Variant report

Variant	nsv1049903
Chromosome Location	chr12:9521487-9546454
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:19)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:9530894..9532008-chr12:9621312..9622244,4	MCF-7	breast:
2	chr12:9483967..9484695-chr12:9530892..9531873,3	MCF-7	breast:
3	chr12:9532106..9535030-chr12:9800116..9802366,2	MCF-7	breast:
4	chr12:9516871..9518767-chr12:9528942..9530878,2	MCF-7	breast:
5	chr12:9530855..9531819-chr12:9772155..9773338,3	MCF-7	breast:
6	chr12:9483381..9483965-chr12:9531043..9531743,2	MCF-7	breast:
7	chr12:9483413..9484009-chr12:9524583..9525215,2	MCF-7	breast:
8	chr12:9536927..9538446-chr12:9539967..9542011,2	K562	blood:
9	chr12:9536927..9538446-chr12:9539967..9542011,2	K562	blood:
10	chr12:9526563..9529363-chr12:9530052..9533405,3	MCF-7	breast:
11	chr12:9536132..9537679-chr12:9542165..9544182,2	MCF-7	breast:
12	chr12:9531253..9531816-chr12:9860516..9861214,2	MCF-7	breast:
13	chr12:9522809..9525392-chr12:9798242..9800347,2	K562	blood:
14	chr12:9526563..9529363-chr12:9530052..9533405,3	MCF-7	breast:
15	chr12:9539959..9542936-chr12:9543055..9546745,3	K562	blood:
16	chr12:9539959..9542936-chr12:9543055..9546745,3	K562	blood:
17	chr12:9216318..9217819-chr12:9520696..9522982,2	MCF-7	breast:
18	chr12:9216794..9217363-chr12:9524530..9525508,3	MCF-7	breast:
19	chr12:9536132..9537679-chr12:9542165..9544182,2	MCF-7	breast:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC2D-3	chr12:9520060-9522192	ENSG00000260423.1
2	lnc-PZP-11	chr12:9524266-9524628	NONHSAT026813
3	lnc-CLEC2D-3	chr12:9528409-9528682	NONHSAT026814
4	lnc-PZP-11	chr12:9533948-9534263	NONHSAT026813
5	lnc-CLEC2D-3	chr12:9529770-9529807	NONHSAT026815
6	lnc-CLEC2D-3	chr12:9528454-9528682	ENSG00000260423.1
7	lnc-CLEC2D-3	chr12:9528409-9528682	NONHSAT026815
8	lnc-CLEC2D-3	chr12:9520084-9522661	NONHSAT026811

No data

Variant related genes	Relation type
ENSG00000214851	chromatin interactions
ENSG00000256442	chromatin interactions
ENSG00000256594	chromatin interactions
ENSG00000245105	chromatin interactions

Extended variants
information (count: 742 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:742 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10771596	chr12:9521487-9521488	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs74062815	chr12:9521490-9521491	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs187047928	chr12:9521513-9521514	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs117798143	chr12:9521625-9521626	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs34271761	chr12:9521668-9521669	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs35672088	chr12:9521774-9521775	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs146507653	chr12:9521921-9521922	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs59757251	chr12:9522065-9522066	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs74792301	chr12:9522066-9522067	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs78797361	chr12:9522067-9522068	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs75303801	chr12:9522074-9522075	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs398018366	chr12:9522075-9522076	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs12309868	chr12:9522087-9522088	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs11050527	chr12:9522144-9522145	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs191866481	chr12:9522205-9522206	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs182234452	chr12:9522211-9522212	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs146830723	chr12:9522237-9522238	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs11050530	chr12:9522306-9522307	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs375020106	chr12:9522331-9522332	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs4883252	chr12:9522350-9522351	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs373756938	chr12:9522355-9522356	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs113230649	chr12:9522386-9522387	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs544246097	chr12:9522454-9522455	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs58713999	chr12:9522472-9522473	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
25	rs368251611	chr12:9522566-9522567	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
26	rs562431041	chr12:9522610-9522611	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs11050535	chr12:9522703-9522704	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs188025966	chr12:9522777-9522778	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs139930917	chr12:9522857-9522858	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs193093035	chr12:9522861-9522862	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs143409248	chr12:9522876-9522877	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs10743683	chr12:9522932-9522933	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs185486631	chr12:9523011-9523012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs573170807	chr12:9523029-9523030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs190413973	chr12:9523081-9523082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs554953952	chr12:9523112-9523113	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs7135599	chr12:9523115-9523116	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs191935289	chr12:9523163-9523164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs544161666	chr12:9523177-9523178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs545414262	chr12:9523211-9523212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs184407269	chr12:9523217-9523218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs114685296	chr12:9523415-9523416	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188466860	chr12:9523466-9523467	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs116529793	chr12:9523480-9523481	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs531083760	chr12:9523486-9523487	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs149558408	chr12:9523514-9523515	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs544823858	chr12:9523570-9523571	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs529849120	chr12:9523588-9523589	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs79379656	chr12:9523732-9523733	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs4882995	chr12:9523741-9523742	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:89)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Epilepsy	21858020	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
craniofacial dysmorphism	21918468	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Alzheimer''s disease	17160897	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	21611746	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
early-passage human iPS cells	21368824	CNVD
Obesity	21131291	CNVD
small cell lung cancer	20016488	CNVD
Incontinentia Pigmenti	22033527	CNVD
Oligozoospermia	20877625	CNVD
Sertoli-cell only syndrome	20877625	CNVD
Cancer	21272361	CNVD
Schizophrenia	20967226	CNVD

Chromatin state (count:169 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9516800-9521600	Enhancers	Fetal Lung	lung
2	chr12:9518600-9521600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:9518800-9527400	Weak transcription	HepG2	liver
4	chr12:9520200-9524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:9520400-9524400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:9521200-9524600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:9521600-9523400	Weak transcription	Fetal Lung	lung
8	chr12:9521600-9524600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:9523400-9525800	Strong transcription	Fetal Lung	lung
10	chr12:9524400-9524800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:9524600-9525600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:9524600-9525800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:9524800-9525200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr12:9524800-9528600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:9525200-9525600	Enhancers	Primary T cells from cord blood	blood
16	chr12:9525800-9526600	Weak transcription	Fetal Lung	lung
17	chr12:9526600-9530200	Strong transcription	Fetal Lung	lung
18	chr12:9527400-9528000	Enhancers	HepG2	liver
19	chr12:9528000-9531400	Weak transcription	HepG2	liver
20	chr12:9528600-9529000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:9528600-9533400	Weak transcription	Gastric	stomach
22	chr12:9529000-9531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:9530200-9533400	Weak transcription	Fetal Lung	lung
24	chr12:9531000-9531200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:9531200-9531400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:9531400-9531600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr12:9531400-9531600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:9531400-9532000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:9531400-9532200	Enhancers	HepG2	liver
30	chr12:9531600-9532600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:9531600-9534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:9531800-9532000	Enhancers	Fetal Muscle Trunk	muscle
33	chr12:9532200-9533400	Weak transcription	HepG2	liver
34	chr12:9532600-9532800	Enhancers	Lung	lung
35	chr12:9532600-9533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:9532800-9533400	Weak transcription	Lung	lung
37	chr12:9533200-9533600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:9533200-9534200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:9533200-9534600	Enhancers	Adipose Nuclei	Adipose
40	chr12:9533200-9535000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:9533400-9533800	Enhancers	Gastric	stomach
42	chr12:9533400-9534000	Strong transcription	Fetal Lung	lung
43	chr12:9533400-9534200	Enhancers	Lung	lung
44	chr12:9533400-9535000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:9533400-9535000	Enhancers	HepG2	liver
46	chr12:9533600-9534200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:9533600-9534400	Enhancers	Spleen	Spleen
48	chr12:9533600-9548800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:9533800-9534800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:9533800-9534800	Enhancers	Monocytes-CD14+_RO01746	blood

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