Variant report

Variant	esv3438102
Chromosome Location	chr9:1041552-1044150
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf66-6	chr9:1041868-1042520	XLOC_007630

Extended variants
information (count: 132 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:132 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138780501	chr9:1041579-1041580	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs192519983	chr9:1041612-1041613	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs553773950	chr9:1041625-1041626	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs573961334	chr9:1041671-1041672	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs184443149	chr9:1041674-1041675	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs137955278	chr9:1041716-1041717	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs556697095	chr9:1041758-1041759	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs149518562	chr9:1041777-1041778	Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs528161795	chr9:1041805-1041806	Bivalent Enhancer Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs544284178	chr9:1041869-1041870	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs573173480	chr9:1041876-1041877	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs564129540	chr9:1041892-1041893	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs577816533	chr9:1041927-1041928	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs540204432	chr9:1041941-1041942	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs189018932	chr9:1041960-1041961	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs145997845	chr9:1041963-1041964	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs372823787	chr9:1041967-1041968	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs78551366	chr9:1041985-1041986	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs562696083	chr9:1041999-1042000	Bivalent Enhancer Bivalent/Poised TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs545351936	chr9:1042047-1042048	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
21	rs368665036	chr9:1042050-1042051	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
22	rs565060426	chr9:1042082-1042083	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
23	rs376266164	chr9:1042096-1042097	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
24	rs531366789	chr9:1042097-1042098	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
25	rs193254809	chr9:1042108-1042109	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
26	rs113159470	chr9:1042118-1042119	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
27	rs111947040	chr9:1042127-1042128	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
28	rs530588101	chr9:1042131-1042132	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
29	rs2279988	chr9:1042166-1042167	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	mRNA abundance
30	rs564092634	chr9:1042167-1042168	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
31	rs73639812	chr9:1042178-1042179	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
32	rs369181490	chr9:1042202-1042203	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
33	rs2279987	chr9:1042215-1042216	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs35086139	chr9:1042221-1042222	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
35	rs536950161	chr9:1042223-1042224	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
36	rs556624356	chr9:1042225-1042226	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
37	rs570337190	chr9:1042238-1042239	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
38	rs12353309	chr9:1042241-1042242	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs368981399	chr9:1042251-1042252	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
40	rs559216880	chr9:1042274-1042275	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
41	rs2279986	chr9:1042284-1042285	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
42	rs139998067	chr9:1042300-1042301	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
43	rs553778859	chr9:1042312-1042313	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
44	rs573600105	chr9:1042315-1042316	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
45	rs542619523	chr9:1042325-1042326	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
46	rs562595875	chr9:1042337-1042338	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
47	rs531657822	chr9:1042348-1042349	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
48	rs544773125	chr9:1042350-1042351	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
49	rs143435464	chr9:1042354-1042355	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
50	rs577953746	chr9:1042367-1042368	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:106)

Disease	PMID	Source
Ovarian cancer	21720365	CNVD
Myelofibrosis	22110671	CNVD
Lynch syndrome	18415027	CNVD
Retinoblastoma	21504564	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Glioblastoma multiforme	22286061	CNVD
Williams-beuren syndrome	18553513	CNVD
Disorders of sex development	21048976	CNVD
Pilocytic astrocytoma	18622384	CNVD
Pilomyxoid astrocytoma	18622384	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
prenatal diagnosis	20453657	CNVD
Gastric cancer	16715143	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Cancer	21272361	CNVD
Autism	22495311	CNVD
Ependymoma	20639864	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Amyotrophic lateral sclerosis	20685689	CNVD
T-cell lymphomas	22341440	CNVD

Chromatin state (count:161 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:1039000-1042200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:1039600-1041800	Enhancers	Adipose Nuclei	Adipose
3	chr9:1040000-1041600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:1041400-1043800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:1041800-1042000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:1041800-1042200	Bivalent Enhancer	Adipose Nuclei	Adipose
7	chr9:1041800-1042400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr9:1041800-1042400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
9	chr9:1042000-1042200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
10	chr9:1042000-1042200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr9:1042000-1042200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr9:1042000-1042200	Bivalent Enhancer	Brain Hippocampus Middle	brain
13	chr9:1042000-1042200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr9:1042000-1042200	Enhancers	Right Atrium	heart
15	chr9:1042000-1042400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr9:1042000-1042400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr9:1042000-1042400	Bivalent Enhancer	Fetal Kidney	kidney
18	chr9:1042000-1042400	Bivalent/Poised TSS	Psoas Muscle	Psoas
19	chr9:1042000-1042600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:1042000-1042600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
21	chr9:1042000-1042600	Bivalent Enhancer	Brain Substantia Nigra	brain
22	chr9:1042000-1042600	Bivalent Enhancer	Fetal Lung	lung
23	chr9:1042000-1042600	Bivalent Enhancer	Fetal Thymus	thymus
24	chr9:1042000-1042800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr9:1042000-1042800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
26	chr9:1042000-1042800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
27	chr9:1042000-1042800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
28	chr9:1042000-1042800	Enhancers	Lung	lung
29	chr9:1042000-1043000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:1042200-1042400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:1042200-1042400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:1042200-1042400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
33	chr9:1042200-1042400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr9:1042200-1042400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:1042200-1042400	Bivalent Enhancer	Aorta	Aorta
36	chr9:1042200-1042400	Bivalent Enhancer	Liver	Liver
37	chr9:1042200-1042400	Bivalent Enhancer	Brain Germinal Matrix	brain
38	chr9:1042200-1042400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
39	chr9:1042200-1042400	Enhancers	Pancreas	Pancrea
40	chr9:1042200-1042400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
41	chr9:1042200-1042400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr9:1042200-1042400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
43	chr9:1042200-1042400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr9:1042200-1042600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
45	chr9:1042200-1042600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr9:1042200-1042600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:1042200-1042600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:1042200-1042600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr9:1042200-1042600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
50	chr9:1042200-1042600	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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