Variant report

Variant	nsv590269
Chromosome Location	chr3:50410778-50413707
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50394292..50396980-chr3:50412055..50414700,2	K562	blood:
2	chr3:50412196..50414182-chr3:50466596..50468838,2	MCF-7	breast:
3	chr3:50387777..50390852-chr3:50409730..50411356,3	K562	blood:
4	chr3:50405624..50407617-chr3:50410447..50413698,3	K562	blood:
5	chr3:50402409..50404056-chr3:50409776..50411818,2	K562	blood:

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

Extended variants
information (count: 92 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:92 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs587759948	chr3:50410784-50410785	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs587657195	chr3:50410811-50410812	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs113506599	chr3:50410870-50410871	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs587612846	chr3:50410919-50410920	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs587613080	chr3:50411049-50411050	Enhancers Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs111210618	chr3:50411051-50411052	Enhancers Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs192148914	chr3:50411076-50411077	Enhancers Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs183573199	chr3:50411139-50411140	Enhancers Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs61121908	chr3:50411169-50411170	Enhancers Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs78671882	chr3:50411188-50411189	Enhancers Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs587677916	chr3:50411276-50411277	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs587750288	chr3:50411279-50411280	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs587625466	chr3:50411332-50411333	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs188570794	chr3:50411538-50411539	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs587682874	chr3:50411641-50411642	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs587764362	chr3:50411645-50411646	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs375703641	chr3:50411840-50411841	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs78773596	chr3:50411846-50411847	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs587687389	chr3:50411952-50411953	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs587727210	chr3:50411954-50411955	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs140772714	chr3:50412074-50412075	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs587618940	chr3:50412077-50412078	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs587701993	chr3:50412084-50412085	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs373427507	chr3:50412157-50412158	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs199862239	chr3:50412208-50412209	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs377584163	chr3:50412249-50412250	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs200831326	chr3:50412250-50412251	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs373256058	chr3:50412258-50412259	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs377394876	chr3:50412267-50412268	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs371625053	chr3:50412270-50412271	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs72934827	chr3:50412299-50412300	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs141683679	chr3:50412324-50412325	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs370929154	chr3:50412327-50412328	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs374605359	chr3:50412378-50412379	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs79686924	chr3:50412379-50412380	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs375634251	chr3:50412398-50412399	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs587757073	chr3:50412412-50412413	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs587670913	chr3:50412422-50412423	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs587727863	chr3:50412427-50412428	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs190270790	chr3:50412472-50412473	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs587678693	chr3:50412504-50412505	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs587737636	chr3:50412597-50412598	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs587593931	chr3:50412625-50412626	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs587672338	chr3:50412653-50412654	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs12489057	chr3:50412712-50412713	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs182565438	chr3:50412714-50412715	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs587738742	chr3:50412715-50412716	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs587630506	chr3:50412767-50412768	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs370941440	chr3:50412777-50412778	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs587687907	chr3:50412787-50412788	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:97)

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

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50403200-50417200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:50404600-50415400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:50405000-50416400	Weak transcription	Gastric	stomach
4	chr3:50405800-50411200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:50406000-50411000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:50407400-50413400	Enhancers	Brain Germinal Matrix	brain
7	chr3:50407600-50411000	Enhancers	Fetal Muscle Leg	muscle
8	chr3:50408200-50410800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:50408200-50411000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:50408200-50411000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:50408400-50410800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:50408400-50411400	Enhancers	Fetal Stomach	stomach
13	chr3:50408400-50413200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:50408600-50413000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:50408800-50411000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:50408800-50412000	Weak transcription	Lung	lung
17	chr3:50408800-50413000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:50408800-50423800	Weak transcription	Fetal Brain Female	brain
19	chr3:50409000-50419600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:50409200-50420200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:50409400-50410800	Enhancers	A549	lung
22	chr3:50409400-50412200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:50409400-50412800	Enhancers	Fetal Thymus	thymus
24	chr3:50409600-50410800	Enhancers	Fetal Intestine Small	intestine
25	chr3:50409600-50410800	Enhancers	Fetal Muscle Trunk	muscle
26	chr3:50409600-50411200	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:50409600-50411400	Enhancers	Fetal Brain Male	brain
28	chr3:50409800-50411000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr3:50409800-50411600	Enhancers	Primary T cells from cord blood	blood
30	chr3:50409800-50412200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:50409800-50412600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:50409800-50412600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:50410000-50410800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:50410000-50410800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:50410000-50410800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:50410000-50412200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:50410000-50413400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:50410200-50410800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:50410200-50411400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:50410200-50411400	Enhancers	Fetal Kidney	kidney
41	chr3:50410200-50415800	Weak transcription	Spleen	Spleen
42	chr3:50410600-50410800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr3:50410600-50411000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:50410600-50411400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:50410600-50412000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:50410600-50412200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:50410800-50412000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:50410800-50412000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:50410800-50412000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:50410800-50412000	Weak transcription	A549	lung

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