Variant report

Variant	nsv983321
Chromosome Location	chr12:50589529-50591229
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	EP300	chr12:50590277-50590770	T-47D	breast:	n/a	chr12:50590443-50590452
2	EP300	chr12:50590295-50590713	T-47D	breast:	n/a	chr12:50590443-50590452
3	FOS	chr12:50591222-50591527	HUVEC	blood vessel:	n/a	chr12:50591352-50591363
4	FOXA1	chr12:50590276-50590741	T-47D	breast:	n/a	n/a
5	FOXA1	chr12:50590302-50590633	T-47D	breast:	n/a	n/a
6	FOXP2	chr12:50589691-50589946	SK-N-MC	brain:	n/a	n/a
7	GATA2	chr12:50590292-50590714	HUVEC	blood vessel:	n/a	chr12:50590345-50590356
8	GATA3	chr12:50590077-50590734	MCF-7	breast:	n/a	chr12:50590345-50590356
9	GATA3	chr12:50590210-50590743	MCF-7	breast:	n/a	chr12:50590345-50590356
10	GATA3	chr12:50590242-50590749	T-47D	breast:	n/a	chr12:50590345-50590356
11	GATA3	chr12:50590269-50590844	SK-N-SH	brain:	n/a	chr12:50590345-50590356
12	GATA3	chr12:50590205-50590717	T-47D	breast:	n/a	chr12:50590345-50590356
13	JUND	chr12:50590217-50590785	T-47D	breast:	n/a	chr12:50590441-50590450
14	NFIC	chr12:50591002-50591645	ECC-1	luminal epithelium:	n/a	chr12:50591219-50591235
15	POLR2A	chr12:50589637-50590372	U87	brain:	n/a	n/a
16	POLR2A	chr12:50589537-50589999	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr12:50589586-50590383	U87	brain:	n/a	n/a
18	SIN3AK20	chr12:50590152-50590801	MCF-7	breast:	n/a	n/a
19	TCF7L2	chr12:50590256-50590792	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50590965..50593256-chr12:50639470..50642013,2	K562	blood:
2	chr12:50589265..50591468-chr12:50615588..50617139,2	K562	blood:
3	chr12:50590614..50593286-chr12:50607491..50609533,2	K562	blood:
4	chr12:50581029..50583186-chr12:50589961..50592504,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CERS5-4	chr12:50589401-50589670	NONHSAT028183

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000257298	TF binding region
ENSG00000050405	chromatin interactions

Extended variants
information (count: 58 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541384011	chr12:50589551-50589552	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs561726310	chr12:50589564-50589565	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs527341854	chr12:50589575-50589576	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs200568910	chr12:50589593-50589594	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs376669656	chr12:50589613-50589614	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs184928153	chr12:50589614-50589615	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs145757087	chr12:50589626-50589627	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs373214767	chr12:50589640-50589641	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs11169313	chr12:50589673-50589674	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs373254884	chr12:50589674-50589675	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs74820163	chr12:50589676-50589677	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs188717812	chr12:50589744-50589745	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs569341780	chr12:50589788-50589789	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs181196616	chr12:50589802-50589803	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs7300549	chr12:50589836-50589837	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs376393193	chr12:50589839-50589840	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs370407807	chr12:50589843-50589844	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs568441419	chr12:50589860-50589861	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs185983765	chr12:50589870-50589871	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs191635950	chr12:50589881-50589882	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs75214463	chr12:50589891-50589892	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs533120502	chr12:50590012-50590013	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs35710904	chr12:50590024-50590025	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs78404708	chr12:50590026-50590027	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs114533806	chr12:50590027-50590028	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs575685306	chr12:50590039-50590040	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs541520757	chr12:50590049-50590050	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs561672183	chr12:50590050-50590051	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs563915528	chr12:50590077-50590078	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs183550356	chr12:50590137-50590138	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs187182156	chr12:50590196-50590197	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs564375342	chr12:50590276-50590277	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs150064921	chr12:50590339-50590340	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs549963841	chr12:50590361-50590362	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs563477807	chr12:50590414-50590415	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs61255936	chr12:50590438-50590439	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs142341155	chr12:50590590-50590591	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs568497473	chr12:50590617-50590618	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs370874423	chr12:50590618-50590619	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs79934390	chr12:50590629-50590630	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs547496585	chr12:50590639-50590640	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs570768605	chr12:50590740-50590741	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs200160960	chr12:50590851-50590852	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs67330834	chr12:50590857-50590858	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs34487829	chr12:50590873-50590874	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs374079510	chr12:50590890-50590891	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs539746843	chr12:50590943-50590944	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs146447245	chr12:50590948-50590949	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs576219766	chr12:50590979-50590980	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs566822110	chr12:50591015-50591016	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:73)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
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
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	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
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	16616336	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD
Cancer	17160897	CNVD
Ependymoma	20639864	CNVD
Breast cancer	21858162	CNVD
Urothelial carcinoma	21177765	CNVD
Prostate cancer	19363497	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:165 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
6	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
8	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
11	chr12:50576600-50595000	Weak transcription	A549	lung
12	chr12:50579600-50598000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:50580400-50595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50582000-50592000	Weak transcription	Fetal Kidney	kidney
16	chr12:50582000-50596000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:50582400-50596200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:50582400-50598200	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:50582400-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:50582600-50593000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:50582600-50597000	Weak transcription	Fetal Brain Female	brain
22	chr12:50582600-50598000	Weak transcription	Psoas Muscle	Psoas
23	chr12:50582600-50598200	Weak transcription	Pancreas	Pancrea
24	chr12:50582800-50592000	Weak transcription	Spleen	Spleen
25	chr12:50582800-50592600	Weak transcription	Fetal Brain Male	brain
26	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
27	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:50583000-50592800	Weak transcription	Esophagus	oesophagus
29	chr12:50583000-50592800	Weak transcription	Gastric	stomach
30	chr12:50583000-50594200	Weak transcription	Ovary	ovary
31	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:50583200-50592800	Weak transcription	Small Intestine	intestine
33	chr12:50583400-50598200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
35	chr12:50583600-50591800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:50584600-50594200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:50584600-50595400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:50584600-50595800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:50584600-50596400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:50585200-50591600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:50585200-50592000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:50585400-50589800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:50585400-50594000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:50586000-50599600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:50586400-50589800	Weak transcription	Left Ventricle	heart
48	chr12:50586400-50592000	Weak transcription	K562	blood
49	chr12:50586400-50592600	Weak transcription	Aorta	Aorta
50	chr12:50586600-50590600	Weak transcription	Fetal Thymus	thymus

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