Variant report

Variant	nsv1000857
Chromosome Location	chr3:53031724-53045913
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53045411..53048406-chr3:53050370..53052257,2	K562	blood:
2	chr3:53037209..53039730-chr3:53079605..53081876,2	MCF-7	breast:
3	chr3:53029648..53031787-chr3:53078604..53081365,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	chromatin interactions

Extended variants
information (count: 565 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:565 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs569624224	chr3:53031774-53031775	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs145254428	chr3:53031782-53031783	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs554739136	chr3:53031788-53031789	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs532851939	chr3:53031850-53031851	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs76760818	chr3:53031854-53031855	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs564728709	chr3:53031872-53031873	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs11708675	chr3:53031912-53031913	Weak transcription Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs547190274	chr3:53031927-53031928	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs140899260	chr3:53031928-53031929	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs189111706	chr3:53031933-53031934	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs549560886	chr3:53031939-53031940	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs149662063	chr3:53032002-53032003	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs72965340	chr3:53032016-53032017	Weak transcription Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs181841801	chr3:53032023-53032024	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs145479960	chr3:53032053-53032054	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs534984728	chr3:53032062-53032063	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs554800424	chr3:53032070-53032071	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs565470279	chr3:53032133-53032134	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs574856373	chr3:53032153-53032154	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs375248220	chr3:53032154-53032155	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs148849073	chr3:53032169-53032170	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs577466686	chr3:53032202-53032203	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs546541897	chr3:53032203-53032204	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs559961278	chr3:53032208-53032209	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs145299408	chr3:53032218-53032219	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs540998540	chr3:53032222-53032223	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs35197205	chr3:53032224-53032225	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs376135196	chr3:53032235-53032236	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs560864467	chr3:53032245-53032246	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs532620977	chr3:53032264-53032265	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs529728764	chr3:53032265-53032266	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs549422240	chr3:53032281-53032282	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs569520737	chr3:53032301-53032302	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs532150252	chr3:53032313-53032314	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs9823865	chr3:53032349-53032350	Weak transcription Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs187360661	chr3:53032359-53032360	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs534737883	chr3:53032385-53032386	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs554947798	chr3:53032403-53032404	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs568608298	chr3:53032445-53032446	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs563189246	chr3:53032460-53032461	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs537552178	chr3:53032483-53032484	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs190956662	chr3:53032486-53032487	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs56026870	chr3:53032488-53032489	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
44	rs140645591	chr3:53032572-53032573	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs145818482	chr3:53032573-53032574	Weak transcription Enhancers Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs73839786	chr3:53032639-53032640	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs566403224	chr3:53032644-53032645	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs560945235	chr3:53032686-53032687	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs527370884	chr3:53032694-53032695	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs529593766	chr3:53032707-53032708	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
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
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
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
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
Adrenocortical carcinoma	18281524	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:215 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
2	chr3:53012600-53032600	Weak transcription	Pancreas	Pancrea
3	chr3:53018000-53044200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:53018200-53045200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:53018600-53032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:53019200-53032800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:53019200-53039600	Weak transcription	GM12878-XiMat	blood
9	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:53019800-53044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:53020600-53057000	Weak transcription	Dnd41	blood
12	chr3:53022600-53043000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:53022600-53050400	Weak transcription	Primary B cells from cord blood	blood
14	chr3:53025200-53032600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:53025200-53039000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:53025600-53061600	Weak transcription	Lung	lung
17	chr3:53026200-53032600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:53026200-53037800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:53026200-53042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:53026200-53044200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:53027200-53043400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:53027600-53061600	Weak transcription	Liver	Liver
23	chr3:53027800-53051000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:53028000-53032800	Weak transcription	Esophagus	oesophagus
25	chr3:53028400-53044200	Weak transcription	Adipose Nuclei	Adipose
26	chr3:53028600-53032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:53028800-53032400	Weak transcription	Fetal Stomach	stomach
28	chr3:53029600-53033200	Weak transcription	A549	lung
29	chr3:53029800-53032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:53030000-53033200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:53030200-53034200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:53030400-53052400	Weak transcription	Primary T cells from cord blood	blood
34	chr3:53030800-53050400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:53031000-53033200	Weak transcription	Gastric	stomach
36	chr3:53031000-53039800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:53031400-53032800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:53031400-53033800	Strong transcription	Fetal Intestine Small	intestine
39	chr3:53031600-53031800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:53031600-53031800	Enhancers	Hela-S3	cervix
41	chr3:53031600-53034600	Weak transcription	Thymus	Thymus
42	chr3:53031600-53038000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:53031800-53032400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:53031800-53032800	Weak transcription	Right Ventricle	heart
45	chr3:53031800-53033600	Active TSS	Hela-S3	cervix
46	chr3:53032000-53032600	Weak transcription	Spleen	Spleen
47	chr3:53032000-53035200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:53032400-53032600	Enhancers	Placenta	Placenta
49	chr3:53032400-53033600	Strong transcription	Fetal Stomach	stomach
50	chr3:53032400-53033800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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