Table 2. SNPs associated with allele-specific expression of lncRNA windows with published trait- or disease-associations from genome-wide association studies.

	ASE				GWAS
Genomicregion oflncRNA	Distance toGWASSNP (bp)1	In or closeto histonemark	ASEp-value	Slope2	SNP3	Trait4
1: 22224268–22229983	16228	H3K4m15	2.41E-7	0.13	rs2501276	Immune responseto smallpoxvaccine (IL-6)
1: 22224268–22229983	128475		3.03E-7	0.07	rs16826658	Endometriosis
1: 41480834–41523120	177376		2.66E-12	0.09	rs66868426	Height
1: 220153613–220218488	13083	H3K4m1	8.46E-17	0.22	rs6687758	Colorectalcancer
2: 19067188–19369296	68959		1.36E-7	0.06	rs1876040	Cognitive testperformance
2: 101944950–101970061	59999		1.32E-7	0.08	rs2310173	Ankylosingspondylitis
2: 166359613–166410847	68123		5.60E-9	0.06	rs6710518	Bone mineraldensity
2: 166359613–166410847	50321		1.82E-9	0.06	rs13460047	Bone mineraldensity
3: 157947829–158017517	91268		3.72E-25	0.08	rs12638253	Multiplesclerosis(severity)
6: 28237538–28245351	184924	H3K4m15H3K27ac5	2.25E-8	0.06	rs69038238	Pulmonaryfunction
6: 30050868–30054162	7639	H3K4m1	5.90E-11	0.08	rs3893464	Graves’disease
6: 29802357–29824805	257099	H3K27ac5	6.18E-7	0.08	rs43130349	Graves’disease
6: 30874410–30906415	204180		4.05E-12	0.11	rs4248154	Graves’disease
6: 58380311–58395738	21176		3.60E-21	0.07	rs950025610	Eosinophilicesophagitis(pediatric)
7: 1166536–1171429	161007		3.40E-14	0.07	rs10256972	Longevity
7: 7261310–7283935	26354		4.86E-9	0.07	rs10259085	Multiplesclerosis(severity)
7: 7261310–7283935	0	H3K4m15	3.41E-7	0.06	rs1299548	Amount of visceraladipose tissue adjustedfor body massindex (BMI)
8: 23138679–23144384	0	H3K4m15H3K27ac5	9.45E-89	0.27	rs13278062	Age-relatedmacular degeneration
9: 122645199–122654702	25619	H3K4m1H3K27ac5	4.09E-16	0.13	rs1953126	Celiac disease andRheumatoid arthritis
9: 122645199–122654702	38017		1.02E-16	0.13	rs881375	Rheumatoidarthritis
9: 122645199–122654702	75358	H3K4m15H3K27ac5	4.13E-17	0.13	rs3761847	Rheumatoidarthritis
9: 135120874–135140438	0		3.39E-50	0.43	rs687621	D-dimerlevels
9: 135120874–135140438	0		2.69E-66	0.43	rs657152	Liver enzymelevels
9: 135120874–135140438	0		2.69E-66	0.43	rs643434	Inflammatorybiomarkers
9: 135120874–135140438	0		5.66E-52	0.44	rs612169	Metabolictraits
9: 135120874–135140438	0		1.00E-50	0.44	rs505922	Proteinquantitativetrait loci
9: 135120874–135140438	0		3.80E-22	0.43	rs507666	SolubleICAM-1
9: 135120874–135140438	3551		8.83E-26	0.43	rs579459	Soluble E-selectinlevels
9: 135120874–135140438	4250		7.93E-25	0.43	rs495828	Angiotensin-convertingenzyme activity
15: 43458687–43481812	30170		1.24E-21	0.14	rs245353311	Chronickidney disease
15: 82975686–82986699	245274		4.86E-13	0.05	rs374316212	Alzheimer’sdisease (ageof onset)
17: 26060783–26121168	150673	H3K4m1	1.28E-8	0.06	rs3760318	Height

¹The distance to the lncRNA region is 0 if the SNP is located within the region and the smallest distance otherwise,

²Slope is given in absolute numbers,

³Listed are all cis-rSNPs that are also found in the GWAS catalog together with the associated lncRNA,

⁴The trait is taken from the GWAS catalog,

⁵Within 2.5 kb,

⁶rs6663565 as proxy,

⁷rs2303393 as proxy,

⁸rs6922111 as proxy,

⁹rs7739434 as proxy,

¹⁰rs13214831 as proxy,

¹¹rs1153862 as proxy,

¹²rs12442557 as proxy.