Variant report

Variant	nsv967106
Chromosome Location	chr3:195562795-195566184
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:367)
Chromatin interactive
region (count:7)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:195565366-195565388	GM13976	blood:	n/a	n/a
2	RCOR1	chr3:195565719-195566000	GM12878	blood:	n/a	n/a
3	RUNX3	chr3:195565486-195565963	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:195565511-195565860	GM12878	blood:	n/a	n/a
5	SETDB1	chr3:195565026-195565258	U2OS	brain:	n/a	n/a
6	TBL1XR1	chr3:195565781-195565981	GM12878	blood:	n/a	n/a
7	ZNF143	chr3:195565642-195565867	GM12878	blood:	n/a	n/a
8	ZNF143	chr3:195565760-195565802	K562	blood:	n/a	n/a

(count:367 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:195565002-195565052	HMEC	breast:	n/a
2	chr3:195565002-195565052	HMEC	breast:	n/a
3	chr3:195564878-195564928	Jurkat	blood:	n/a
4	chr3:195566068-195566118	HIPEpiC	eye:	n/a
5	chr3:195565002-195565052	Jurkat	blood:	n/a
6	chr3:195565002-195565052	Hepatocyte	liver:	n/a
7	chr3:195564951-195565001	GM06990	blood:	n/a
8	chr3:195564951-195565001	ECC-1	luminal epithelium:	n/a
9	chr3:195563279-195563329	MCF-7	breast:	n/a
10	chr3:195564951-195565001	HMEC	breast:	n/a
11	chr3:195564748-195564798	HCPEpiC	choroid plexus:	n/a
12	chr3:195566068-195566118	HRCEpiC	kidney:	n/a
13	chr3:195563279-195563329	GM12891	blood:	n/a
14	chr3:195564748-195564798	GM19239	blood:	n/a
15	chr3:195563279-195563329	HIPEpiC	eye:	n/a
16	chr3:195564748-195564798	HMEC	breast:	n/a
17	chr3:195566068-195566118	SAEC	small airway:	n/a
18	chr3:195565002-195565052	GM12892	blood:	n/a
19	chr3:195564748-195564798	MCF-7	breast:	n/a
20	chr3:195563279-195563329	RPTEC	kidney:	n/a
21	chr3:195564951-195565001	HIPEpiC	eye:	n/a
22	chr3:195565002-195565052	Hela-S3	cervix:	n/a
23	chr3:195563279-195563329	PrEC	prostate:	n/a
24	chr3:195564878-195564928	HPAEpiC	pulmonary alveolar:	n/a
25	chr3:195564878-195564928	PANC-1	pancreas:	n/a
26	chr3:195564951-195565001	K562	blood:	n/a
27	chr3:195566068-195566118	Jurkat	blood:	n/a
28	chr3:195564878-195564928	PFSK-1	brain:	n/a
29	chr3:195563279-195563329	GM19239	blood:	n/a
30	chr3:195563279-195563329	Hepatocyte	liver:	n/a
31	chr3:195564748-195564798	BJ	skin:	n/a
32	chr3:195565002-195565052	GM06990	blood:	n/a
33	chr3:195564951-195565001	MCF-7	breast:	n/a
34	chr3:195564951-195565001	HRPEpiC	eye:	n/a
35	chr3:195565002-195565052	HPAEpiC	pulmonary alveolar:	n/a
36	chr3:195564951-195565001	A549	lung:	n/a
37	chr3:195564748-195564798	U87	brain:	n/a
38	chr3:195564878-195564928	HNPCEpiC	eye:	n/a
39	chr3:195566068-195566118	RPTEC	kidney:	n/a
40	chr3:195564951-195565001	GM12891	blood:	n/a
41	chr3:195565002-195565052	MCF-7	breast:	n/a
42	chr3:195563279-195563329	HUVEC	blood vessel:	n/a
43	chr3:195565002-195565052	SK-N-SH_RA	brain:	n/a
44	chr3:195564878-195564928	NH-A	brain:	n/a
45	chr3:195563279-195563329	PFSK-1	brain:	n/a
46	chr3:195563279-195563329	HCF	heart:	n/a
47	chr3:195564748-195564798	SK-N-SH	brain:	n/a
48	chr3:195565002-195565052	A549	lung:	n/a
49	chr3:195564748-195564798	IMR90	lung:	fetal
50	chr3:195566068-195566118	BE2_C	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:195557190..195561504-chr3:195561743..195563468,3	K562	blood:
2	chr3:195561374..195564288-chr3:195569433..195571276,2	K562	blood:
3	chr3:195564688..195566453-chr3:195572036..195574100,2	K562	blood:
4	chr3:195557190..195560097-chr3:195561743..195563468,2	K562	blood:
5	chr3:195562017..195564300-chr3:195564370..195566279,2	MCF-7	breast:
6	chr3:195549072..195550801-chr3:195564516..195566947,2	K562	blood:
7	chr3:195552617..195555555-chr3:195561700..195563483,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNK2-1	chr3:195563205-195563486	ENSG00000223783
2	lnc-TNK2-1	chr3:195563625-195563916	ENSG00000223783
3	lnc-TNK2-1	chr3:195563211-195563486	ENSG00000223783
4	lnc-TNK2-1	chr3:195563064-195563486	ENSG00000223783

No data

Variant related genes	Relation type
ENSG00000235836	TF binding region
ENSG00000223783	TF binding region
ENSG00000235836	CpG island
ENSG00000223783	CpG island
ENSG00000223783	chromatin interactions
ENSG00000235836	chromatin interactions

Extended variants
information (count: 200 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:200 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546917011	chr3:195562807-195562808	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs372334483	chr3:195562808-195562809	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs551027215	chr3:195562822-195562823	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs569753381	chr3:195562827-195562828	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs537223534	chr3:195562828-195562829	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs536060486	chr3:195562831-195562832	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs62283271	chr3:195562838-195562839	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	mRNA abundance
8	rs569743002	chr3:195562854-195562855	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs536786287	chr3:195562898-195562899	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs182023575	chr3:195562914-195562915	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs535385318	chr3:195562915-195562916	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs62283272	chr3:195562917-195562918	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs578047786	chr3:195562927-195562928	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs137891619	chr3:195562935-195562936	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs576944969	chr3:195562960-195562961	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs563612787	chr3:195562971-195562972	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs34516577	chr3:195562981-195562982	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs142321223	chr3:195562990-195562991	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs186610855	chr3:195563006-195563007	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs553320664	chr3:195563035-195563036	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs561964736	chr3:195563053-195563054	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs554090112	chr3:195563059-195563060	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs574520849	chr3:195563091-195563092	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs199866489	chr3:195563118-195563119	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs190730577	chr3:195563145-195563146	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs532738868	chr3:195563146-195563147	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs370024806	chr3:195563167-195563168	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs542008919	chr3:195563168-195563169	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs569632292	chr3:195563174-195563175	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs537189035	chr3:195563178-195563179	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs182015569	chr3:195563202-195563203	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs138420346	chr3:195563214-195563215	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs62283273	chr3:195563233-195563234	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs73205778	chr3:195563248-195563249	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs373210259	chr3:195563260-195563261	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs114886240	chr3:195563280-195563281	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs144783137	chr3:195563307-195563308	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs539019241	chr3:195563337-195563338	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs528500718	chr3:195563359-195563360	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs186383669	chr3:195563411-195563412	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs190000687	chr3:195563426-195563427	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs543062954	chr3:195563483-195563484	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
43	rs371364304	chr3:195563512-195563513	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs75748934	chr3:195563565-195563566	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs199856557	chr3:195563572-195563573	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs78393845	chr3:195563573-195563574	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs111405013	chr3:195563590-195563591	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs114196117	chr3:195563613-195563614	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs546853844	chr3:195563641-195563642	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
50	rs9812304	chr3:195563643-195563644	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195556800-195566600	Weak transcription	Spleen	Spleen
2	chr3:195559200-195566600	Weak transcription	Right Atrium	heart
3	chr3:195561600-195563000	Enhancers	Colonic Mucosa	Colon
4	chr3:195562000-195562800	Bivalent Enhancer	Stomach Mucosa	stomach
5	chr3:195562400-195563000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:195562800-195563000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr3:195563000-195564600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:195563600-195564000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:195563600-195564600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:195563800-195564000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:195564000-195566000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:195564200-195564800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:195564400-195564600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:195564600-195564800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:195564600-195564800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:195564600-195565600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:195564800-195565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:195564800-195566000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:195564800-195566200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:195565200-195565800	Enhancers	GM12878-XiMat	blood
21	chr3:195565200-195566800	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:195565600-195567000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:195565800-195566200	Flanking Active TSS	GM12878-XiMat	blood
24	chr3:195565800-195567000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:195565800-195567000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:195565800-195567000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:195565800-195567000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:195565800-195567000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:195566000-195566200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:195566000-195566600	Enhancers	Brain Hippocampus Middle	brain
31	chr3:195566000-195566800	Enhancers	Brain Angular Gyrus	brain
32	chr3:195566000-195567000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:195566000-195567000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:195566000-195567000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:195566000-195567000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:195566000-195567000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr3:195566000-195567000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:195566000-195567000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:195566000-195567000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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