Variant report

Variant	esv3369484
Chromosome Location	chr3:49586448-49590446
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:49588802-49588875	NB4	blood:	n/a	chr3:49588856-49588866
2	POLR2A	chr3:49588410-49588798	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:49587113-49587227	HepG2	liver:	n/a	n/a
4	YY1	chr3:49588712-49588961	K562	blood:	n/a	n/a
5	YY1	chr3:49588742-49588975	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49588245-49588295	HCT-116	colon:	n/a
2	chr3:49588245-49588295	HEK293	kidney:	embryo
3	chr3:49588245-49588295	HPAEpiC	pulmonary alveolar:	n/a
4	chr3:49588245-49588295	AoSMC	blood vessel:	n/a
5	chr3:49588245-49588295	HUVEC	blood vessel:	n/a
6	chr3:49588245-49588295	K562	blood:	n/a
7	chr3:49588245-49588295	Hepatocyte	liver:	n/a
8	chr3:49588245-49588295	NT2-D1	testis:	n/a
9	chr3:49588245-49588295	AG09309	skin:	n/a
10	chr3:49588245-49588295	HAEpiC	amniotic membrane:	n/a
11	chr3:49588245-49588295	BJ	skin:	n/a
12	chr3:49588245-49588295	HRPEpiC	eye:	n/a
13	chr3:49588245-49588295	HCF	heart:	n/a
14	chr3:49588245-49588295	NB4	blood:	n/a
15	chr3:49588245-49588295	HMEC	breast:	n/a
16	chr3:49588245-49588295	T-47D	breast:	n/a
17	chr3:49588245-49588295	SK-N-SH_RA	brain:	n/a
18	chr3:49588245-49588295	PrEC	prostate:	n/a
19	chr3:49588245-49588295	BE2_C	brain:	n/a
20	chr3:49588245-49588295	AG04449	skin:	fetal
21	chr3:49588245-49588295	GM12891	blood:	n/a
22	chr3:49588245-49588295	GM12878	blood:	n/a
23	chr3:49588245-49588295	NH-A	brain:	n/a
24	chr3:49588245-49588295	SKMC	muscle:	n/a
25	chr3:49588245-49588295	HepG2	liver:	n/a
26	chr3:49588245-49588295	HRE	kidney:	n/a
27	chr3:49588245-49588295	SK-N-MC	brain:	n/a
28	chr3:49588245-49588295	NHDF-neo	bronchial:	n/a
29	chr3:49588245-49588295	HNPCEpiC	eye:	n/a
30	chr3:49588245-49588295	HCPEpiC	choroid plexus:	n/a
31	chr3:49588245-49588295	HL-60	blood:	n/a
32	chr3:49588245-49588295	SAEC	small airway:	n/a
33	chr3:49588245-49588295	SK-N-SH	brain:	n/a
34	chr3:49588245-49588295	Caco-2	colon:	n/a
35	chr3:49588245-49588295	HCM	heart:	n/a
36	chr3:49588245-49588295	AG04450	lung:	fetal
37	chr3:49588245-49588295	Hela-S3	cervix:	n/a
38	chr3:49588245-49588295	AG10803	skin:	n/a
39	chr3:49588245-49588295	HEEpiC	esophagus:	n/a
40	chr3:49588245-49588295	PANC-1	pancreas:	n/a
41	chr3:49588245-49588295	A549	lung:	n/a
42	chr3:49588245-49588295	MCF10A-Er-Src	breast:	n/a
43	chr3:49588245-49588295	PFSK-1	brain:	n/a
44	chr3:49588245-49588295	H1-hESC	embryonic stem cell:	embryo
45	chr3:49588245-49588295	CMK	blood:	n/a
46	chr3:49588245-49588295	U87	brain:	n/a
47	chr3:49588245-49588295	GM19239	blood:	n/a
48	chr3:49588245-49588295	Jurkat	blood:	n/a
49	chr3:49588245-49588295	NHBE	bronchial:	n/a
50	chr3:49588245-49588295	LNCaP	prostate:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49585320..49587935-chr3:49676099..49678339,2	K562	blood:
2	chr3:49582614..49585275-chr3:49588937..49591341,2	K562	blood:
3	chr3:49584919..49586555-chr3:49711963..49713638,2	MCF-7	breast:
4	chr3:49588932..49590951-chr3:49710802..49712975,2	K562	blood:
5	chr3:49588369..49590572-chr3:49704819..49707525,2	K562	blood:
6	chr3:49576628..49579352-chr3:49585412..49588058,3	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NICN1-1	chr3:49588728-49588875	ENSG00000226913
2	lnc-NICN1-1	chr3:49590374-49591536	NONHSAT089709
3	lnc-NICN1-1	chr3:49587676-49588875	NONHSAT089707
4	lnc-NICN1-1	chr3:49586739-49588875	XLOC_003118
5	lnc-NICN1-1	chr3:49586739-49588875	ENSG00000226913

No data

Variant related genes	Relation type
BSN	TF binding region
BSN	CpG island
ENSG00000164062	chromatin interactions
CHL1	miRNA target sites
KLHL28	miRNA target sites

Extended variants
information (count: 111 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:111 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553061832	chr3:49586466-49586467	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs148961138	chr3:49586496-49586497	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs554690242	chr3:49586512-49586513	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs142853520	chr3:49586540-49586541	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs146557783	chr3:49586542-49586543	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs564850754	chr3:49586597-49586598	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs569221710	chr3:49586628-49586629	Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs554803996	chr3:49586661-49586662	Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs541306555	chr3:49586671-49586672	Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs75470186	chr3:49586700-49586701	Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs529814586	chr3:49586829-49586830	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs367712376	chr3:49586979-49586980	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs77701561	chr3:49586985-49586986	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs548013550	chr3:49587026-49587027	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs375773602	chr3:49587054-49587055	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs563168314	chr3:49587064-49587065	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs200704753	chr3:49587074-49587075	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs531650257	chr3:49587110-49587111	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs550018017	chr3:49587178-49587179	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs571607774	chr3:49587202-49587203	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs59579780	chr3:49587211-49587212	Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs572871097	chr3:49587240-49587241	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs193207104	chr3:49587393-49587394	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs566279791	chr3:49587407-49587408	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs114465719	chr3:49587448-49587449	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs555173212	chr3:49587463-49587464	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs139009816	chr3:49587466-49587467	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs77682947	chr3:49587468-49587469	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs369215887	chr3:49587527-49587528	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs558408147	chr3:49587536-49587537	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs183623920	chr3:49587646-49587647	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs540695873	chr3:49587653-49587654	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs553214584	chr3:49587675-49587676	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs574353654	chr3:49587729-49587730	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs541726598	chr3:49587752-49587753	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs112108559	chr3:49587812-49587813	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs187335718	chr3:49587872-49587873	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs530660537	chr3:49587877-49587878	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs140694974	chr3:49587937-49587938	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs191816303	chr3:49587957-49587958	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs183895482	chr3:49587983-49587984	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs547439924	chr3:49588058-49588059	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs371016925	chr3:49588095-49588096	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs35883547	chr3:49588109-49588110	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs566101402	chr3:49588124-49588125	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs377609188	chr3:49588125-49588126	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs115541747	chr3:49588138-49588139	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs568277527	chr3:49588157-49588158	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs570252062	chr3:49588172-49588173	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs150456231	chr3:49588189-49588190	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:100)

Disease	PMID	Source
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49585200-49590600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:49585400-49590600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:49585800-49590400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:49586000-49590800	Weak transcription	Right Ventricle	heart
5	chr3:49586600-49586800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:49587400-49588200	Enhancers	HUVEC	blood vessel
7	chr3:49587400-49589800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:49587400-49590600	Enhancers	HepG2	liver
9	chr3:49587600-49587800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:49587600-49587800	Enhancers	Spleen	Spleen
11	chr3:49587600-49588400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:49587600-49590600	Weak transcription	Right Atrium	heart
13	chr3:49587800-49588000	Enhancers	Lung	lung
14	chr3:49587800-49590600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:49588000-49588200	Enhancers	Adipose Nuclei	Adipose
16	chr3:49588000-49588200	Enhancers	Brain Angular Gyrus	brain
17	chr3:49588000-49589800	Weak transcription	Lung	lung
18	chr3:49588000-49590600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:49588200-49590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:49588200-49590800	Weak transcription	HUVEC	blood vessel
21	chr3:49588200-49591000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:49588400-49590400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:49588400-49590600	Weak transcription	Adipose Nuclei	Adipose
24	chr3:49588600-49590400	Weak transcription	Brain Angular Gyrus	brain
25	chr3:49588600-49590600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:49588800-49591000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:49589000-49590200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr3:49589000-49590400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:49589000-49591200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:49589200-49589400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:49589200-49589400	Enhancers	Fetal Intestine Large	intestine
32	chr3:49589200-49590600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:49589400-49589600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:49589400-49590800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:49589400-49590800	Weak transcription	Fetal Intestine Large	intestine
36	chr3:49589400-49591200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr3:49589600-49589800	Bivalent Enhancer	Primary T cells from cord blood	blood
38	chr3:49589600-49590000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr3:49589600-49590600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:49589600-49591200	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:49589800-49590000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:49589800-49590200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:49589800-49590600	Enhancers	Dnd41	blood
44	chr3:49589800-49590800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:49589800-49591000	Enhancers	Lung	lung
46	chr3:49590200-49590800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:49590200-49590800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:49590400-49590600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:49590400-49590600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr3:49590400-49590600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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