Table 2.

Thirty-two unique cis-sQTL associations found to be in a canonical splice site (NCBI dbSNP v137 database)

Gene	Affymetrix probe set	rs ID	Chr.	Position (bp)	Effect allele	Non-effect allele	Observed EAF	Estimate	SE	PsQTL	Function
IRF5	3023264	rs2004640	7	128,578,301	G	T	0.47	0.549	0.015	1.46 × 10−262	Splice-5
KIF20B	3257353	rs12264026	10	91,534,702	T	C	0.78	−0.424	0.0128	9.07 × 10−220	Splice-5
MS4A14	3332343	rs4938941	11	60,173,360	G	A	0.67	−0.338	0.012	7.48 × 10−163	Splice-3
WDR82	2676049	rs2276834	3	52,325,759	G	A	0.52	−0.374	0.0175	1.16 × 10−97	Splice-3
NME2	3726971	rs115848216	17	49,243,859	G	A	0.96	0.441	0.0209	2.45 × 10−95	Splice-5
PNPLA2	3316308	rs61876746	11	827,713	A	T	0.69	0.49	0.0235	7.74 × 10−93	Splice-5
MTMR9	3085893	rs2736277	8	11,218,893	A	G	0.52	−0.214	0.0117	4.73 × 10−72	Splice-3
ADNP2	3795520	rs7233511	18	77,915,113	C	T	0.79	−0.202	0.0133	1.93 × 10−51	Splice-5
PPIP5K1	3621297	rs7169097	15	43,925,134	T	A	0.71	0.291	0.0202	3.89 × 10−46	Splice-3
UBTF	3758978	rs7220138	17	42,254,011	G	C	0.31	−0.0939	0.00812	1.56 × 10−30	Splice-3
PTDSS2	3315872	rs12419209	11	494,510	T	C	0.89	0.179	0.0155	2.44 × 10−30	Splice-5
C19orf53	3822350	rs8108058	19	13,889,589	C	T	0.74	−0.1	0.00895	1.04 × 10−28	Splice-5
HNRNPF	3286287	rs10899795	10	43,869,097	C	A	0.76	−0.101	0.0094	9.36 × 10−27	splice-3
PTGS1a	3188118	rs3842788	9	125,140,206	G	A	0.96	0.547	0.0523	2.24 × 10−25	Splice-3
RNF216P1	2988420	rs9689983	7	5,024,540	G	A	0.95	0.361	0.0359	1.31 × 10−23	Splice-3
RHOT2	3643270	rs35915772	16	679,274	G	A	0.78	−0.171	0.0176	6.45 × 10−22	Splice-5
APOL6	3944259	rs67090823	22	36,064,455	R	D	0.93	0.163	0.0178	7.21 × 10−20	Splice-5
GOLGA2P5	3467744	rs11110268	12	100,560,416	T	C	0.94	0.197	0.0219	3.03 × 10−19	Splice-3
RNF213	3737392	rs41298712	17	78,396,004	A	G	0.95	−0.261	0.0297	1.67 × 10−18	Splice-3
MOK	3580293	rs56377169	14	102,729,881	A	G	0.93	0.202	0.0233	7.69 × 10−18	Splice-5
ASB16	3722813	rs7220138	17	42,254,011	G	C	0.31	−0.0648	0.00751	8.11 × 10−18	Splice-3
TMUB2	3722846	rs7220138	17	42,254,011	G	C	0.31	−0.0559	0.00673	1.20 × 10−16	Splice-3
CYP2D7P1	3962303	rs3892097	22	42,524,947	C	T	0.81	−0.121	0.0154	5.39 × 10−15	Splice-3
STRC	3621380	rs7169097	15	43,925,134	T	A	0.71	−0.0713	0.0091	5.59 × 10−15	Splice-3
TMEM8B	3168220	rs2381409	9	35,829,390	T	C	0.62	0.069	0.00938	2.16 × 10−13	Splice-5
NCL	2603490	rs28685161	2	232,378,792	C	T	0.76	0.0534	0.00729	2.85 × 10−13	Splice-5
BZW1	2522472	rs62623595	2	201,637,798	G	A	0.89	−0.0889	0.0126	2.34 × 10−12	Splice-5
IFIH1	2584224	rs35337543	2	163,136,505	C	G	0.98	0.69	0.0995	4.49 × 10−12	Splice-5
LLGL2	3734961	rs73998360	17	73,586,325	G	A	0.93	0.136	0.0207	6.66 × 10−11	Splice-5
WDR46	2950587	rs3130099	6	33,282,181	G	A	0.51	−0.0655	0.0101	1.18 × 10−10	Splice-5
ISG15	4053546	rs3813194	1	998,582	C	G	0.53	−0.0941	0.0146	1.27 × 10−10	Splice-5
BMP8A	2331542	rs79473113	1	40,020,020	C	A	0.96	0.261	0.0413	2.67 × 10−10	Splice-5

Chr., chromosome; EAF, effect allele frequency; SE, standard error.

^aAn example of the PTGS1 gene with its associated cis sQTL is shown in Figure 2.