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Table 1 Concordant SNPs recovered from TCGA and AGS data, and associated genes

From: Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk

SNP chr gene location left_gene right_gene Genes correlated with SNP (R2) AGS (P1) TCGA (P2) FDR
rs2736100+ 5 TERT 5p15.33 SLC6A18 CLPTM1L NA 5.30E-13 2.66E-04 7.38E-09
rs1412829*+ 9 CDKN2A/B 9p21.3 LOC100130239 LOC729983 CDKN2A(1.0);
CDKN2B(1.0);
C9orf53(0.87)
3.40E-08 3.26E-03 1.27E-03
rs2157719 9 CDKN2A/B 9p21.3 LOC100130239 LOC729983 CDKN2A(0.97);
CDKN2B(0.97);
C9orf53(0.93);
RP11-145E5.4(0.97);
LOC100130239(0.97)
6.10E-08 8.00E-03 5.40E-03
rs1063192+ 9 CDKN2A/B 9p21.3 CDKN2A LOC100130239 CDKN2A(0.97);
CDKN2B(0.97);
C9orf53(0.93);
RP11-145E5.4(0.97);
LOC100130239(0.97)
9.20E-08 8.31E-03 7.95E-03
rs4977756+ 9 CDKN2A/B 9p21.3 LOC100130239 LOC729983 CDKN2A(0.97);
CDKN2B(0.97);
C9orf53(0.93);
RP11-145E5.4(0.97);
LOC100130239(0.97)
4.20E-07 1.12E-02 3.90E-02
rs7530361 1 SLC35A3 1p21.2 LOC730081 HIAT1 SLC35A3(1.0);
CCDC76(0.95);
HIAT1(1.0);
LRRC39(0.95);
SASS6(1.0);
BRI3P1(0.95);
LOC730081(1.0)
6.50E-07 2.19E-06 4.29E-05
rs501700 1 HIAT1 1p21.2 SLC35A3 SASS6 DBT(0.95);
RTCD1(0.89);
SLC35A3(1.0);
CCDC76(0.95);
HIAT1(1.0);
LRRC39(0.94);
SASS6(1.0);
BRI3P1(0.94);
LOC730081(1.0)
7.10E-07 5.99E-06 9.72E-05
rs1920116 3 LRRC31 3q26.2 LRRIQ4 KRT18P43 MYNN(0.89);
LRRC31(1);
ARPM1(0.85);
KRT18P43(1)
LRRC34(1)
1.40E-06 2.88E-03 2.81E-02
rs506044 1 SASS6 1p21.2 SASS6 LRRC39 DBT(1.0);
RTCD1(0.89);
SLC35A3(0.95);
CCDC76(1.0);
HIAT1(1.0);
LRRC39(1.0);
SASS6(1.0);
BRI3P1(0.95);
LOC730081(0.94)
2.10E-06 2.45E-06 1.57E-04
rs640030 1 SASS6 1p21.2 HIAT1 CCDC76 DBT(1.0);
RTCD1(0.89);
SLC35A3(0.95);
CCDC76(1.0);
HIAT1(1.0);
LRRC39(1.0);
SASS6(1.0);
BRI3P1(0.95);
LOC730081(0.94)
2.40E-06 2.57E-06 1.86E-04
rs687513 1 SASS6 1p21.2 SASS6 LRRC39 DBT(0.95);
RTCD1(0.90);
SLC35A3(0.94);
CCDC76(1.0);
HIAT1(1.0);
LRRC39(1.0);
SASS6(1.0);
BRI3P1(0.95);
LOC730081(0.90)
2.90E-06 3.91E-06 3.03E-04
rs3779505 7 ITGB8 7p15.3 MACC1 LOC100130234 ITGB8(1.0) 3.00E-06 5.67E-04 1.35E-02
  1. Concordant SNPs (FDR < 0.05) recovered from TCGA (n = 97) and AGS data (n = 692), and associated genes. The blue boldface indicates the genes that are known to be cancer-associated.
  2. + reported by Shete et, al.
  3. * reported by Wrensch et, al. and validated on Mayo Clinic population
  4. FDR: Bonferroni corrected False Discovery Rate = 3 × 105P12 (eq. 1)