Variant report

Variant	esv2752272
Chromosome Location	chr9:104839357-104961860
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:104846252..104847873-chr9:104851668..104854284,2	K562	blood:
2	chr9:104828978..104830886-chr9:104836828..104839477,2	K562	blood:
3	chr9:104846252..104847873-chr9:104851668..104854284,2	K562	blood:
4	chr11:118868629..118869144-chr9:104880609..104881109,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIN3A-3	chr9:104942626-104945366	NONHSAT133756
2	lnc-GRIN3A-3	chr9:104942631-104945366	ucscGeneNc_uc004bbt_2
3	lnc-GRIN3A-3	chr9:104946414-104946469	ucscGeneNc_uc004bbt_2
4	lnc-GRIN3A-3	chr9:104946414-104946469	NONHSAT133756

No data

Variant related genes	Relation type
ENSG00000186166	chromatin interactions
ENSG00000255121	chromatin interactions

Extended variants
information (count: 906 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:906 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs320288	chr9:104839357-104839358	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs148271372	chr9:104839391-104839392	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs10820047	chr9:104839414-104839415	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs535981769	chr9:104839431-104839432	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs555572578	chr9:104839461-104839462	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs575796131	chr9:104839464-104839465	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs180808824	chr9:104839465-104839466	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs564802697	chr9:104839476-104839477	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs141382422	chr9:104839533-104839534	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs320287	chr9:104839556-104839557	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs569048203	chr9:104839579-104839580	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs79628977	chr9:104839620-104839621	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs528873154	chr9:104839625-104839626	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs542754373	chr9:104839651-104839652	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs185266200	chr9:104839661-104839662	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs531543563	chr9:104839673-104839674	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs375018717	chr9:104839687-104839688	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs150610372	chr9:104839697-104839698	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs79457963	chr9:104839707-104839708	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs140038099	chr9:104839708-104839709	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs79147488	chr9:104839745-104839746	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs10989804	chr9:104839778-104839779	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs547700840	chr9:104839796-104839797	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs10760837	chr9:104839839-104839840	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs375092753	chr9:104839861-104839862	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs535432917	chr9:104839874-104839875	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs555837459	chr9:104839935-104839936	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs569217607	chr9:104839963-104839964	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs190561085	chr9:104839970-104839971	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs557956365	chr9:104839974-104839975	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs12002182	chr9:104839981-104839982	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs113934794	chr9:104839996-104839997	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs540564943	chr9:104840003-104840004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs558158583	chr9:104840008-104840009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs573584892	chr9:104840022-104840023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs376090862	chr9:104840023-104840024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs542218787	chr9:104840031-104840032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs562620462	chr9:104840072-104840073	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs531279540	chr9:104840109-104840110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs75573208	chr9:104840110-104840111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs182267510	chr9:104840117-104840118	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs552189156	chr9:104840161-104840162	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs527475342	chr9:104840172-104840173	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs547764226	chr9:104840204-104840205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs567405125	chr9:104840209-104840210	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs540233279	chr9:104840217-104840218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs549077625	chr9:104840233-104840234	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs186844080	chr9:104840293-104840294	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs577106998	chr9:104840317-104840318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs146322146	chr9:104840328-104840329	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Fukuyama congenital muscular dystrophy	21572526	CNVD
Testicular germ cell tumor	18059402	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Neuroblastoma	20406844	CNVD
Schizophrenia	23813976	CNVD
early-passage human iPS cells	21368824	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104835000-104842400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:104839200-104840000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:104842400-104842600	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr9:104849400-104850000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr9:104849600-104850000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:104875800-104876200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:104876600-104877200	Enhancers	Adipose Nuclei	Adipose
8	chr9:104877200-104877600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr9:104878600-104879600	Enhancers	Fetal Heart	heart
10	chr9:104886400-104886800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:104886600-104887400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:104893200-104893800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:104897000-104897600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:104897600-104898400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:104897800-104899000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr9:104898000-104898400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:104904600-104905000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:104915600-104916000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr9:104940400-104941800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:104940600-104941400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:104947400-104950200	Enhancers	Fetal Heart	heart
22	chr9:104947800-104948000	Enhancers	Ovary	ovary
23	chr9:104947800-104948400	Enhancers	Stomach Smooth Muscle	stomach
24	chr9:104947800-104948800	Enhancers	Adipose Nuclei	Adipose
25	chr9:104948000-104948800	Enhancers	Fetal Kidney	kidney
26	chr9:104948200-104948800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:104948600-104949200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr9:104948800-104949800	Weak transcription	Fetal Kidney	kidney
29	chr9:104949200-104949600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr9:104949600-104950400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr9:104950000-104950200	Enhancers	Fetal Kidney	kidney
32	chr9:104950000-104950800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr9:104950000-104950800	Enhancers	Ovary	ovary

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