Slides I showed at the meeting organized by the GTEx folks at the Broad in Oct 2011.

1. eQTLs as playground
Chris Cotsapas
cotsapaslab.info

3. Co-occurrence in Denmark
T1D Celiac MS CD Ps RA SLE
T1D -- 108 147 217 442 616 46
Celiac 4.2 -- 6 101 13 21 3
MS 1.2 1.0 -- 36 39 43 14
CD 1.7 16.7 1.2 -- 95 148 13
Ps 3.2 2.3 1.4 3.3 -- 372 19
RA 1.9 1.7 0.8 2.8 6.4 -- 226
SLE 2.2 2.7 2.5 2.5 4.1 24.0 --
Lower tri is pairwise OR
Upper tri is overlapping cases
condensed from
Eaton et al J Autoimm 2007

4. Cross-phenotype meta-analysis
l=1 l¹1 l¹1
−log(p) −log(p) −log(p)
L(data | λ≠1)
SCPMA ~
L(data | λ=1)
Cotsapas et al, PLoS Genetics

5. 18.4
−log(p)
OLIG3 TNFAIP3
0
rs6920220 rs5029939
rs10499194
RA rs2230926
Celiac rs2327832
SLE
Psoriasis rs9321619 rs610604
MS
137.9 138 138.1 138.2
Position on Chr 6q23.3 (Mb)

6. 18.4
−log(p)
Shared/distinct alleles: fine mapping OLIG3 TNFAIP3
0
rs6920220 rs5029939
rs10499194
RA rs2230926
Celiac rs2327832
SLE
Psoriasis rs9321619 rs610604
MS
137.9 138 138.1 138.2
Position on Chr 6q23.3 (Mb)
1
8
−1
Spearman's r (f = 10; d = 5)
6
MS
−log10 (p)
CD
4
2
0
199.0 199.1 199.2 199.3 199.4 199.5
Chr 1 (Mb)

7. TF binding site variation
Lizzie Rossin, Martha Bulyk, Mark
Daly