International Journal of Genomics

Research Article

Common Expression Quantitative Trait Loci Shared by Histone Genes

Table 1

Genome-wide associations of SNPs with expression of histone genes.


SNP^a	Gene	Effect^b	Location^c	A1^d	A2^d	MAF	Genetic associations	Beta

rs10919229	SELE (2Kb upstream)		1:169735986	T	A	0.05	HIST1H4B	1.035	2.51E−10

rs191508159	Intergenic		2:35957035	T	C	0.06	HIST1H4A	0.466	3.41E−11

rs79103588	Intergenic		2:48891009	A	T	0.05	HIST1H4B	1.045	1.02E−10

rs10490124	Intergenic		2:48897335	G	A	0.06	HIST1H4B	1.023	1.65E−10

rs7562208	Intergenic		2:48898231	C	T	0.06	HIST1H4B	1.023	1.65E−10

rs12468670	Intergenic		2:48902054	T	G	0.06	HIST1H4B	1.023	1.65E−10

rs7563070	Intergenic		2:48902202	T	C	0.06	HIST1H4B	1.023	1.65E−10

rs7563889	Intergenic	CTCF	2:48902751	T	G	0.06	HIST1H4B	1.023	1.65E−10

rs115071514	Intergenic		2:48902928	T	C	0.06	HIST1H4B	1.023	1.65E−10

rs7600883	Intergenic		2:48905331	G	A	0.06	HIST1H4B	1.023	1.65E−10

rs10170423	Intergenic		2:48906784	G	A	0.06	HIST1H4B	1.023	1.65E−10

rs10208418	Intergenic		2:48912244	A	T	0.05	HIST1H4B	1.079	3.82E−11

rs10208981	Intergenic		2:48912890	G	T	0.05	HIST1H4B	1.049	8.60E−11

rs79335804	Intergenic		2:48915424	T	C	0.05	HIST1H4B	1.079	3.82E−11

rs13430743	Intergenic		2:48916396	T	G	0.05	HIST1H4B	1.079	3.82E−11

rs13429699	Intergenic		2:48921530	G	C	0.05	HIST1H4B	1.049	8.60E−11

rs13432631	Intergenic		2:48921948	A	C	0.05	HIST1H4B	1.108	1.78E−11

rs13385591	Intergenic		2:48923227	T	C	0.05	HIST1H4B	1.079	3.82E−11

rs7602404	Intergenic		2:48923414	A	G	0.05	HIST1H4B	1.049	8.60E−11

rs142402253	Intergenic		2:48924921	A	G	0.05	HIST1H4B	1.049	8.60E−11

rs189340111	Intergenic		2:68450091	G	A	0.06	HIST1H4B	0.995	2.99E−12
							HIST1H1B	2.319	2.91E−11
							HIST1H1E	2.044	6.90E−11
							HIST1H3J	1.044	8.17E−11
							HIST1H2AH	0.745	2.34E−10
							HIST1H2BM	1.027	2.58E−10

rs75372391	LRP1B (intron 2)		2:141415941	G	A	0.05	HIST1H2BM	1.268	6.19E−12
							HIST1H4B	1.102	1.39E−11
							HIST1H1B	2.645	2.92E−11
							HIST1H3B	2.016	2.00E−10

rs79503131	LRP1B (intron 2)		2:141417401	T	C	0.05	HIST1H2BM	1.268	6.19E−12
							HIST1H4B	1.102	1.39E−11
							HIST1H1B	2.645	2.92E−11
							HIST1H3B	2.016	2.00E−10

rs76908315	LRP1B (intron 2)		2:141428575	G	A	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs75358328	LRP1B (intron 2)		2:141435763	C	T	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs79931187	LRP1B (intron 2)		2:141440679	C	T	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs114273249	LRP1B (intron 2)		2:141441139	T	C	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs74871811	LRP1B (intron 2)		2:141441981	T	A	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs114288750	LRP1B (intron 2)		2:141442588	A	C	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs137985802	LRP1B (intron 2)		2:141442673	T	C	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs114372180	LRP1B (intron 2)		2:141442782	A	G	0.05	HIST1H2BM	1.246	9.09E−12
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.590	4.75E−11

rs75148923	LRP1B (intron 2)		2:141454893	T	C	0.05	HIST1H2BM	1.236	1.33E−11
							HIST1H4B	1.080	2.15E−11
							HIST1H1B	2.588	4.96E−11

rs72853591	LRP1B (intron 2)	OC	2:141557777	C	T	0.06	HIST1H4B	1.015	9.68E−11

rs73963540	LRP1B (intron 2)		2:141710041	T	C	0.05	HIST1H1B	2.975	1.62E−14
							HIST1H2BM	1.369	3.12E−14
							HIST1H3B	2.277	1.75E−13
							HIST1H4B	1.154	4.90E−13
							HIST1H2AB	0.310	8.94E−13
							HIST1H3J	1.273	1.28E−12
							HIST1H1E	2.439	3.33E−12
							HIST1H2AJ	1.711	4.01E−12
							HIST1H2AL	0.552	9.35E−12
							HIST2H2AB	0.263	1.43E−11
							HIST2H3C	0.609	4.10E−11
							HIST1H4K	1.649	4.54E−11
							HIST1H4J	2.204	4.67E−11
							HIST1H3H	1.277	5.05E−11
							HIST1H3I	0.574	6.66E−11
							HIST3H2BB	0.268	6.82E−11
							HIST1H4A	0.474	1.04E−10

rs17801458	LRP1B (intron 2)		2:141710903	T	C	0.05	HIST1H1B	2.975	1.62E−14
							HIST1H2BM	1.369	3.12E−14
							HIST1H3B	2.277	1.75E−13
							HIST1H4B	1.154	4.90E−13
							HIST1H2AB	0.310	8.94E−13
							HIST1H3J	1.273	1.28E−12
							HIST1H1E	2.439	3.33E−12

							HIST1H2AJ	1.711	4.01E−12
							HIST1H2AL	0.552	9.35E−12
							HIST2H2AB	0.263	1.43E−11
							HIST2H3C	0.609	4.10E−11
							HIST1H4K	1.649	4.54E−11
							HIST1H4J	2.204	4.67E−11
							HIST1H3H	1.277	5.05E−11
							HIST1H3I	0.574	6.66E−11
							HIST3H2BB	0.268	6.82E−11
							HIST1H4A	0.474	1.04E−10

rs7570091	LRP1B (intron 2)		2:141714131	G	T	0.05	HIST1H2BM	1.297	1.36E−13
							HIST1H1B	2.787	1.48E−13
							HIST1H3B	2.132	1.34E−12
							HIST1H2AL	0.543	4.65E−12
							HIST1H4B	1.074	4.79E−12
							HIST1H3J	1.201	5.93E−12
							HIST1H2AB	0.289	7.28E−12
							HIST1H2AJ	1.628	1.12E−11
							HIST2H2AB	0.256	1.13E−11
							HIST3H2BB	0.267	1.89E−11
							HIST1H1E	2.277	2.38E−11
							HIST2H3C	0.583	7.77E−11
							HIST1H3I	0.545	1.78E−10
							HIST1H3H	1.199	2.26E−10

rs11684178	LRP1B (intron 2)		2:141788340	C	G	0.06	HIST1H2BM	1.090	6.71E−12
							HIST1H1B	2.283	2.56E−11
							HIST1H3B	1.778	6.72E−11
							HIST2H2AB	0.221	1.04E−10
							HIST1H3J	1.019	1.10E−10
							HIST1H2AL	0.455	1.67E−10

rs6718590	LRP1B (intron 1)		2:141817609	G	C	0.07	HIST1H2BM	0.968	1.15E−10

rs111875224	Intergenic		2:202309382	A	C	0.05	HIST1H2AM	0.594	1.24E−11
rs111875224	Intergenic		2:202309382	A	C	0.05	HIST1H4B	1.023	8.51E−11

rs849583	NRP2 (intron 7)		2:205737518	A	G	0.08	HIST1H4A	0.398	8.66E−11

rs849578^#	NRP2 (intron 7)		2:205738798	T	G	0.08	HIST1H4A	0.390	1.69E−10

rs849577	NRP2 (intron 7)		2:205739705	A	G	0.07	HIST1H4A	0.407	4.48E−11

rs849573	NRP2 (intron 8)		2:205741099	T	C	0.08	HIST1H4A	0.407	4.48E−11

rs849572	NRP2 (intron 8)		2:205741317	A	G	0.08	HIST1H4A	0.398	8.98E−11

rs849567	NRP2 (intron 9)		2:205744540	T	C	0.07	HIST1H4A	0.403	7.11E−11

rs830612	Intergenic		3:71634179	C	T	0.08	HIST1H4B	0.889	1.28E−10

rs150958961	Intergenic		4:9006930	C	A	0.1	HIST1H4A	0.341	8.77E−11

rs148619316	Intergenic		5:14080602	T	C	0.06	HIST1H4B	1.006	4.81E−11

rs1992368	Intergenic		5:14092868	A	G	0.06	HIST1H4B	0.974	9.25E−11

rs55989629	Intergenic		5:14093354	T	C	0.06	HIST1H4B	0.974	9.25E−11

rs11956277	Intergenic		5:14095038	T	C	0.06	HIST1H4B	0.974	9.25E−11

rs66689811	Intergenic		5:14095266	T	C	0.06	HIST1H4B	0.974	9.25E−11

rs6863067	Intergenic		5:14098914	A	C	0.06	HIST1H4B	0.974	9.25E−11

rs10041963	Intergenic		5:14099801	A	G	0.06	HIST1H4B	0.974	9.25E−11

rs10072716	Intergenic		5:14101222	T	C	0.06	HIST1H4B	0.974	9.25E−11

rs6861945	Intergenic		5:53398953	A	G	0.11	HIST1H3J	0.780	2.75E−10

rs61564830	Intergenic		6:129768950	T	C	0.06	HIST1H3J	1.036	2.62E−10

rs144499291	UTRN (intron 22)		6:144471095	G	A	0.06	HIST1H4A	0.461	2.88E−10

rs71560740	Intergenic		7:85896218	C	T	0.06	HIST1H2AJ	1.491	1.48E−10
rs71560740	Intergenic		7:85896218	C	T	0.06	HIST1H3A	0.228	2.41E−10

rs118052517	Intergenic		7:153287269	C	T	0.06	HIST1H3J	1.234	8.16E−13
							HIST1H4A	0.494	1.89E−12
							HIST1H2BM	1.222	2.40E−12
							HIST1H2AJ	1.648	3.64E−12
							HIST1H3B	2.052	6.16E−12
							HIST1H1B	2.540	1.39E−11
							HIST1H1E	2.269	1.78E−11
							HIST1H2AB	0.270	1.16E−10
							HIST1H4K	1.532	2.14E−10
							HIST1H4J	2.039	2.62E−10
							HIST1H3I	0.534	2.77E−10
							HIST1H3H	1.180	2.95E−10

rs77957383	Intergenic		9:1715766	T	C	0.07	HIST1H4B	0.894	1.85E−10

rs113936625	Intergenic		10:111124417	C	G	0.05	HIST1H4B	1.056	2.76E−10

rs75201173	Intergenic	CTCF	11:1062030	C	A	0.07	HIST1H2BM	1.092	1.45E−11
							HIST2H3C	0.529	1.22E−10
							HIST1H1B	2.227	1.75E−10
							HIST1H3B	1.766	1.94E−10

rs11245920	Intergenic	CTCF	11:1062519	C	T	0.07	HIST1H2BM	1.092	1.45E−11
							HIST2H3C	0.529	1.22E−10
							HIST1H1B	2.227	1.75E−10
							HIST1H3B	1.766	1.94E−10

rs111452409	Intergenic		11:1064929	G	A	0.07	HIST1H2BM	1.092	1.45E−11
							HIST2H3C	0.529	1.22E−10
							HIST1H1B	2.227	1.75E−10
							HIST1H3B	1.766	1.94E−10

rs113659777	MUC2 (intron 2)		11:1088149	A	G	0.07	HIST1H2BM	1.101	2.89E−11
rs113659777	MUC2 (intron 2)		11:1088149	A	G	0.07	HIST1H4B	0.951	8.17E−11

rs184239416	MUC2 (intron 2)		11:1088154	G	A	0.06	HIST1H2BM	1.262	1.56E−12
							HIST1H4B	1.077	9.13E−12
							HIST1H1B	2.566	2.84E−11
							HIST1H3J	1.174	3.88E−11
							HIST1H3B	1.979	1.17E−10
							HIST1H1E	2.206	2.06E−10
							HIST3H2BB	0.257	2.37E−10

rs41392245	MUC2 (intron 2)		11:1089095	T	C	0.07	HIST1H2BM	1.068	4.19E−11
							HIST2H3C	0.528	1.34E−10
							HIST1H3B	1.761	2.23E−10
							HIST1H1B	2.201	2.90E−10

rs11033879	MMP26 (intron 1)		11:4786997	G	A	0.05	HIST1H2AJ	1.711	2.53E−13
							HIST1H1E	2.374	9.71E−13
							HIST1H3B	2.102	9.80E−13
							HIST2H2AB	0.263	1.12E−12
							HIST1H1B	2.635	1.18E−12
							HIST1H4A	0.490	1.62E−12
							HIST1H2BM	1.195	4.53E−12
							HIST2H3C	0.594	1.15E−11
							HIST1H3J	1.148	2.08E−11
							HIST1H4K	1.593	2.16E−11
							HIST1H2AB	0.275	3.14E−11
							HIST1H4J	2.095	4.85E−11
							HIST1H3I	0.544	7.46E−11
							HIST1H3H	1.190	1.28E−10
							HIST1H2AH	0.793	2.70E−10

rs80143982	Intergenic		11:110990257	A	G	0.05	HIST1H4A	0.482	2.65E−10

rs75349221	Intergenic		14:44176974	T	A	0.05	HIST1H4A	0.471	2.75E−10

rs72846811	RBFOX3 (intron 3)		17:79231229	A	G	0.06	HIST1H4A	0.489	1.90E−11

rs183898825	TAF4B (intron 9)		18:26303160	C	A	0.05	HIST1H4A	0.466	2.60E−10

rs57185274	CACNA1A (intron 3)		19:13406972	A	T	0.05	HIST1H4B	1.034	2.04E−10

^aSNP in bold indicates the representative variant in each linkage disequilibrium block. SNP with superscript “#” was associated with autism in a Chinese population [15]. ^bThe effects were predicted using Ensembl Variant Effect Predictor program [11]. OC: open chromatin region; CTCF: CTCF binding site. ^cChromosome: base pair position from GRCh38.p2. ^dA1: minor allele; A2: major allele. SNP: single-nucleotide polymorphism; MAF: minor allele frequency.