Variant report

Variant	nsv1016401
Chromosome Location	chr9:2255397-2410590
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:28)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:2266333..2269283-chr9:2269848..2272589,2	K562	blood:
2	chr9:2321723..2322570-chr9:2728160..2728820,2	MCF-7	breast:
3	chr9:2257367..2260216-chr9:2810940..2813820,2	MCF-7	breast:
4	chr9:2353709..2356767-chr9:2357162..2361529,4	K562	blood:
5	chr9:2367757..2369969-chr9:2374700..2376724,2	K562	blood:
6	chr9:2255030..2255773-chr9:2600478..2601011,2	MCF-7	breast:
7	chr9:2353709..2355330-chr9:2357162..2359493,2	K562	blood:
8	chr9:2244966..2246945-chr9:2263682..2266605,2	MCF-7	breast:
9	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
10	chr9:2291871..2293597-chr9:2622079..2623974,2	MCF-7	breast:
11	chr9:2333652..2336415-chr9:2621221..2622791,2	MCF-7	breast:
12	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
13	chr9:2335749..2336338-chr9:2727775..2728597,3	MCF-7	breast:
14	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
15	chr9:2353709..2356767-chr9:2357162..2361529,4	K562	blood:
16	chr9:2334689..2336340-chr9:2621369..2623518,2	MCF-7	breast:
17	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
18	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
19	chr9:2353709..2355330-chr9:2357162..2359493,2	K562	blood:
20	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
21	chr9:2377530..2380377-chr9:2380910..2383194,2	MCF-7	breast:
22	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:
23	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
24	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:
25	chr9:2266333..2269283-chr9:2269848..2272589,2	K562	blood:
26	chr9:2377530..2380377-chr9:2380910..2383194,2	MCF-7	breast:
27	chr9:2367757..2369969-chr9:2374700..2376724,2	K562	blood:
28	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCA2-6	chr9:2287708-2288332	NONHSAT129989
2	lnc-SMARCA2-6	chr9:2291976-2293037	NONHSAT129989
3	lnc-SMARCA2-6	chr9:2276007-2276253	NONHSAT129989
4	lnc-SMARCA2-5	chr9:2264485-2264628	NONHSAT129991
5	lnc-VLDLR-2	chr9:2390027-2390054	XLOC_007266
6	lnc-VLDLR-2	chr9:2408820-2408888	XLOC_007266
7	lnc-SMARCA2-5	chr9:2273475-2274167	NONHSAT129991

No data

Variant related genes	Relation type
ENSG00000147852	chromatin interactions
ENSG00000236404	chromatin interactions

Extended variants
information (count: 7393 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:7393 , 50 per page) page: 1 2 3 4 5 6 7 ... 148

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1555646	chr9:2255397-2255398	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs539668463	chr9:2255431-2255432	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs190471167	chr9:2255434-2255435	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs182028211	chr9:2255447-2255448	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs548401864	chr9:2255448-2255449	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs568257299	chr9:2255454-2255455	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs557828366	chr9:2255483-2255484	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs187063316	chr9:2255497-2255498	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs543022751	chr9:2255508-2255509	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs557052239	chr9:2255525-2255526	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs576907784	chr9:2255534-2255535	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs539390338	chr9:2255554-2255555	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs553406148	chr9:2255623-2255624	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs12550896	chr9:2255632-2255633	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs370014390	chr9:2255633-2255634	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs144913242	chr9:2255645-2255646	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs561993988	chr9:2255665-2255666	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs575424853	chr9:2255667-2255668	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs1555645	chr9:2255676-2255677	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs542834163	chr9:2255682-2255683	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs149216951	chr9:2255711-2255712	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs369411512	chr9:2255735-2255736	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs143406887	chr9:2255744-2255745	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs111686365	chr9:2255762-2255763	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs528417188	chr9:2255770-2255771	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs548176798	chr9:2255825-2255826	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs112381261	chr9:2255859-2255860	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs537193700	chr9:2255864-2255865	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs192185424	chr9:2255909-2255910	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs201731932	chr9:2255938-2255939	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs150239196	chr9:2255939-2255940	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs570528155	chr9:2255948-2255949	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs115047300	chr9:2255949-2255950	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs35173753	chr9:2255972-2255973	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs72691295	chr9:2255978-2255979	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs4741665	chr9:2255979-2255980	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs142158859	chr9:2255982-2255983	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs565831283	chr9:2255983-2255984	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs555600550	chr9:2256049-2256050	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs145676232	chr9:2256055-2256056	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs200253811	chr9:2256074-2256075	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs544374813	chr9:2256088-2256089	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs16938145	chr9:2256092-2256093	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	disease
44	rs77529977	chr9:2256140-2256141	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs186620144	chr9:2256151-2256152	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs369076308	chr9:2256155-2256156	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs560573891	chr9:2256167-2256168	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs189893991	chr9:2256184-2256185	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs535424176	chr9:2256231-2256232	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs542146254	chr9:2256245-2256246	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:103)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	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
Disorders of sex development	21048976	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
Oral squamous cell carcinoma	17134496	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
Melanoma	18172304	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
Ovarian cancer	21720365	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
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
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Renal cell carcinoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:846 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2248600-2263800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:2248800-2257000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:2252200-2260400	Weak transcription	A549	lung
4	chr9:2253600-2255400	Enhancers	Fetal Muscle Leg	muscle
5	chr9:2253600-2255800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:2254000-2255600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:2254400-2255800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:2254600-2255400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:2254600-2257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:2254600-2262800	Weak transcription	Ovary	ovary
11	chr9:2254800-2255400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr9:2255000-2255600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:2255200-2255400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:2255200-2255400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:2255200-2255600	Enhancers	Fetal Heart	heart
16	chr9:2255400-2255600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr9:2255400-2260400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:2255400-2262800	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:2255600-2255800	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr9:2255600-2257200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:2255800-2256200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr9:2255800-2257400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:2256200-2263200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:2257000-2257400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr9:2257000-2258000	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:2257000-2258200	Enhancers	Primary B cells from cord blood	blood
27	chr9:2257200-2257400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:2257400-2257600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:2257400-2257800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:2257400-2257800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:2257400-2257800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr9:2257400-2257800	Enhancers	GM12878-XiMat	blood
33	chr9:2257400-2258000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:2257400-2275000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:2257600-2262800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:2257800-2258200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr9:2257800-2260200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:2257800-2260600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:2258000-2260400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:2258000-2263000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:2258200-2258400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr9:2258200-2263000	Weak transcription	Primary B cells from cord blood	blood
43	chr9:2258400-2266200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr9:2259400-2259800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:2259600-2261400	Enhancers	Brain Germinal Matrix	brain
46	chr9:2259800-2260200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:2259800-2261200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:2259800-2261200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr9:2260200-2260600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:2260200-2260800	Enhancers	Fetal Brain Male	brain

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