Variant report

Variant	nsv546304
Chromosome Location	chr1:56195659-56240015
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:56221833..56223709-chr6:26204838..26207511,2	K562	blood:
2	chr1:56195823..56198284-chr1:56202189..56204581,2	K562	blood:
3	chr1:56195823..56198284-chr1:56202189..56204581,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCSK9-3	chr1:56196853-56200675	ENSG00000234810

Variant related genes	Relation type
ENSG00000198518	chromatin interactions

Extended variants
information (count: 1354 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:1354 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4111070	chr1:56195659-56195660	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs554949331	chr1:56195666-56195667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs143770644	chr1:56195715-56195716	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs57681335	chr1:56195753-56195754	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs528009151	chr1:56195761-56195762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs368810471	chr1:56195808-56195809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs554239886	chr1:56195809-56195810	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs146369507	chr1:56195846-56195847	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs545881369	chr1:56195851-56195852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs186238254	chr1:56195860-56195861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs376741424	chr1:56195874-56195875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs114492210	chr1:56195898-56195899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs544119220	chr1:56195945-56195946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs560996888	chr1:56196005-56196006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs555425495	chr1:56196019-56196020	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs529903692	chr1:56196030-56196031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs549666662	chr1:56196070-56196071	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs190810353	chr1:56196082-56196083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs532292093	chr1:56196100-56196101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs3972660	chr1:56196127-56196128	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs370161169	chr1:56196129-56196130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs568905776	chr1:56196145-56196146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs537807389	chr1:56196210-56196211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs370492101	chr1:56196273-56196274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs139737672	chr1:56196300-56196301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs534411581	chr1:56196302-56196303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs549820947	chr1:56196309-56196310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs554109989	chr1:56196328-56196329	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs577002905	chr1:56196343-56196344	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs545930229	chr1:56196362-56196363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs529122710	chr1:56196399-56196400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs182611892	chr1:56196415-56196416	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs368216639	chr1:56196422-56196423	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs561245726	chr1:56196426-56196427	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs188860296	chr1:56196506-56196507	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs1165510	chr1:56196527-56196528	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs560116567	chr1:56196540-56196541	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs144512007	chr1:56196571-56196572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs190755045	chr1:56196593-56196594	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs568944391	chr1:56196607-56196608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs113189903	chr1:56196623-56196624	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs547831487	chr1:56196646-56196647	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs1165509	chr1:56196649-56196650	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs534269731	chr1:56196673-56196674	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs1165508	chr1:56196678-56196679	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs570729995	chr1:56196706-56196707	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs115227933	chr1:56196767-56196768	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs36000701	chr1:56196781-56196782	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs397863928	chr1:56196784-56196785	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs187357288	chr1:56196793-56196794	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:95)

Disease	PMID	Source
Papillary thyroid carcinoma	21436994	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Rett syndrome	21593744	CNVD
Meckel-Gruber syndrome	21572526	CNVD
Breast cancer	16620391	CNVD
Multiple myeloma	16616336	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Prostate cancer	16573809	CNVD
Gastric adenocarcinoma	19115996	CNVD
Parathyroid adenoma	22454399	CNVD
Breast cancer	16608533	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Developmental delay	19490664	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	21720365	CNVD

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56186400-56207600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:56193000-56200600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:56193000-56206600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:56193800-56200400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:56196400-56197000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:56197000-56197400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:56197400-56197600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:56197600-56200200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:56200000-56201400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:56200200-56201200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:56200200-56201400	Enhancers	NHDF-Ad	bronchial
12	chr1:56200200-56201600	Enhancers	Fetal Muscle Leg	muscle
13	chr1:56200400-56201200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:56200400-56201200	Enhancers	Osteobl	bone
15	chr1:56200600-56201000	Enhancers	NHLF	lung
16	chr1:56200600-56201200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:56200600-56201200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:56200600-56201200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:56200600-56201200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:56200600-56201400	Enhancers	HSMMtube	muscle
21	chr1:56200800-56201200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:56200800-56201400	Enhancers	HSMM	muscle
23	chr1:56201000-56206400	Weak transcription	NHLF	lung
24	chr1:56201200-56206400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:56201200-56206400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:56201400-56202800	Weak transcription	HSMM	muscle
27	chr1:56201400-56206200	Weak transcription	NHDF-Ad	bronchial
28	chr1:56201400-56206600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:56201600-56202800	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:56202800-56203400	Enhancers	HSMM	muscle
31	chr1:56203400-56203600	Weak transcription	HSMM	muscle
32	chr1:56204200-56204800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr1:56205600-56207800	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:56206200-56207200	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:56206200-56208400	Enhancers	NHDF-Ad	bronchial
36	chr1:56206400-56207000	Enhancers	Fetal Kidney	kidney
37	chr1:56206400-56207000	Enhancers	Fetal Stomach	stomach
38	chr1:56206400-56207000	Enhancers	Ovary	ovary
39	chr1:56206400-56207600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:56206400-56207800	Enhancers	Fetal Lung	lung
41	chr1:56206400-56208200	Enhancers	NHLF	lung
42	chr1:56206400-56208400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:56206600-56207200	Enhancers	Brain Hippocampus Middle	brain
44	chr1:56206600-56207800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:56206600-56208200	Enhancers	Brain Substantia Nigra	brain
46	chr1:56206600-56208400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:56206800-56207800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr1:56206800-56207800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:56206800-56208200	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr1:56206800-56208200	Enhancers	HUES6 Cell Line	embryonic stem cell

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