Table 1.

Top Transcript-SNP Pairs with a Significant Effect of Diagnosis

Probe IDa	Symbolb	Chr.c	Bp Positiond	Best SNPe	S_Chr.f	S_Pos.g	Otherh	Loc.i	Raw p Valuej	1K p Valuek	Inter p Valuel	r2 CAm	r2 COn	Dir.o
GI_34147330-S	ABDH12	20	25.2–25.3	rs6050598	20	25.3	40	cis	1.540 × 10−65	9.990 × 10−4	3.770 × 10−2	0.44	0.38	+
GI_14149802-S	ANKRD27	19	37.8–37.9	rs259228	19	37.8	13	cis	1.190 × 10−31	9.990 × 10−4	4.160 × 10−2	0.17	0.31	-
GI_14916517-S	AP3M1	10	75.6	rs26133	5	14.2	1	trans	3.280 × 10−9	1.500 × 10−2	7.080 × 10−7	0.13	−0.05	+/−
GI_38261968-S	APG12L	5	115.2	rs2483589	10	116.4	1	trans	7.930 × 10−9	2.000 × 10−2	9.490 × 10−4	0.12	−0.04	-
GI_29739147-S	ARL16	17	77.3	rs6565624	17	77.3	3	cis	4.360 × 10−12	9.990 × 10−4	4.520 × 10−2	0.04	0.13	-
GI_38327635-S	C14orf4	14	76.6	rs1120277	14	76.5	0	cis	1.840 × 10−27	9.990 × 10−4	2.900 × 10−2	0.08	0.27	-
GI_23346408-S	C20orf111	20	42.3	a-2038955	1	19.6	0	trans	2.040 × 10−9	2.000 × 10−2	3.440 × 10−6	0.14	−0.05	−/+
GI_25092657-S	C7orf27	7	2.5–2.6	rs3936086	16	13.6	1	trans	5.520 × 10−9	1.600 × 10−2	1.050 × 10−6	0.15	−0.05	−/+
GI_37059735-S	CWF19L1	10	102	rs11594333	10	101.9	6	cis	4.650 × 10−11	9.990 × 10−4	7.120 × 10−2	−0.01	0.13	+
GI_39995081-S	FLJ20303	5	6.7	rs4701742	5	66.7	10	cis	1.180 × 10−51	9.990 × 10−4	5.820 × 10−4	0.24	0.41	+
GI_32698961-S	GDPD1	17	54.7	rs7223491	17	54.6	5	cis	5.770 × 10−15	9.990 × 10−4	3.110 × 10−2	0.15	0.01	-
GI_30061497-I	GGTL3	20	32.9	rs6087619	20	32.8	23	cis	2.220 × 10−33	9.990 × 10−4	4.230 × 10−2	0.14	0.33	-
GI_22095346-S	IGSF4	11	114.5–114.9	rs7125361	11	114.6	5	cis	3.020 × 10−26	9.990 × 10−4	1.270 × 10−2	0.24	0.14	-
GI_29171690-I	ILVBL	19	15.1	rs11851301	14	94.2	0	trans	1.780 × 10−9	5.990 × 10−3	2.990 × 10−3	0.12	−0.05	-
GI_37059782-S	KIAA0980	20	25.4–25.5	rs6132819	20	25.2	35	cis	1.750 × 10−29	9.990 × 10−4	2.580 × 10−2	0.29	0.15	+
GI_41393558-I	KIF1B	1	10.2–10.4	rs12120191	1	10.3	22	cis	1.530 × 10−79	9.990 × 10−4	3.530 × 10−2	0.5	0.41	-
GI_42658911-S	LOC401470	8	93.2	rs11171739	12	54.8	5	trans	4.540 × 10−58	9.990 × 10−4	3.120 × 10−2	0.48	0.27	+
GI_38455399-S	MADH5	5	135.5	rs2483589	10	116.4	1	trans	3.010 × 10−8	2.100 × 10−2	1.090 × 10−3	0.12	−0.04	-
GI_5174552-S	MFAP1	15	41.9	rs17546037	5	7.3	1	trans	7.340 × 10−9	5.990 × 10−3	1.050 × 10−3	0.13	−0.04	-
GI_7662347-S	MONDOA	12	121.0–121.2	rs3741452	12	121.2	1	cis	2.620 × 10−28	9.990 × 10−4	3.550 × 10−5	0.04	0.32	-
GI_31881619-A	PPA2	4	106.5–106.6	rs2866799	4	106.7	19	cis	1.260 × 10−24	9.990 × 10−4	3.380 × 10−2	0.27	0.1	-
GI_45439315-I	PPIE	1	40	rs1180341	1	39.8	2	cis	3.260 × 10−14	9.990 × 10−4	2.800 × 10−2	0.21	0.02	-
GI_19557635-A	PPIL3	2	201.4–201.5	rs6715380	2	201.9	14	cis	2.340 × 10−12	9.990 × 10−4	2.470 × 10−2	0.02	0.13	-
GI_15011935-S	RPS26	12	54.7	rs11171739	12	54.8	5	cis	1.150 × 10−70	9.990 × 10−4	2.740 × 10−2	0.51	0.33	+
GI_7657430-S	SND1	7	127.1–127.5	rs1408015	13	106.9	1	trans	3.150 × 10−8	3.800 × 10−2	1.790 × 10−3	0.14	−0.05	+
GI_5730084-S	TCTEL1	6	159	rs10843090	12	28.1	0	trans	1.430 × 10−8	3.000 × 10−2	1.760 × 10−3	0.13	−0.04	+/−
GI_8922751-S	TYW1	7	66.1–66.3	rs6966142	7	66	8	cis	1.180 × 10−12	9.990 × 10−4	2.330 × 10−2	0	0.14	+
GI_41281748-I	ZNF323	6	28.4	rs149970	6	28.1	8	cis	8.350 × 10−10	6.990 × 10−3	2.510 × 10−2	0.12	−0.02	+

This table shows the list of transcript-SNP pairs that had transcript-specific empirically significant p values by our 2 df model and where there was a significant diagnosis interaction term. Listed is a subset of the effects, generated from the full list of associated transcript-SNP pairs (Table S5). Criteria for generation of subset includes: transcript-specific 2 df model empirical p value from 1000 simulations ≤ 0.05, gene-expression detection rate within both cases and controls ≥ 99%, SNP call rate ≥ 99% overall, minor-allele frequency ≥ 5% in cases and controls, no LD between eQTL SNP and any polymorphism in probe (r² < 0.8), and SNP accounting for 12% or greater of the variance in transcript expression in either cases of controls (adjusted r² in cases or controls ≥ 0.12). Genes are listed in alphabetical order. All data are also represented in Table S5.

^aGI illumina probe identifiers.

^bCorrelated transcripts.

^cTranscript chromosome.

^dTranscript position (listed in Mb).

^eSNP with the smallest 2 df model–corrected (1000 permutations) p value for that transcript (dbSNP or Affymetrix identifiers listed).

^fSNP chromosome.

^gSNP position (listed in Mb).

^hNumber of other SNPs with a 2 df model p value for the transcript that was significant after 1000 permutations (α = 0.05).

ⁱWhere the SNP was in cis or trans to the transcript.

^jUncorrected p value for the 2 df model.

^kp value after correction of the 2 df model using 1000 permutations.

^lp values for the interaction term in the 2 df model.

^mAdjusted correlation coefficients for the 2 df model in cases.

ⁿAdjusted correlation coefficients for the 2 df model in controls.

^oDirection of the effect as indicated by the sample-specific β values. A plus sign indicates positive correlation and a major allele associated with high expression, and a minus sign indicates negative correlation and a minor allele associated with high expression. “+/−” or “−/+” indicates that direction of effect is different in case and controls, with the data given as direction in cases/direction in controls. Note that the latter effects were seen in trans and suggest a more complex model for effect whereby the uncaptured intermediary acts differently within case and control samples.