Variant report

Variant	nsv976580
Chromosome Location	chr12:12401869-12402529
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	BCL11A	chr12:12402210-12402539	GM12878	blood:	n/a	n/a
2	IKZF1	chr12:12402305-12402495	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:12402102-12403079	SK-N-MC	brain:	n/a	n/a
4	RUNX3	chr12:12402113-12402538	GM12878	blood:	n/a	n/a
5	RUNX3	chr12:12402182-12402549	GM12878	blood:	n/a	n/a
6	SPI1	chr12:12402284-12402508	GM12878	blood:	n/a	chr12:12402426-12402433 chr12:12402424-12402437
7	YY1	chr12:12402136-12402440	GM12878	blood:	n/a	chr12:12402248-12402256 chr12:12402249-12402259
8	YY1	chr12:12402182-12402465	GM12878	blood:	n/a	chr12:12402248-12402256 chr12:12402249-12402259
9	YY1	chr12:12402160-12402331	K562	blood:	n/a	chr12:12402248-12402256 chr12:12402249-12402259
10	YY1	chr12:12402119-12402430	GM12891	blood:	n/a	chr12:12402248-12402256 chr12:12402249-12402259

No.	Distal block	Cell Line	Cell type
1	chr12:12395975..12398553-chr12:12399397..12402094,2	MCF-7	breast:
2	chr12:12401851..12404835-chr12:12418306..12421349,3	MCF-7	breast:
3	chr12:12399860..12402436-chr12:12417674..12420343,2	K562	blood:
4	chr12:12400936..12406172-chr12:12417674..12422348,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BCL2L14-2	chr12:12401925-12402361	NONHSAT026966

Variant related genes	Relation type
ENSG00000270857	TF binding region
LRP6	TF binding region
ENSG00000070018	chromatin interactions

Extended variants
information (count: 25 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539395628	chr12:12401883-12401884	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs373637398	chr12:12401944-12401945	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs367618370	chr12:12401946-12401947	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs574016530	chr12:12401982-12401983	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs180984106	chr12:12402008-12402009	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs540846041	chr12:12402011-12402012	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs559543121	chr12:12402063-12402064	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs576723376	chr12:12402064-12402065	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs111564595	chr12:12402067-12402068	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs184601071	chr12:12402079-12402080	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs12427198	chr12:12402108-12402109	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs149023837	chr12:12402140-12402141	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs549232610	chr12:12402146-12402147	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs371458908	chr12:12402160-12402161	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs555018287	chr12:12402230-12402231	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs144622728	chr12:12402235-12402236	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs115032830	chr12:12402236-12402237	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs571851797	chr12:12402248-12402249	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs539122786	chr12:12402277-12402278	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs138572494	chr12:12402283-12402284	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs572388035	chr12:12402297-12402298	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs569634750	chr12:12402305-12402306	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs374044137	chr12:12402378-12402379	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs537026860	chr12:12402396-12402397	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs202041147	chr12:12402411-12402412	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
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
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	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
Malignant fibrous histiocytomas	21085701	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	21611746	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Lung cancer	18438408	CNVD
Myelofibrosis	22110671	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Squamous cell cancer	19607727	CNVD
Prostate cancer	16573809	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute myeloid leukemia	17268525	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16461572	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:12377800-12407200	Weak transcription	NH-A	brain
3	chr12:12384800-12417200	Weak transcription	K562	blood
4	chr12:12385000-12404000	Weak transcription	Lung	lung
5	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:12385200-12409200	Weak transcription	Pancreas	Pancrea
7	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
8	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:12392200-12403000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:12392400-12407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:12392600-12408200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:12393200-12405000	Weak transcription	HUVEC	blood vessel
13	chr12:12394200-12407200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:12394200-12407200	Weak transcription	Osteobl	bone
15	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
17	chr12:12394600-12407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:12394800-12405800	Weak transcription	HMEC	breast
19	chr12:12394800-12407600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:12395200-12407200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:12395600-12409200	Weak transcription	Ovary	ovary
23	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:12395800-12406600	Weak transcription	Brain Germinal Matrix	brain
25	chr12:12396000-12407400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:12397000-12403600	Weak transcription	Fetal Intestine Small	intestine
27	chr12:12397000-12408400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:12397400-12403200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:12397400-12409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:12397600-12402200	Weak transcription	Fetal Thymus	thymus
31	chr12:12397600-12404600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:12397600-12404600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:12397600-12404800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:12397600-12404800	Weak transcription	Left Ventricle	heart
35	chr12:12397600-12406200	Weak transcription	Primary T cells from cord blood	blood
36	chr12:12397600-12407600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:12397600-12409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:12397600-12416600	Weak transcription	Fetal Stomach	stomach
39	chr12:12397800-12405200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:12397800-12416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:12397800-12417200	Weak transcription	Brain Anterior Caudate	brain
42	chr12:12398200-12404400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:12398200-12404600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:12398200-12407400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:12398400-12406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:12400800-12402200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:12401000-12407200	Weak transcription	Liver	Liver
48	chr12:12401000-12408200	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:12401200-12402200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:12401200-12402200	Weak transcription	A549	lung

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