Variant report

Variant	nsv819688
Chromosome Location	chr12:406038-415530
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr12:413597-413695	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:407286-407334	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:407358-407371	MCF-7	breast:	n/a	n/a
4	POLR2A	chr12:412647-412689	Gliobla	brain:	n/a	n/a
5	SETDB1	chr12:408727-408968	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:402335..404067-chr12:405685..407593,2	K562	blood:

Variant related genes	Relation type
KDM5A	TF binding region

Extended variants
information (count: 405 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:405 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs531714998	chr12:406071-406072	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs550247220	chr12:406098-406099	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs571904857	chr12:406100-406101	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs532569040	chr12:406113-406114	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs547541796	chr12:406132-406133	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs527281571	chr12:406151-406152	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs375881033	chr12:406174-406175	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs373495550	chr12:406218-406219	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs368675098	chr12:406244-406245	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs561267177	chr12:406267-406268	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs375254444	chr12:406278-406279	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs2229351	chr12:406292-406293	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs535912611	chr12:406319-406320	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs372573598	chr12:406326-406327	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs531280433	chr12:406350-406351	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs75348779	chr12:406363-406364	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs377600159	chr12:406384-406385	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs554630160	chr12:406449-406450	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs200421844	chr12:406524-406525	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs537043462	chr12:406600-406601	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs139559074	chr12:406636-406637	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs80154723	chr12:406656-406657	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs143321988	chr12:406683-406684	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs373358420	chr12:406684-406685	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs549446580	chr12:406701-406702	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs572594252	chr12:406706-406707	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs140240645	chr12:406756-406757	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs561424230	chr12:406757-406758	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs531654101	chr12:406772-406773	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs77205979	chr12:406868-406869	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs569471651	chr12:407019-407020	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs188453640	chr12:407021-407022	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs536438519	chr12:407025-407026	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs548910256	chr12:407030-407031	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs547603752	chr12:407041-407042	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs559551687	chr12:407045-407046	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191629251	chr12:407051-407052	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs183833200	chr12:407106-407107	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs569730797	chr12:407129-407130	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs536647050	chr12:407142-407143	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs145873005	chr12:407145-407146	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs570775720	chr12:407212-407213	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs534195346	chr12:407226-407227	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs553287864	chr12:407244-407245	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs574725768	chr12:407256-407257	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs149015260	chr12:407258-407259	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs577287710	chr12:407270-407271	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs554767640	chr12:407278-407279	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs188159751	chr12:407280-407281	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs543466370	chr12:407334-407335	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

Disease	PMID	Source
Cancer	20164920	CNVD
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
small cell lung cancer	20016488	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	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
Acute myeloid leukemia	20729466	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Autism	22495309	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Glioblastoma multiforme	22291905	CNVD

Chromatin state (count:441 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:384600-414600	Weak transcription	Psoas Muscle	Psoas
2	chr12:387600-407200	Strong transcription	Primary B cells from cord blood	blood
3	chr12:387600-408000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:388000-407200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:388200-408400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:388200-408600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:389400-455200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:389600-408200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:389600-409600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr12:389800-407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:389800-408400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:391200-407800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:391400-408400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:391400-408400	Strong transcription	Fetal Thymus	thymus
15	chr12:391600-407000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:391600-407600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:392000-409000	Strong transcription	Dnd41	blood
18	chr12:394000-474400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:394600-413800	Weak transcription	Fetal Heart	heart
20	chr12:394800-414800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:395000-416200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:397000-408400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:397800-407000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:397800-407000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr12:398200-416000	Weak transcription	Stomach Mucosa	stomach
26	chr12:398600-408200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:399000-407000	Strong transcription	GM12878-XiMat	blood
28	chr12:399000-407200	Strong transcription	Placenta	Placenta
29	chr12:399000-408200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:399000-408400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:399200-406200	Strong transcription	A549	lung
32	chr12:399200-407000	Strong transcription	HSMM	muscle
33	chr12:399200-407600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:399200-407800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:399200-408400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:399600-407200	Strong transcription	HepG2	liver
37	chr12:400000-407800	Strong transcription	Liver	Liver
38	chr12:400200-407800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:400400-406400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:400400-406400	Strong transcription	Brain Anterior Caudate	brain
41	chr12:400400-406600	Strong transcription	HMEC	breast
42	chr12:400400-407000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:400400-407000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:400400-407600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:400400-407600	Strong transcription	Adipose Nuclei	Adipose
46	chr12:400400-407600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:400400-407800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:400400-407800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:400400-409000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:400600-406400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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