Variant report

Variant	esv20613
Chromosome Location	chr12:66609223-66609834
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	chr12:66562009..66565017-chr12:66607672..66610931,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HELB-3	chr12:66609321-66609434	l_669_chr12:66609320-66613349_heart

Variant related genes	Relation type
ENSG00000155957	chromatin interactions

Extended variants
information (count: 30 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76560317	chr12:66609276-66609277	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs376418040	chr12:66609312-66609313	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs189369580	chr12:66609336-66609337	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs74100118	chr12:66609378-66609379	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs544241415	chr12:66609390-66609391	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs192700876	chr12:66609419-66609420	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs577897434	chr12:66609459-66609460	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs140947281	chr12:66609500-66609501	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs149842421	chr12:66609517-66609518	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs150339586	chr12:66609565-66609566	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs368883846	chr12:66609566-66609567	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs375264640	chr12:66609568-66609569	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs201234408	chr12:66609570-66609571	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs56931740	chr12:66609572-66609573	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs71096080	chr12:66609586-66609587	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs185690823	chr12:66609608-66609609	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs59834759	chr12:66609609-66609610	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs201811324	chr12:66609610-66609611	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs549154366	chr12:66609647-66609648	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs562618180	chr12:66609696-66609697	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs531423110	chr12:66609709-66609710	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs201929920	chr12:66609712-66609713	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs371153918	chr12:66609730-66609731	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs551428589	chr12:66609740-66609741	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs571132215	chr12:66609748-66609749	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs527251789	chr12:66609750-66609751	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs114529150	chr12:66609777-66609778	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs567112734	chr12:66609778-66609779	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs190551496	chr12:66609793-66609794	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs57546002	chr12:66609797-66609798	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Wilms tumour	21544195	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
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
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	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
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	CNVD
Fibroblasts	20926602	CNVD
Metanephric adenoma	20802469	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Mental retardation	17220210	CNVD
Osteopoikilosis	17220210	CNVD
short stature	17220210	CNVD
Burkitt''s lymphoma	20823134	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Ovarian neoplasms	16753589	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	16620391	CNVD
Neuroticism	17667963	CNVD
Breast cancer	21364760	CNVD
Urothelial cell carcinoma	18451213	CNVD
Breast cancer	22048815	CNVD
Congenital anomalies of the kidney and urinary tract	21113617	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Myxofibrosarcoma	16751306	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Lung cancer	17925434	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Disease	21505450	CNVD
craniofacial dysmorphism	21918468	CNVD

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66583800-66623400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66589600-66623400	Weak transcription	Spleen	Spleen
3	chr12:66592400-66628400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:66593400-66613400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:66597600-66623400	Weak transcription	Aorta	Aorta
6	chr12:66604000-66620200	Weak transcription	Lung	lung
7	chr12:66604400-66628800	Weak transcription	Right Ventricle	heart
8	chr12:66604800-66610600	Strong transcription	Fetal Lung	lung
9	chr12:66605200-66628800	Weak transcription	Psoas Muscle	Psoas
10	chr12:66605400-66628200	Weak transcription	NHDF-Ad	bronchial
11	chr12:66605600-66611400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:66606000-66610400	Weak transcription	Primary B cells from cord blood	blood
13	chr12:66606200-66609400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:66606200-66609800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr12:66606200-66610600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:66606400-66620000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:66606800-66611600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:66606800-66612400	Weak transcription	Adipose Nuclei	Adipose
19	chr12:66606800-66623000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:66606800-66625800	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:66607000-66611200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:66607200-66611000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:66608000-66609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:66608000-66611000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:66608600-66610000	Enhancers	Fetal Intestine Large	intestine
26	chr12:66608600-66610000	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr12:66608800-66610000	Enhancers	Fetal Intestine Small	intestine
28	chr12:66608800-66628800	Weak transcription	Gastric	stomach
29	chr12:66609000-66609600	Enhancers	HepG2	liver
30	chr12:66609000-66609800	Enhancers	Stomach Mucosa	stomach
31	chr12:66609000-66610000	Enhancers	Duodenum Mucosa	Duodenum
32	chr12:66609000-66610200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:66609000-66610400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:66609000-66628800	Weak transcription	Left Ventricle	heart
35	chr12:66609200-66609400	Enhancers	Small Intestine	intestine
36	chr12:66609200-66610600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:66609200-66610800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:66609200-66628800	Weak transcription	Colonic Mucosa	Colon
39	chr12:66609200-66629000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:66609400-66612000	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:66609400-66613400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:66609400-66626200	Weak transcription	Small Intestine	intestine
43	chr12:66609800-66610000	Active TSS	Rectal Smooth Muscle	rectum
44	chr12:66609800-66612000	Genic enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links