Variant report

Variant	nsv590259
Chromosome Location	chr3:50408398-50411819
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:50402409..50404056-chr3:50409776..50411818,2	K562	blood:
2	chr3:50407190..50409972-chr3:50577719..50580221,2	K562	blood:
3	chr3:50407737..50410112-chr3:50424315..50425913,2	K562	blood:
4	chr3:50407840..50408665-chr3:50579653..50580547,2	MCF-7	breast:
5	chr3:50401635..50404173-chr3:50408002..50409529,2	MCF-7	breast:
6	chr3:50387777..50390852-chr3:50409730..50411356,3	K562	blood:
7	chr3:50407329..50410054-chr3:50589199..50591435,2	K562	blood:
8	chr3:50405624..50407617-chr3:50410447..50413698,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272104	chromatin interactions
ENSG00000271858	chromatin interactions
ENSG00000007402	chromatin interactions
ENSG00000114388	chromatin interactions
ENSG00000114395	chromatin interactions

Extended variants
information (count: 90 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:90 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12629047	chr3:50408398-50408399	Weak transcription Bivalent Enhancer Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs147611392	chr3:50408429-50408430	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs587677244	chr3:50408461-50408462	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs376593320	chr3:50408487-50408488	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs587731584	chr3:50408537-50408538	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs587627404	chr3:50408631-50408632	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs587686684	chr3:50408699-50408700	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs140537855	chr3:50408727-50408728	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs144490133	chr3:50408737-50408738	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs587665955	chr3:50408745-50408746	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs587731330	chr3:50408773-50408774	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs35155126	chr3:50408777-50408778	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs113335665	chr3:50408778-50408779	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs587628719	chr3:50408781-50408782	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs587660947	chr3:50408800-50408801	Enhancers Bivalent Enhancer Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs397716409	chr3:50408801-50408802	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs11914549	chr3:50408855-50408856	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs181277136	chr3:50408892-50408893	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs185464449	chr3:50409070-50409071	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs587765050	chr3:50409087-50409088	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs587621890	chr3:50409133-50409134	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs587697576	chr3:50409159-50409160	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs587759162	chr3:50409166-50409167	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs587674909	chr3:50409183-50409184	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs116702923	chr3:50409190-50409191	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs587775581	chr3:50409251-50409252	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs372833045	chr3:50409275-50409276	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs587664089	chr3:50409295-50409296	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs587718886	chr3:50409308-50409309	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs112492607	chr3:50409309-50409310	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs3216199	chr3:50409338-50409339	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs397840202	chr3:50409339-50409340	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs587673850	chr3:50409398-50409399	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs587699406	chr3:50409439-50409440	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs587744874	chr3:50409487-50409488	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs375898638	chr3:50409541-50409542	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs587605044	chr3:50409629-50409630	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs12629853	chr3:50409632-50409633	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs369706795	chr3:50409639-50409640	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs148813323	chr3:50409659-50409660	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs114601421	chr3:50409702-50409703	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs587659827	chr3:50409802-50409803	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
43	rs2236948	chr3:50409826-50409827	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs189872875	chr3:50409837-50409838	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
45	rs587698428	chr3:50409844-50409845	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
46	rs587772104	chr3:50409847-50409848	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs587652119	chr3:50409885-50409886	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
48	rs587709230	chr3:50409889-50409890	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
49	rs57053520	chr3:50409920-50409921	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
50	rs2236949	chr3:50410041-50410042	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:98)

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
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:148 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50403200-50408400	Weak transcription	Fetal Lung	lung
2	chr3:50403200-50417200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:50403400-50408400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:50403400-50410000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:50403600-50408400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:50403800-50408400	Weak transcription	Fetal Stomach	stomach
7	chr3:50403800-50409600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:50403800-50409600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:50403800-50409800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:50403800-50409800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:50403800-50410000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:50404000-50409400	Weak transcription	Fetal Thymus	thymus
13	chr3:50404000-50409800	Weak transcription	Thymus	Thymus
14	chr3:50404200-50410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:50404600-50409800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:50404600-50410000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:50404600-50415400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:50405000-50409800	Weak transcription	Primary T cells from cord blood	blood
19	chr3:50405000-50416400	Weak transcription	Gastric	stomach
20	chr3:50405200-50409800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:50405600-50409800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:50405600-50410000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:50405800-50411200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:50406000-50411000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:50406800-50409800	Weak transcription	Spleen	Spleen
26	chr3:50407200-50410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:50407400-50408800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:50407400-50408800	Strong transcription	Lung	lung
29	chr3:50407400-50409600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr3:50407400-50413400	Enhancers	Brain Germinal Matrix	brain
31	chr3:50407600-50411000	Enhancers	Fetal Muscle Leg	muscle
32	chr3:50408000-50408400	Enhancers	Fetal Heart	heart
33	chr3:50408000-50408800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:50408000-50408800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:50408000-50408800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:50408000-50409200	Enhancers	Brain Angular Gyrus	brain
37	chr3:50408000-50409200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr3:50408000-50409200	Enhancers	Fetal Brain Male	brain
39	chr3:50408000-50410200	Enhancers	K562	blood
40	chr3:50408200-50408400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:50408200-50408400	Enhancers	A549	lung
42	chr3:50408200-50408600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:50408200-50408600	Weak transcription	Fetal Brain Female	brain
44	chr3:50408200-50408800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:50408200-50408800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr3:50408200-50410800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:50408200-50411000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:50408200-50411000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr3:50408400-50408800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:50408400-50408800	Enhancers	HUES64 Cell Line	embryonic stem cell

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