Table 4.

Expression quantitative trait locus analysis for 11 out of the 14 WHR signals.

WHR SNP	Tissue	Gene	Effecta	WHR SNP association with transcript (P)		Transcript peak SNP b	r2c	Peak SNP association with transcript (P)
				Unadj.	Adj. for peak SNP			Unadj.	Adj. for WHR SNP
rs9491696	SAT-D	RSPO3	+	1.10E-07	0.03	rs1936795	0.26	2.20E-13	7.40E-08
rs984222	Omental	TBX15	+	7.90E-10	1.00	rs984222	1.00	7.90E-10	1.00
	Omental	WARS2	+	5.11E-36	0.03	rs10802075	0.27	1.31E-163	1.33E-88
	Subcutaneous fat	WARS2	+	1.67E-25	0.01	rs10802075	0.22	3.88E-110	1.01E-63
	Lymph.	WARS2	−	4.30E-18	5.47E-05	rs2645305	0.27	5.57E-40	6.88E-26
	Liver	WARS2	+	2.57E-17	0.07	rs1057990	0.26	6.69E-59	1.97E-32
	SAT-D	WARS2	+	1.10E-18	0.51	rs1057990	0.26	5.80E-130	5.80E-100
	Blood	WARS2	+	6.10E-17	0.11	rs1057990	0.26	6.30E-75	1.10E-54
rs1055144	SAT-D	AA553656d	−	1.20E-11	0.96	rs7798002	0.95	7.20E-12	0.32
	SAT-M	AA553656d	−	2.46E-07	0.65	rs1451385	0.77	5.93E-08	0.38
rs10195252	SAT-D	GRB14	+	4.40E-11	1.00	rs10195252	1.00	4.40E-11	1.00
	SAT-M	GRB14	+	5.51E-06	1.00	rs10184004	1.00	5.51E-06	1.00
	Omental	GRB14	+	1.02E-13	1.00	rs10195252	1.00	1.02E-13	1.00
	SAT-M	SLC38A11	−	3.93E-06	0.66	rs10184126	0.18	7.76E-44	8.57E-34
	SAT-D	SLC38A11	−	3.70E-09	0.35	rs10184126	0.18	2.40E-94	7.40E-82
rs1011731	Blood	C1orf105	+	3.80E-16	0.20	rs2157451	0.28	1.30E-33	8.20E-18
	Lymph.	PIGC	−	5.87E-10	1.00	rs991790	1.00	5.65E-10	1.00
rs718314	Lymph.	ITPR2	+	1.79E-09	0.98	rs7976877	0.45	2.21E-18	1.91E-06
	Blood	ITPR2	−	2.40E-09	0.20	rs2570	0.41	2.40E-37	1.80E-28
rs1294421	SAT-M	BC039678	−	2.43E-07	0.38	rs1294404	0.64	1.89E-16	3.42E-04
	Omental	BC039678	−	1.09E-06	0.33	rs912056	0.71	8.28E-17	4.26E-05
rs6795735	SAT-D	ADAMTS9	−	1.50E-06	0.04	rs7372321	0.11	1.10E-09	2.30E-05
	Omental	AK022320	−	7.99E-15	0.64	rs4521216	0.02	5.15E-42	1.49E-19
	SAT-D	AK022320	−	2.24E-10	0.98	rs4521216	0.02	9.62E-37	7.58E-19
rs4823006	SAT-D	ZNRF3	−	2.40E-08	0.63	rs3178915	0.81	6.70E-11	8.90E-04
	SAT-M	ZNRF3	−	1.08E-18	0.93	rs6005975	0.79	1.59E-19	0.50
	Omental	ZNRF3	−	9.13E-18	0.98	rs6005975	0.79	6.07E-21	0.27
rs6784615	Blood	STAB1	+	2.80E-09	0.32	rs9846089	0.83	9.40E-10	0.08
rs6861681	Lymph.	CPEB4	+	3.79E-22	0.89	rs7705502	0.87	4.95E-29	2.00E-03
	Blood	HMP19	+	1.60E-16	0.97	rs10516107	0.83	1.10E-21	4.30E-06

Association between the 14 WHR SNPs and expression of transcripts located within 1 Mb of the WHR SNP in two sets of abdominal subcutaneous adipose tissue (SAT-D from deCODE and SAT-M from Massachusetts General Hospital), omental fat, liver, lymphocytes, and blood (see Supplementary Note): results are given if the unadjusted WHR SNP association showed P < 1.00E-05. Findings are highlighted in bold font, where the WHR SNP was the transcript peak SNP or where the WHR signal and the cis-eQTL signal were considered coincident (i.e. the transcript peak SNP was highly correlated with the WHR SNP, r² > 0.7, and the transcript peak association disappeared by adjusting on the WHR SNP, P >0.05); see also Online Methods

Unadj. = unadjusted. Adj. = adjusted.

^aEffect direction for the WHR increasing allele.

^bSNP with the strongest association with the transcript in the region (transcript peak SNP).

^cCorrelation (Hapmap CEU, B36) between the WHR SNP and transcript peak SNP.

^dThe transcript labeled AA553656 was detected as Contig27623_RC and corresponds to chr7: 25,854,143-25,854,203 (B36)