Variant report

Variant	nsv560047
Chromosome Location	chr12:104529349-104531705
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:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104456335..104459744-chr12:104529847..104533076,5	K562	blood:
2	chr12:104531440..104533678-chr17:57914653..57916695,2	MCF-7	breast:
3	chr12:104234047..104236214-chr12:104531313..104532962,2	MCF-7	breast:
4	chr12:104487179..104490226-chr12:104527814..104531447,3	K562	blood:
5	chr12:104528672..104531458-chr12:104545242..104548166,3	K562	blood:
6	chr12:104529888..104531745-chr12:104641591..104644080,2	MCF-7	breast:
7	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
8	chr12:104531449..104532221-chr9:72873633..72874142,2	Hela-S3	cervix:
9	chr12:104526354..104529452-chr12:104565610..104568678,3	MCF-7	breast:
10	chr12:104529986..104533486-chr12:104678703..104682517,5	MCF-7	breast:
11	chr12:104530782..104534411-chr12:104679881..104682289,3	K562	blood:
12	chr12:104528832..104532197-chr12:105351511..105353407,3	MCF-7	breast:
13	chr12:104481200..104483346-chr12:104529918..104531545,2	K562	blood:
14	chr12:104456193..104459744-chr12:104529847..104533076,6	K562	blood:
15	chr12:104455182..104458865-chr12:104529769..104532559,3	MCF-7	breast:
16	chr12:104358049..104359986-chr12:104530882..104532737,3	K562	blood:
17	chr12:104528011..104530810-chr12:104621683..104623795,2	K562	blood:
18	chr12:104531363..104532174-chr20:25228138..25229130,2	NB4	blood:
19	chr12:104529689..104531446-chr12:104719514..104721289,2	K562	blood:
20	chr12:104357850..104359549-chr12:104531019..104533949,2	K562	blood:
21	chr12:104510515..104519727-chr12:104525085..104533754,15	MCF-7	breast:
22	chr12:104531384..104532055-chr2:26568058..26568772,2	Hela-S3	cervix:
23	chr12:104530239..104532383-chr12:105499797..105502736,2	MCF-7	breast:
24	chr12:72079541..72080318-chr12:104531306..104531990,2	NB4	blood:
25	chr12:104530514..104533012-chr12:104679009..104681675,2	K562	blood:
26	chr12:104530429..104534144-chr12:104679811..104684673,6	MCF-7	breast:
27	chr12:104531360..104532346-chr4:185395679..185396224,2	Hela-S3	cervix:
28	chr12:104348297..104351124-chr12:104530392..104533056,3	MCF-7	breast:
29	chr12:104531573..104532274-chr3:49058505..49059412,2	Hela-S3	cervix:
30	chr1:167905681..167906352-chr12:104531146..104532073,2	Hela-S3	cervix:
31	chr12:104490343..104492832-chr12:104530682..104533569,2	MCF-7	breast:
32	chr12:104528672..104531458-chr12:104545242..104548166,2	K562	blood:
33	chr12:104530438..104533662-chr12:104564030..104567253,5	K562	blood:
34	chr12:104322684..104325586-chr12:104530441..104532019,2	K562	blood:
35	chr12:104530672..104533179-chr6:154830934..154833113,2	MCF-7	breast:
36	chr12:104531343..104532062-chr14:24036745..24037302,2	HCT-116	colon:

No data

Variant related genes	Relation type
ENSG00000213983	chromatin interactions
ENSG00000178149	chromatin interactions
ENSG00000178057	chromatin interactions
ENSG00000062716	chromatin interactions
ENSG00000100994	chromatin interactions
ENSG00000214198	chromatin interactions
ENSG00000257193	chromatin interactions
ENSG00000173567	chromatin interactions
ENSG00000199415	chromatin interactions
ENSG00000166598	chromatin interactions
ENSG00000111727	chromatin interactions
ENSG00000136051	chromatin interactions
ENSG00000143164	chromatin interactions
ENSG00000198887	chromatin interactions
ENSG00000257999	chromatin interactions
ENSG00000204954	chromatin interactions
ENSG00000120820	chromatin interactions
ENSG00000153721	chromatin interactions
ENSG00000268364	chromatin interactions
ENSG00000168310	chromatin interactions
ENSG00000271646	chromatin interactions
ENSG00000111696	chromatin interactions
ENSG00000139291	chromatin interactions
ENSG00000257327	chromatin interactions
ENSG00000198431	chromatin interactions
ENSG00000136052	chromatin interactions
ENSG00000143158	chromatin interactions
ENSG00000139372	chromatin interactions
ENSG00000265072	chromatin interactions

Extended variants
information (count: 77 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:77 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4257050	chr12:104529349-104529350	Enhancers Weak transcription Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs570556517	chr12:104529369-104529370	Enhancers Weak transcription Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs74241079	chr12:104529395-104529396	Enhancers Weak transcription Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs556000859	chr12:104529406-104529407	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs117408628	chr12:104529407-104529408	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs186531763	chr12:104529423-104529424	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs200141325	chr12:104529436-104529437	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs555389837	chr12:104529463-104529464	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs572819810	chr12:104529476-104529477	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs541360269	chr12:104529524-104529525	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs564757135	chr12:104529536-104529537	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs578120466	chr12:104529567-104529568	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs73392511	chr12:104529616-104529617	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs563467317	chr12:104529623-104529624	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs529329937	chr12:104529628-104529629	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs565918954	chr12:104529717-104529718	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs17806516	chr12:104529766-104529767	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs559318262	chr12:104529874-104529875	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
19	rs528438298	chr12:104529875-104529876	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs554396612	chr12:104529882-104529883	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs368093882	chr12:104529897-104529898	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
22	rs570692117	chr12:104529916-104529917	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
23	rs539279092	chr12:104529952-104529953	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
24	rs147270583	chr12:104529968-104529969	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
25	rs189414619	chr12:104530002-104530003	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
26	rs140775209	chr12:104530072-104530073	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
27	rs549341643	chr12:104530116-104530117	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
28	rs572075575	chr12:104530130-104530131	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
29	rs572822401	chr12:104530136-104530137	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
30	rs144727407	chr12:104530138-104530139	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
31	rs558187511	chr12:104530192-104530193	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
32	rs77043454	chr12:104530214-104530215	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
33	rs74972331	chr12:104530215-104530216	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
34	rs578178561	chr12:104530234-104530235	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
35	rs73392513	chr12:104530258-104530259	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs563527897	chr12:104530289-104530290	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
37	rs181976999	chr12:104530337-104530338	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
38	rs567571816	chr12:104530367-104530368	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
39	rs542715236	chr12:104530401-104530402	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
40	rs559378621	chr12:104530450-104530451	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
41	rs528491874	chr12:104530455-104530456	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
42	rs57998452	chr12:104530467-104530468	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
43	rs551725404	chr12:104530485-104530486	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
44	rs564253212	chr12:104530495-104530496	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
45	rs7979648	chr12:104530548-104530549	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs550043090	chr12:104530634-104530635	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
47	rs373828807	chr12:104530721-104530722	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
48	rs151293640	chr12:104530737-104530738	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
49	rs556078323	chr12:104530742-104530743	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
50	rs529054084	chr12:104530753-104530754	Active TSS Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
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
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	22032731	CNVD
Cancer	16751803	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
lymphocytic leukemia	21291569	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16397240	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Neurocytoma	17123091	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:443 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104493800-104530600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104495600-104530800	Weak transcription	Esophagus	oesophagus
3	chr12:104520000-104530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:104523600-104530600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:104523800-104529800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:104523800-104530400	Enhancers	Fetal Heart	heart
7	chr12:104523800-104530600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:104525200-104530400	Weak transcription	Stomach Mucosa	stomach
9	chr12:104525400-104529600	Genic enhancers	Dnd41	blood
10	chr12:104525600-104530400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:104526200-104530200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:104526600-104529800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:104526600-104530400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:104526600-104530600	Weak transcription	Psoas Muscle	Psoas
15	chr12:104526600-104531000	Weak transcription	Lung	lung
16	chr12:104526800-104529800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:104526800-104529800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:104526800-104529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:104526800-104530800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:104526800-104530800	Weak transcription	Gastric	stomach
21	chr12:104526800-104531000	Weak transcription	Spleen	Spleen
22	chr12:104527000-104529400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:104527200-104530000	Weak transcription	Fetal Kidney	kidney
24	chr12:104527200-104530200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:104527400-104530000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:104527400-104530000	Weak transcription	Fetal Stomach	stomach
27	chr12:104527600-104529400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr12:104527600-104530400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:104527800-104529400	Weak transcription	HUVEC	blood vessel
30	chr12:104527800-104529800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:104527800-104530400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:104527800-104530600	Weak transcription	Colonic Mucosa	Colon
33	chr12:104528000-104529400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:104528000-104529800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:104528000-104530000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:104528000-104530000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:104528000-104530000	Weak transcription	NH-A	brain
38	chr12:104528000-104530200	Weak transcription	HMEC	breast
39	chr12:104528000-104530400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:104528000-104530600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr12:104528000-104530600	Weak transcription	Placenta	Placenta
42	chr12:104528200-104530000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:104528200-104530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:104528200-104530000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:104528400-104529800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr12:104528400-104529800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:104528400-104530000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:104528400-104530400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:104528400-104530400	Enhancers	Brain Angular Gyrus	brain
50	chr12:104528600-104530400	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links