 chr2:73649928 G/A cg20560298 chr2:73613845 ALMS1 -0.62 -8.32 -0.39 1.59E-15 Metabolite levels;
BLCA cis rs3008870 1 rs1925408 chr1:67365034 C/T cg08660285 chr1:67390436 MIER1;WDR78 1.07 18.36 0.69 2.26E-54 Lymphocyte percentage of white cells;
BLCA cis rs7017914 0.934 rs1993862 chr8:71579362 A/G cg08952539 chr8:71862263 NA 0.33 6.26 0.31 1.03E-9 Bone mineral density;
BLCA cis rs4665809 1 rs2053367 chr2:26293413 T/C cg04944784 chr2:26401820 FAM59B -0.62 -8.56 -0.4 2.76E-16 Gut microbiome composition (summer);
BLCA cis rs11124272 0.717 rs2082185 chr2:32155175 A/G cg02381751 chr2:32503542 YIPF4 -0.56 -7.4 -0.35 8.76E-13 Interleukin-18 levels;
BLCA cis rs4722166 0.63 rs2091115 chr7:22810166 G/T cg26061582 chr7:22766209 IL6 0.53 9.38 0.43 6.33E-19 Lung cancer;
BLCA cis rs806215 1 rs2106186 chr7:127241352 G/C cg25922125 chr7:127225783 GCC1 0.49 6.61 0.32 1.28E-10 Type 2 diabetes;
BLCA cis rs523522 0.962 rs2168319 chr12:120933217 C/T cg27279351 chr12:120934652 DYNLL1 0.67 9.95 0.45 6.97E-21 High light scatter reticulocyte count;
BLCA cis rs3617 0.625 rs2239548 chr3:52854186 A/C cg11645453 chr3:52864694 ITIH4 0.29 6.88 0.33 2.52E-11 Red blood cell count;Autism spectrum disorder or schizophrenia;
BLCA cis rs12893668 0.572 rs2273175 chr14:104160141 T/C cg24130564 chr14:104152367 KLC1 -0.41 -6.05 -0.3 3.48E-9 Reticulocyte count;
BLCA cis rs9381040 0.61 rs2294694 chr6:41046177 G/A cg04346459 chr6:41068666 NFYA;LOC221442 -0.36 -6.09 -0.3 2.71E-9 Alzheimer's disease (late onset);
BLCA cis rs6061231 0.631 rs2427317 chr20:60975725 C/T cg15674680 chr20:60982522 CABLES2 0.42 6.1 0.3 2.65E-9 Colorectal cancer;
BLCA cis rs28386778 0.897 rs2584617 chr17:61925298 C/T cg06873352 chr17:61820015 STRADA 0.62 12.69 0.55 5.37E-31 Prudent dietary pattern;
BLCA cis rs28386778 0.831 rs2584618 chr17:61923611 T/C cg23090583 chr17:61904693 PSMC5;FTSJ3 1.08 22 0.75 9.42E-70 Prudent dietary pattern;
BLCA cis rs1801251 0.711 rs2592117 chr2:233735693 C/T cg25237894 chr2:233734115 C2orf82 -0.59 -11.1 -0.49 5.3E-25 Coronary artery disease;