Variant report

Variant	nsv1006542
Chromosome Location	chr1:172253765-172304690
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:3)
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	chr1:172290323..172292944-chr1:172297056..172298732,2	MCF-7	breast:
2	chr1:172290799..172293766-chr1:172293837..172296183,4	MCF-7	breast:
3	chr1:172262678..172264424-chr1:172266629..172268521,2	K562	blood:
4	chr1:172248264..172251646-chr1:172254476..172256076,3	K562	blood:
5	chr1:172230387..172232137-chr1:172254891..172256764,2	K562	blood:
6	chr1:172253395..172255527-chr1:172290385..172292894,2	MCF-7	breast:
7	chr1:172290799..172293766-chr1:172293837..172296183,4	MCF-7	breast:
8	chr1:172256870..172259800-chr1:172260361..172262827,2	MCF-7	breast:
9	chr1:172223489..172225833-chr1:172289738..172293302,4	MCF-7	breast:
10	chr1:172262678..172264424-chr1:172266629..172268521,2	K562	blood:
11	chr1:171710381..171712610-chr1:172281687..172284320,2	K562	blood:
12	chr1:172261558..172263643-chr1:172263765..172267506,3	MCF-7	breast:
13	chr1:172253395..172255527-chr1:172290385..172292894,2	MCF-7	breast:
14	chr1:172294512..172295506-chr1:172329394..172330284,2	MCF-7	breast:
15	chr1:172290323..172292944-chr1:172297056..172298732,2	MCF-7	breast:
16	chr1:172256870..172259800-chr1:172260361..172262827,2	MCF-7	breast:
17	chr1:172244510..172246522-chr1:172290374..172293118,2	MCF-7	breast:
18	chr1:172290820..172291829-chr1:172368303..172369352,3	MCF-7	breast:
19	chr1:172261558..172263643-chr1:172263765..172267506,3	MCF-7	breast:
20	chr1:172293750..172296257-chr1:172325539..172327779,3	MCF-7	breast:
21	chr1:172227773..172230310-chr1:172254726..172257439,2	MCF-7	breast:
22	chr1:172063383..172065738-chr1:172289085..172291783,2	MCF-7	breast:
23	chr1:172291112..172293715-chr1:172326566..172328931,2	MCF-7	breast:
24	chr1:172290966..172293542-chr1:172305681..172308662,2	MCF-7	breast:
25	chr1:172250146..172252710-chr1:172254053..172256076,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-3	chr1:172257872-172258194	expReg_chr1_17771_-
2	lnc-C1orf105-2	chr1:172258270-172258401	NONHSAT007606
3	lnc-C1orf105-2	chr1:172258544-172258746	NONHSAT007606

No data

Variant related genes	Relation type
ENSG00000117533	chromatin interactions

Extended variants
information (count: 1922 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:1922 , 50 per page) page: 1 2 3 4 5 6 7 ... 39

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3850640	chr1:172253765-172253766	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs553001937	chr1:172253766-172253767	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs116349556	chr1:172253799-172253800	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs115713387	chr1:172253810-172253811	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs527641774	chr1:172253840-172253841	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs143296157	chr1:172253903-172253904	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs114157640	chr1:172253997-172253998	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs548079721	chr1:172254003-172254004	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs543691067	chr1:172254026-172254027	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs564964503	chr1:172254098-172254099	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs543399875	chr1:172254108-172254109	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs2586392	chr1:172254193-172254194	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs182205730	chr1:172254208-172254209	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs75609615	chr1:172254329-172254330	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs147097914	chr1:172254352-172254353	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs116155888	chr1:172254360-172254361	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs537372949	chr1:172254384-172254385	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs564867072	chr1:172254406-172254407	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs12161561	chr1:172254407-172254408	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs185996598	chr1:172254420-172254421	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs534574246	chr1:172254441-172254442	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs12161563	chr1:172254483-172254484	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs370453589	chr1:172254492-172254493	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs552798676	chr1:172254552-172254553	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs190900802	chr1:172254578-172254579	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs574524369	chr1:172254610-172254611	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs138452321	chr1:172254657-172254658	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs549941593	chr1:172254658-172254659	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs555177046	chr1:172254683-172254684	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs143925466	chr1:172254720-172254721	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs543726711	chr1:172254725-172254726	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs2255707	chr1:172254777-172254778	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs150629302	chr1:172254870-172254871	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs541368364	chr1:172254871-172254872	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs563586012	chr1:172255003-172255004	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs559484506	chr1:172255022-172255023	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs368925834	chr1:172255027-172255028	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs548372064	chr1:172255028-172255029	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs182608543	chr1:172255046-172255047	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs368472665	chr1:172255062-172255063	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs139697410	chr1:172255091-172255092	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs528952438	chr1:172255146-172255147	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs60257339	chr1:172255168-172255169	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs149362774	chr1:172255186-172255187	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs143628364	chr1:172255208-172255209	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs373603586	chr1:172255209-172255210	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs72131604	chr1:172255210-172255211	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs10687290	chr1:172255226-172255227	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs548755209	chr1:172255229-172255230	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs186924586	chr1:172255231-172255232	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	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
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	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
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	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
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21509527	CNVD
Autism	20531469	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:438 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172239000-172262000	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:172247800-172255800	Weak transcription	Left Ventricle	heart
3	chr1:172247800-172256000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172248200-172255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:172248200-172255400	Weak transcription	HSMM	muscle
6	chr1:172248200-172255400	Weak transcription	NHLF	lung
7	chr1:172248200-172255800	Weak transcription	Aorta	Aorta
8	chr1:172249200-172255400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:172249200-172255600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:172249400-172256000	Weak transcription	Esophagus	oesophagus
11	chr1:172249600-172255000	Weak transcription	NHDF-Ad	bronchial
12	chr1:172251800-172257000	Weak transcription	Right Ventricle	heart
13	chr1:172253000-172253800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:172253000-172253800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:172253000-172257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:172253600-172254200	Enhancers	Colon Smooth Muscle	Colon
17	chr1:172253600-172254800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:172253800-172254800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:172253800-172255200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:172254200-172254400	Enhancers	Ovary	ovary
21	chr1:172254200-172254400	Weak transcription	Right Atrium	heart
22	chr1:172254200-172255600	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:172254400-172254600	Enhancers	Psoas Muscle	Psoas
24	chr1:172254400-172254600	ZNF genes & repeats	Right Atrium	heart
25	chr1:172254400-172255800	Weak transcription	Ovary	ovary
26	chr1:172254600-172255800	Weak transcription	Right Atrium	heart
27	chr1:172254800-172255400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:172254800-172256000	Weak transcription	Psoas Muscle	Psoas
29	chr1:172254800-172257200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:172254800-172258400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:172255000-172255400	Enhancers	NHDF-Ad	bronchial
32	chr1:172255000-172256600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr1:172255000-172256600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:172255200-172256400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:172255400-172255800	Flanking Active TSS	NHDF-Ad	bronchial
36	chr1:172255400-172256000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:172255400-172256000	Enhancers	HSMM	muscle
38	chr1:172255400-172256000	Enhancers	Osteobl	bone
39	chr1:172255400-172256200	Enhancers	Brain Anterior Caudate	brain
40	chr1:172255400-172256200	Enhancers	Brain Hippocampus Middle	brain
41	chr1:172255400-172256400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:172255400-172256400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:172255400-172256400	Enhancers	HSMMtube	muscle
44	chr1:172255400-172256600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr1:172255400-172256600	Enhancers	Fetal Lung	lung
46	chr1:172255400-172256600	Enhancers	Hela-S3	cervix
47	chr1:172255400-172256800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:172255400-172256800	Enhancers	HMEC	breast
49	chr1:172255400-172257200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:172255400-172257600	Enhancers	NHLF	lung

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