Table 3. Celiac risk variants correlated with cis gene expression.

SNPa	Chr	SNP positionb	Probe Centre Positionb	Illumina ArrayAddressID	Expression datasetc	Gene name	eQTL P valued
Loci with genome-wide significant evidence (Pcombined <5 × 10−8)
rs3748816	1	2516606	2412221	650452	HT-12	PLCH2	1.66 × 10−5
rs3748816	1	2516606	2482955	6520725	Ref-8v2 + HT-12	TNFRSF14	1.30 × 10−3
rs3748816	1	2516606	2510429	6250338	Ref-8v2	C1orf93	1.16 × 10−4
rs3748816	1	2516606	2533115	2070246	Ref-8v2 + HT-12	MMEL1	1.03 × 10−20
rs296547	1	199158760	198880146	1300279	Ref-8v2 + HT-12	DDX59	2.45 × 10−5
rs842647	2	60972975	61263810	1170220	Ref-8v2 + HT-12	AHSA2	3.30 × 10−10
rs13003464e	2	61040333	61263810	1170220	Ref-8v2 + HT-12	AHSA2	6.39 × 10−11
rs3816281f	2	68461451	68461957	4810020	Ref-8v2 + HT-12	PLEK	7.97 × 10−26
rs917997	2	102437000	102418571	6520180	Ref-8v2 + HT-12	IL18RAP	7.35 × 10−87
rs13010713	2	181704290	181593865	1780433	HT-12	UBE2E3	4.93 × 10−5
rs13098911	3	46210205	45964449	6550333	Ref-8v2 + HT-12	CXCR6	9.66 × 10−6
rs13098911	3	46210205	46255176g	2190671	HT-12	CCR3	5.50 × 10−10
rs13098911	3	46210205	46255176g	7570670	Ref-8v2	CCR3	5.69 × 10−4
rs6441961d	3	46327388	46255176h	2190671	HT-12	CCR3	2.87 × 10−19
rs6441961d	3	46327388	46255176h	7570670	Ref-8v2	CCR3	1.02 × 10−4
rs11922594f	3	120608512	120683364i	6550288	Ref-8v2 + HT-12	KTELC1	5.09 × 10−17
rs11922594f	3	120608512	120683364i	3850161	Ref-8v2 + HT-12	KTELC1	7.34 × 10−6
rs10806425	6	90983333	90878075	3520349	HT-12	BACH2	1.92 × 10−3
rs1738074	6	159385965	159380068	5890739	Ref-8v2 + HT-12	TAGAP	1.99 × 10−3
rs1738074	6	159385965	159381094 j	5360364	HT-12	TAGAP	3.23 × 10−4
rs1738074	6	159385965	159381094 j	4860242	HT-12	TAGAP	2.18 × 10−3
rs1250552	10	80728033	80622540	2450131	Ref-8v2 + HT-12	ZMIZ1	1.80 × 10−3
rs653178	12	110492139	110399552	6560301	Ref-8v2 + HT-12	SH2B3	9.24 × 10−12
rs653178	12	110492139	110710447	840253	Ref-8v2 + HT-12	ALDH2	1.44 × 10−4
rs653178	12	110492139	110894406 k	2070736	HT-12	TMEM116	3.68 × 10−4
rs653178	12	110492139	110894406 k	3190129	Ref-8v2	TMEM116	1.51 × 10−3
rs12928822	16	11311394	11335627	4540072	Ref-8v2 + HT-12	C16orf75	1.02 × 10−8
rs4819388	21	44471849	44049567	7200373	Ref-8v2	RRP1	2.62 × 10−3
Loci with suggestive evidence (either A. 10−6>Pcombined>5×10−8 and/or B. PGWAS<10−4 and Pfollow-up<0.01)
rs12727642	1	7969259	7956138	610193	Ref-8v2 + HT-12	PARK7	9.76 × 10−15
rs864537	1	165678008	165710482 l	6290400	Ref-8v2 + HT-12	CD247	1.77 × 10−9
rs864537	1	165678008	165710482 l	3890689	HT-12	CD247	2.93 × 10−7
rs6974491	7	37341035	37157761	2750154	Ref-8v2 + HT-12	ELMO1	5.40 × 10−6
rs2074404	17	42220599	41824345	3520672	Ref-8v2 + HT-12	LRRC37A	1.17 × 10−4
rs2074404	17	42220599	42106695 m	5260138	Ref-8v2 + HT-12	NSF	1.20 × 10−5
rs2074404	17	42220599	42106695 m	1410484	HT-12	NSF	4.28 × 10−4
rs2074404	17	42220599	42223012	4070615	HT-12	WNT3	2.77 × 10−3
rs2074404	17	42220599	42485154	4880037	HT-12	LOC388397	1.78 × 10−9
rs2298428	22	20312892	20308188	1230242	Ref-8v2 + HT-12	UBE2L3	1.96 × 10−90
rs5979785	X	12881445	12842944 n	6480360	Ref-8v2 + HT-12	TLR8	3.88 × 10−13
rs5979785	X	12881445	12842944 n	3390612	Ref-8v2 + HT-12	TLR8	1.07 × 10−7

See Supplementary Figures 2 & 3 for detailed results, and Supplementary Table 3 for more detail of Illumina expression probes.

^aWe tested the SNP with the strongest association from 34 of 39 non-HLA loci (P_combined<10⁻⁶, Table 2), Hap300 proxy SNPs for 4 further loci, and a second independently associated SNP from 6 loci, for correlation with gene expression in PAXgene blood RNA in up to 1,349 individuals. 1 locus (containing ETS1) where an adequate proxy SNP was not available was not included for the eQTL analysis. SNP-gene expression correlations were tested for probes within a 1Mb window. Results are presented for SNPs showing significant correlations with cis gene expression after controlling false discovery rate at 5% (corresponding to P<0.0028).

^bAll chromosomal positions are based on NCBI build-36 coordinates. Probe centre position was determined by re-mapping probe sequences to the human transcriptome and calculated from the mid-point of the transcript start and transcript end positions in genomic co-ordinates.

^c‘HT-12’ comprise 1240 individuals with blood gene expression assayed using Illumina Human HT-12v3 arrays, ‘Ref-8v2’ comprise 229 individuals with blood gene expression assayed using Illumina Human-Ref-8v2 arrays (Online Methods).

^dSpearman rank correlation of genotype and residual variance in transcript expression. Meta-analysis eQTL P value shown if both datasets had identical probes.

^eSecond, independently associated SNP from this locus.

^fProxy SNP, r²=0.61 in HapMap CEU with most associated SNP rs11712165.

^gDifferent Illumina probe sequences with the same Probe Centre Position.

^hDifferent Illumina probe sequences with the same Probe Centre Position.

ⁱDifferent Illumina probe sequences with the same Probe Centre Position.

^jDifferent Illumina probe sequences with the same Probe Centre Position.

^kDifferent Illumina probe sequences with the same Probe Centre Position.

^lDifferent Illumina probe sequences with the same Probe Centre Position.

^mDifferent Illumina probe sequences with the same Probe Centre Position.

ⁿDifferent Illumina probe sequences with the same Probe Centre Position.