Variant report

Variant	nsv548504
Chromosome Location	chr1:189301911-189456312
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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:189399166..189401720-chr1:189433273..189435659,2	K562	blood:
2	chr1:189409498..189411737-chr1:189422806..189424517,2	MCF-7	breast:
3	chr1:189424671..189426547-chr1:189428199..189429967,2	K562	blood:
4	chr1:189416774..189418507-chr1:189422911..189425482,2	K562	blood:
5	chr1:189121464..189123287-chr1:189388904..189390413,2	K562	blood:
6	chr1:189119463..189122039-chr1:189394507..189396400,2	K562	blood:
7	chr1:189390529..189394907-chr1:189395498..189400534,5	K562	blood:
8	chr1:189398752..189399352-chr1:190289866..190290710,2	MCF-7	breast:
9	chr1:188762438..188765055-chr1:189455240..189458166,2	MCF-7	breast:
10	chr1:189398408..189399387-chr1:189661985..189662829,2	MCF-7	breast:
11	chr1:189390529..189394907-chr1:189395498..189400534,5	K562	blood:
12	chr1:189398440..189399083-chr1:189642226..189643036,4	MCF-7	breast:
13	chr1:189416774..189418507-chr1:189422911..189425482,2	K562	blood:
14	chr1:189409498..189411737-chr1:189422806..189424517,2	MCF-7	breast:
15	chr1:189398256..189399319-chr1:190290193..190290907,3	MCF-7	breast:
16	chr1:189424671..189426547-chr1:189428199..189429967,2	K562	blood:
17	chr1:189398245..189398855-chr3:191237330..191238213,2	MCF-7	breast:
18	chr1:189408828..189411419-chr1:189412082..189414422,2	K562	blood:
19	chr1:189389640..189390412-chr9:79530846..79531642,2	MCF-7	breast:
20	chr1:189189341..189190044-chr1:189398354..189398974,2	MCF-7	breast:
21	chr1:189399166..189401720-chr1:189433273..189435659,2	K562	blood:
22	chr1:188746632..188749210-chr1:189368064..189370522,2	K562	blood:
23	chr1:189408828..189411419-chr1:189412082..189414422,2	K562	blood:
24	chr1:189275475..189276987-chr1:189302090..189304788,2	K562	blood:
25	chr1:189398509..189399144-chr1:189660311..189661261,2	MCF-7	breast:

No data

Extended variants
information (count: 636 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:636 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs373725014	chr1:189305035-189305036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs568809802	chr1:189305039-189305040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs375019193	chr1:189305041-189305042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs565332089	chr1:189305052-189305053	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs71118401	chr1:189305069-189305070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs11388514	chr1:189305070-189305071	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs57030071	chr1:189305097-189305098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs74139427	chr1:189305114-189305115	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs548252688	chr1:189305145-189305146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs568190597	chr1:189305163-189305164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs376172147	chr1:189305164-189305165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs6697824	chr1:189305179-189305180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs193096579	chr1:189305236-189305237	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs185861047	chr1:189305271-189305272	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs371153874	chr1:189305273-189305274	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs577522222	chr1:189305277-189305278	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs532506938	chr1:189305284-189305285	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs74139428	chr1:189305287-189305288	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs144617410	chr1:189305296-189305297	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs556600414	chr1:189305298-189305299	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs576349105	chr1:189305322-189305323	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs541380266	chr1:189305325-189305326	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs541889442	chr1:189305336-189305337	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs74139429	chr1:189305343-189305344	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs572251243	chr1:189305372-189305373	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs559805389	chr1:189305374-189305375	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs374454836	chr1:189305375-189305376	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs74139430	chr1:189305383-189305384	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs74139431	chr1:189305388-189305389	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs189111216	chr1:189305401-189305402	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs562674936	chr1:189305413-189305414	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs531315277	chr1:189305425-189305426	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs57845205	chr1:189305429-189305430	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs140857471	chr1:189305484-189305485	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs533829562	chr1:189305506-189305507	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs549991945	chr1:189305533-189305534	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs12118925	chr1:189305535-189305536	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs181018212	chr1:189305558-189305559	ZNF genes & repeats Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs144716018	chr1:189305604-189305605	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs556797390	chr1:189305622-189305623	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs576689951	chr1:189305680-189305681	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs370308209	chr1:189305703-189305704	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs535837373	chr1:189305734-189305735	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs555517154	chr1:189305751-189305752	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs572113899	chr1:189305784-189305785	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs74139432	chr1:189305785-189305786	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs74139433	chr1:189305786-189305787	ZNF genes & repeats Genic enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs185170476	chr1:189305803-189305804	ZNF genes & repeats Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs201786631	chr1:189305839-189305840	ZNF genes & repeats Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs116495972	chr1:189305896-189305897	ZNF genes & repeats Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	20688739	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21611746	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17899364	CNVD
Non-small cell lung cancer	19010865	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Lung adenocarcinoma	17086460	CNVD
Glioblastoma multiforme	22286061	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189305000-189305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:189305200-189305400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:189305400-189305600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:189305400-189306000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:189305600-189306000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:189305800-189306000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:189306000-189306200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:189306000-189306200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:189318400-189319200	Enhancers	Stomach Mucosa	stomach
10	chr1:189318600-189319000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:189319200-189325200	Weak transcription	Stomach Mucosa	stomach
12	chr1:189320200-189320800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:189320200-189320800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:189320200-189320800	Active TSS	Ovary	ovary
15	chr1:189320200-189320800	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:189320200-189320800	Active TSS	A549	lung
17	chr1:189320200-189321000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:189320400-189320800	Active TSS	Duodenum Mucosa	Duodenum
19	chr1:189320400-189320800	Active TSS	Right Atrium	heart
20	chr1:189320400-189320800	Active TSS	GM12878-XiMat	blood
21	chr1:189320400-189321000	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr1:189320800-189321200	Flanking Active TSS	A549	lung
23	chr1:189321200-189321600	Enhancers	A549	lung
24	chr1:189325000-189325200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:189325200-189325600	Enhancers	Stomach Mucosa	stomach
26	chr1:189325200-189326600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:189325600-189326600	Weak transcription	Stomach Mucosa	stomach
28	chr1:189326600-189327000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:189326600-189327000	Enhancers	Stomach Mucosa	stomach
30	chr1:189343800-189344600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:189344000-189344600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:189370200-189370400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:189370400-189370800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:189372200-189373000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:189373000-189373200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:189373200-189373400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:189373400-189374400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:189374200-189374400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
39	chr1:189374200-189374400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:189374200-189375200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:189374400-189374600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:189374400-189374600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:189374400-189375600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:189374400-189375800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr1:189374600-189374800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:189374600-189374800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:189374600-189374800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:189374600-189375400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:189374800-189375000	Enhancers	H9 Cell Line	embryonic stem cell
50	chr1:189374800-189375400	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links