Table 2 : Comparison of previously replicated loci, and genomic regions with the strongest
and moderate association signals between prGWAS and GWAS.


Table 2a
Collection SNP prGWAS P-value (k) Genotypic
P-value1
n=250 n=500 n=1000
CAD rs4420638 ND ND ND 1.7x10-1
CD rs17221417 1.33x10-15 (3) 9.46x10-9 (2) 1.49x10-13 (3) 4.0x10-11
  rs11805303 1.66x10-10 (9) 1.77x10-10 (6) 6.38x10-13 (5) 5.9x10-12
RA rs615672 3.99x10-20 (7) 7.24x10-15 (9) 6.97x10-34 (3) 7.5x10-27
  rs6679677 1.09x10-4 (9) 2.38x10-25 (8) 2.09x10-26 (2) 5.6x10-25
T1D rs3087243 a a a 1.8x10-5
  rs2104286 2.25x10-2 (8) 8.43x10-7 (2) 6.26x10-10 (2) 4.3x10-5
  rs3788964 a a 1.75x10-3 (2) 7.6x10-3
  rs6679677 1.089x10-8 (9) 7.33x10-23 (9) 2.04x10-30 (5) 5.4x10-26
  rs9270986 3.74x10-136 (4) 6.31x10-148 (2) 3.18x10-301 (2) 2.3x10-122
T2D rs1801282 a 3.88x10-3 (3) 8.07x10-4 (2) 5.4x10-3
  rs4506565 1.41x10-5 (9) 7.32x10-4 (9) 3.24x10-14 (3) 5.1x10-12
  rs5215 a 4.67x10-3 (2) 6.86x10-3 (4) 5.6x10-3

Table 2b
Collection SNP prGWAS P-value (k) Genotypic
P-value1
n=250 n=500 n=1000
BD rs420259 * a 3.82x10-8 (10) 6.29x10-8
CAD rs1333049 8.39x10-15 (3) 1.58x10-12 (4) 1.51x10-13 (3) 1.16x10-13
CD rs11805303 1.66x10-10 (9) 3.19x10-12 (7) 6.38x10-13 (5) 5.85x10-12
  rs10210302 3.76x10-14 (10) 3.17x10-15 (4) 6.50x10-17 (3) 5.26x10-14
  rs9858542 2.53x10-6 (9) 1.02x10-7 (10) 1.94x10-8 (7) 3.58x10-8
  rs17234657 1.34x10-28 (3) 8.01x10-13 (4) 3.73x10-13 (2) 1.99x10-12
  rs1000113 * * 2.03x10-7 (7) 3.15x10-7
  rs10761659 a 9.93x10-5 (9) 5.60x10-5 (8) 1.75x10-6
  rs10883365 * * * 5.82x10-8
  rs17221417 * 1.33x10-15 (3) 1.49x10-13 (3) 3.98x10-11
  rs2542151 a 4.17x10-5 (4) 5.48x10-9 (4) 2.03x10-7
RA rs6679677 * 2.38x10-25 (8) 2.09x10-26 (4) 5.55x10-25
  rs6457617 3.46x10-64 (10) 3.21x10-78 (5) 1.21x10-96 (3) 5.18x10-75
T1D rs6679677 * 7.33x10-23 (10) 2.04x10-30 (5) 5.43x10-26
  rs9272346 1.30x10-132 (8) 3.92x10-162 (4) 1.19x10-128 (2) 5.47x10-134
  rs11171739 a 4.71x10-8 (9) 2.45x10-11 (5) 9.71x10-11
  rs17696736 * 6.07x10-14 (4) 5.33x10-24 (2) 1.51x10-14
  rs12708716 4.90x10-7 (8) * 4.26x10-7 (10) 4.92x10-7
T2D rs9465871 a a a 3.34x10-7
  rs4506565 * * 3.24x10-14 (3) 5.05x10-12
  rs9939609 1.14x10-9 (4) 1.23x10-6 (4) 3.40x10-11 (3) 1.91x10-7

Table 2c
Collection SNP prGWAS P-value (k) Genotypic
P-value1
n= 250 n=500 n=1000
BD rs4027132 8.33x10-6 (8) a 9.88x10-8 (4) 9.68x10-6
  rs7570682 a a 7.58x10-4 (9) 1.64x10-5
  rs1375144 7.7x10-6 (4) 5.93x10-5 (5) 9.64x10-5 (7) 1.31x10-5
  rs2953145 a * 3.91x10-5 (3) 6.57x10-6
  rs4276227 a 5.61x10-9 (2) * 2.62x10-5
  rs683395 ND ND ND 5.11x10-6
  rs6458307 ND ND ND 4.35x10-6
  rs2609653 ND ND ND b
  rs10982256 4.57x10-6 (4) * * 4.41x10-5
  rs10134944 a * 1.68x10-5 (10) 6.89x10-6
  rs11622475 a a 7.58x10-7 (8) 8.14x10-6
  rs1344484 a * 9.99x10-5 (5) 1.03x10-5
  rs3761218 ND ND ND 6.71x10-6
CAD rs17672135 * 6.07x10-10 (9) 2.51x10-4 (5) 2.35x10-6
  rs383830 * * 7.92x10-5 (4) 1.34x10-5
  rs6922269 a * 1.91x10-4 (6) 1.50x10-5
  rs8055236 a 2.09x10-5 (8) 1.26x10-6 (2) 5.60x10-6
  rs7250581 a a 2.48x10-6 (3) 2.50x10-5
  rs688034 a * 3.77x10-6 (5) 3.75x10-6
CD rs12037606 1.08x10-5 (6) 9.54x10-5 (5) * 1.09x10-5
  rs6596075 - 1.04x10-6 (3) * 3.19x10-6
  rs6908425 * a a 1.10x10-5
  rs9469220 * 2.99x10-6 (3) 1.82x10-8 (2) 2.28x10-6
  rs7753394 a 4.34x10-5 (2) 6.06x10-5 (2) 2.59x10-5
  rs7807268 a 1.60x10-5 (7) 2.36x10-7 (2) 4.42x10-6
  rs6601764 * 9.84x10-7 (8) 4.64x10-6 (8) 8.95x10-6
  rs8111071 a 4.88x10-5 (10) 1.45x10-5 (6) 1.75x10-5
HT rs2820037 a * * 7.66x10-7
  rs6997709 a 3.58x10-5 (5) 5.70x10-5 (4) 4.36x10-5
  rs7961152 a * 3.65x10-4 (9) 3.03x10-5
  rs11110912 a a 1.45x10-5 (6) 1.94x10-5
  rs1937506 a a * 4.53x10-5
  rs2398162 a 7.89x10-4 (10) 9.06x10-4 (8) 5.67x10-5
RA rs6684865 a - 9.87x10-5 (6) 3.14x10-5
  rs11162922 a 9.50x10-6 (5) 2.13x10-6 (4) a
  rs3816587 a * a 9.25x10-6
  rs6920220 a a 6.44x10-5 (5) 1.58x10-5
  rs11761231 a * 4.33x10-6 (3) 2.65x10-6
  rs2104286 * 2.44x10-5 (5) 2.85x10-11 (2) 2.52x10-5
  rs9550642 3.24x10-116 (2) 5.19x10-79 (2) 2.31x10-101 (3) 3.90x10-5
  rs2837960 * * - 1.68x10-6
  rs743777 * - 2.67x10-3 (8) 1.15x10-6
T1D rs2639703 a 3.11x10-4 (8) * 1.74x10-5
  rs17388568 a a 3.68x10-9 (4) 3.27x10-6
  rs2544677 a a a 4.43x10-5
  rs17166496 * a a 5.20x10-6
  rs2104286 a 8.43x10-7 (2) 6.26x10-10 (2) 4.32x10-5
  rs11052552 1.80x10-7 (10) 1.40x10-3 (9) a 7.24x10-7
  rs2542151 * * 2.47x10-6 (4) 1.16x10-5
T2D rs4655595 a 1.49x10-6 (5) 5.24x10-9 (2) 1.33x10-5
  rs6718526 1.39x10-5 (7) 2.31x10-7 (6) 1.79x10-9 (2) 1.16x10-5
  rs358806 ND ND ND 3.05x10-6
  rs7659604 a a * 9.42x10-6
  rs9326506 a * * 2.99x10-5
  rs12304921 ND ND ND 7.07x10-6
  rs1495377 a * 2.51x10-7 (5) 6.52x10-6
  rs2930291 * 7.15x10-6 (7) * 4.40x10-5
  rs2903265 * * 1.89x10-5 (9) 4.98x10-5

(a) Comparison of association at previously replicated loci between prGWAS and the GWAS using the full
data. Reported P-values in prGWAS are those closer to the P-values found with the full data.
(b) Comparison of regions with the strongest association signals between prGWAS and Burton et al. [6]
as a function of the master plate’s sample size. Reported P-values in prGWAS are those closer to the
P-values found with the full data.
(c) Comparison of regions of the genome showing moderate association in prGWAS and the GWAS using
the full WTCCC data. Reported P-values in prGWAS are those closer to the P-values found with the full data.
aNot statistically significant.
ND=Not determined as a consequence of not passing quality control (see Methods).
SNP=Single nucleotide polymorphism; Chr=Chromosome; n=sample size of the master plate (see
Methods); k=number of DNA pools being combined. BD=Bipolar disorder; CAD=Coronary artery
disease; CD=Conduct disorder; RA=Rheumatoid arthritis; HT=Hypertension; T1D=Type 1 diabetes;
T2D=Type 2 diabetes.
*Statistically significant in prGWAS but the resulting combined P-value was higher than that obtained
using the full data set.
1As reported in Table 2. of Burton et al [6].

Arcos-Burgos et al.Molecular Biology and Genetic Engineering  2015 3:1DOI : 10.7243/2053-5767-3-1