Variant report

Variant	esv3444193
Chromosome Location	chr12:1979091-1981989
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1978767..1980595-chr12:2025590..2028373,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256706	chromatin interactions
ENSG00000151062	chromatin interactions

Extended variants
information (count: 135 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:135 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558212775	chr12:1979142-1979143	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs573194536	chr12:1979164-1979165	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs76783761	chr12:1979214-1979215	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs561882458	chr12:1979237-1979238	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs529144080	chr12:1979246-1979247	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs77301974	chr12:1979250-1979251	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs562311834	chr12:1979266-1979267	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs532937122	chr12:1979271-1979272	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs13353073	chr12:1979387-1979388	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs35966879	chr12:1979407-1979408	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs566551926	chr12:1979420-1979421	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs185961043	chr12:1979427-1979428	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs548916133	chr12:1979430-1979431	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs568670312	chr12:1979452-1979453	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs190842138	chr12:1979453-1979454	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs138499287	chr12:1979463-1979464	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs112153846	chr12:1979544-1979545	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs34590143	chr12:1979584-1979585	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs538239505	chr12:1979628-1979629	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs558012181	chr12:1979631-1979632	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs144401514	chr12:1979656-1979657	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs533945592	chr12:1979657-1979658	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs80281596	chr12:1979678-1979679	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs183107577	chr12:1979720-1979721	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs374148115	chr12:1979737-1979738	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs187024925	chr12:1979756-1979757	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs562425221	chr12:1979782-1979783	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs116682294	chr12:1979814-1979815	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs578015396	chr12:1979920-1979921	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs534721280	chr12:1979971-1979972	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs190285950	chr12:1980059-1980060	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs149345286	chr12:1980067-1980068	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs559992813	chr12:1980078-1980079	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs527338334	chr12:1980083-1980084	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs548719840	chr12:1980097-1980098	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs560912425	chr12:1980104-1980105	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs147972690	chr12:1980167-1980168	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs551332734	chr12:1980168-1980169	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs7131989	chr12:1980185-1980186	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs536112440	chr12:1980189-1980190	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs141635032	chr12:1980193-1980194	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs150524300	chr12:1980194-1980195	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs372005673	chr12:1980195-1980196	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs374268017	chr12:1980199-1980200	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs202147550	chr12:1980204-1980205	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs534267483	chr12:1980205-1980206	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs112457460	chr12:1980215-1980216	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs555556010	chr12:1980227-1980228	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs182861905	chr12:1980239-1980240	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs200990001	chr12:1980261-1980262	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Glaucoma	21310917	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Squamous cell cancer	19607727	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Mental retardation	17847001	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	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
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Bipolar disorder	22488967	CNVD

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1974400-1979200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:1978800-1980200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:1979200-1979400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:1979400-1980200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:1979400-1980400	Bivalent Enhancer	HepG2	liver
6	chr12:1979400-1980600	Enhancers	Fetal Brain Male	brain
7	chr12:1980000-1983800	Enhancers	Fetal Brain Female	brain
8	chr12:1980200-1980400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:1980200-1980800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:1980200-1980800	ZNF genes & repeats	Fetal Kidney	kidney
11	chr12:1980200-1980800	Bivalent/Poised TSS	Fetal Lung	lung
12	chr12:1980200-1980800	Enhancers	Gastric	stomach
13	chr12:1980200-1980800	ZNF genes & repeats	Spleen	Spleen
14	chr12:1980200-1981000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:1980200-1981000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:1980200-1981000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:1980200-1981000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:1980400-1980600	Enhancers	Right Atrium	heart
19	chr12:1980400-1980800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr12:1980600-1980800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
21	chr12:1980600-1980800	Flanking Active TSS	Fetal Brain Male	brain
22	chr12:1980600-1988600	Weak transcription	Right Atrium	heart
23	chr12:1980800-1981000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:1980800-1981000	Enhancers	Fetal Kidney	kidney
25	chr12:1980800-1981800	Weak transcription	Spleen	Spleen
26	chr12:1980800-1983800	Enhancers	Fetal Brain Male	brain
27	chr12:1981000-1986800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:1981000-1992000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:1981800-1982000	Enhancers	Spleen	Spleen

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