Variant report

Variant	nsv880346
Chromosome Location	chr5:52381216-52385312
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	CEBPB	chr5:52385125-52385681	MCF-7	breast:	n/a	n/a
2	CEBPB	chr5:52385103-52385738	MCF-7	breast:	n/a	n/a
3	EP300	chr5:52385095-52385829	MCF-7	breast:	n/a	chr5:52385422-52385432
4	EP300	chr5:52385274-52385955	SK-N-SH_RA	brain:	n/a	chr5:52385422-52385432
5	EP300	chr5:52385049-52385811	MCF-7	breast:	n/a	chr5:52385422-52385432
6	EP300	chr5:52385230-52385863	SK-N-SH	brain:	n/a	chr5:52385422-52385432
7	ESR1	chr5:52385062-52385418	T-47D	breast:	n/a	chr5:52385261-52385278 chr5:52385260-52385277
8	ESR1	chr5:52385050-52385437	T-47D	breast:	n/a	chr5:52385261-52385278 chr5:52385260-52385277
9	ESR1	chr5:52385105-52385344	ECC-1	luminal epithelium:	n/a	chr5:52385261-52385278 chr5:52385260-52385277
10	ESR1	chr5:52385023-52385486	ECC-1	luminal epithelium:	n/a	chr5:52385261-52385278 chr5:52385260-52385277
11	ESR1	chr5:52385093-52385487	T-47D	breast:	n/a	chr5:52385261-52385278 chr5:52385260-52385277
12	FOXM1	chr5:52384934-52385840	MCF-7	breast:	n/a	n/a
13	FOXM1	chr5:52385035-52385760	MCF-7	breast:	n/a	n/a
14	GATA3	chr5:52385285-52385760	SH-SY5Y	brain:	n/a	chr5:52385496-52385504
15	GATA3	chr5:52385080-52386527	MCF-7	breast:	n/a	chr5:52385496-52385504
16	GATA3	chr5:52384907-52386671	MCF-7	breast:	n/a	chr5:52385496-52385504
17	GATA3	chr5:52385233-52385724	T-47D	breast:	n/a	chr5:52385496-52385504
18	GATA3	chr5:52385121-52385881	MCF-7	breast:	n/a	chr5:52385496-52385504
19	GATA3	chr5:52384627-52386125	SK-N-SH	brain:	n/a	chr5:52385496-52385504
20	GATA3	chr5:52384958-52386571	MCF-7	breast:	n/a	chr5:52385496-52385504
21	GATA3	chr5:52385312-52385883	T-47D	breast:	n/a	chr5:52385496-52385504
22	GATA3	chr5:52385092-52386017	SK-N-SH	brain:	n/a	chr5:52385496-52385504
23	HDAC2	chr5:52385020-52385804	MCF-7	breast:	n/a	chr5:52385422-52385431
24	JUND	chr5:52385209-52385844	SK-N-SH	brain:	n/a	n/a
25	JUND	chr5:52385125-52385745	MCF-7	breast:	n/a	n/a
26	MAFK	chr5:52382129-52382135	HepG2	liver:	n/a	n/a
27	MAZ	chr5:52383836-52383838	HepG2	liver:	n/a	n/a
28	MYC	chr5:52381243-52381246	K562	blood:	n/a	n/a
29	NFIC	chr5:52385095-52386020	SK-N-SH	brain:	n/a	n/a
30	NFIC	chr5:52385286-52385746	SK-N-SH	brain:	n/a	n/a
31	NR2F2	chr5:52385107-52385901	MCF-7	breast:	n/a	chr5:52385267-52385282 chr5:52385256-52385271
32	NR2F2	chr5:52384959-52385905	MCF-7	breast:	n/a	chr5:52385267-52385282 chr5:52385256-52385271
33	PBX3	chr5:52384769-52385942	SK-N-SH	brain:	n/a	n/a
34	PBX3	chr5:52385298-52385937	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr5:52385006-52385060	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr5:52385257-52385960	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr5:52384664-52384739	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr5:52384859-52384932	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr5:52384987-52386000	MCF-7	breast:	n/a	n/a
40	SIN3AK20	chr5:52385126-52385896	MCF-7	breast:	n/a	n/a
41	TCF12	chr5:52384953-52386817	MCF-7	breast:	n/a	n/a
42	TCF12	chr5:52385164-52386004	SK-N-SH	brain:	n/a	n/a
43	TCF12	chr5:52385235-52385929	SK-N-SH	brain:	n/a	n/a
44	TCF12	chr5:52385053-52385794	MCF-7	breast:	n/a	n/a
45	TCF7L2	chr5:52385017-52385811	MCF-7	breast:	n/a	n/a
46	ZNF217	chr5:52385131-52385843	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52285755..52287338-chr5:52380121..52382244,2	MCF-7	breast:
2	chr5:52382323..52385100-chr5:52387808..52389930,2	K562	blood:
3	chr5:52381586..52383200-chr5:52383742..52385269,2	MCF-7	breast:
4	chr5:52380023..52382035-chr5:52385112..52387338,2	K562	blood:
5	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
6	chr5:52381586..52383200-chr5:52383742..52385269,2	MCF-7	breast:
7	chr5:52376435..52379263-chr5:52381516..52385182,3	MCF-7	breast:
8	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MOCS2-4	chr5:52384846-52385298	ENSG00000272123.1

Variant related genes	Relation type
ENSG00000272123	TF binding region
ENSG00000272123	chromatin interactions
ENSG00000249899	chromatin interactions
ENSG00000247796	chromatin interactions
ENSG00000164171	chromatin interactions
ENSG00000164172	chromatin interactions

Extended variants
information (count: 140 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:140 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3212632	chr5:52381216-52381217	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs556105124	chr5:52381239-52381240	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs540609636	chr5:52381249-52381250	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs181163216	chr5:52381258-52381259	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs529739749	chr5:52381260-52381261	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs79356784	chr5:52381358-52381359	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs547987058	chr5:52381372-52381373	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs563457935	chr5:52381405-52381406	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs574538943	chr5:52381480-52381481	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs535394833	chr5:52381536-52381537	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs34599720	chr5:52381604-52381605	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs554062619	chr5:52381652-52381653	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs570638182	chr5:52381738-52381739	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs543768444	chr5:52381743-52381744	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs535056190	chr5:52381744-52381745	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs370881847	chr5:52381752-52381753	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs186389308	chr5:52381765-52381766	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs376677260	chr5:52381814-52381815	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs374954915	chr5:52381840-52381841	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs139184769	chr5:52381860-52381861	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs557603478	chr5:52381896-52381897	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs190461341	chr5:52381902-52381903	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs183022586	chr5:52381908-52381909	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs3212633	chr5:52381933-52381934	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs573330796	chr5:52381967-52381968	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs577673342	chr5:52381986-52381987	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs142486049	chr5:52382001-52382002	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs540674411	chr5:52382018-52382019	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs186245626	chr5:52382092-52382093	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs80048813	chr5:52382205-52382206	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs546342977	chr5:52382207-52382208	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs12521915	chr5:52382218-52382219	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs190959281	chr5:52382281-52382282	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs563213949	chr5:52382285-52382286	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs530764964	chr5:52382291-52382292	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs34996589	chr5:52382293-52382294	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs76407780	chr5:52382311-52382312	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs12515364	chr5:52382349-52382350	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs528347916	chr5:52382397-52382398	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs547024575	chr5:52382406-52382407	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs183993885	chr5:52382412-52382413	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs529430986	chr5:52382417-52382418	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs146113719	chr5:52382423-52382424	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs76529944	chr5:52382442-52382443	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs540066157	chr5:52382449-52382450	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs547668786	chr5:52382481-52382482	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs558068940	chr5:52382494-52382495	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs527678819	chr5:52382515-52382516	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs567159893	chr5:52382531-52382532	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs3212697	chr5:52382606-52382607	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Cancer	16751803	CNVD
Autism	22495311	CNVD
Intellectual disability	22102821	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
adenomatous polyposis	22470819	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	20729466	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	21911935	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:174 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52341200-52396400	Strong transcription	HMEC	breast
5	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52342600-52383800	Strong transcription	NHEK	skin
7	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
8	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
10	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
11	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
14	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
16	chr5:52362200-52387800	Strong transcription	HepG2	liver
17	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
20	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
22	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:52367800-52386000	Strong transcription	NH-A	brain
25	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
26	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:52369400-52382600	Weak transcription	Brain Angular Gyrus	brain
28	chr5:52369400-52383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
31	chr5:52372000-52382600	Weak transcription	Brain Anterior Caudate	brain
32	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
33	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:52372200-52382600	Weak transcription	Lung	lung
35	chr5:52372200-52382800	Weak transcription	Spleen	Spleen
36	chr5:52372200-52384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:52372200-52394800	Weak transcription	Gastric	stomach
39	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
40	chr5:52372400-52385000	Weak transcription	Osteobl	bone
41	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
43	chr5:52373000-52385600	Weak transcription	Ovary	ovary
44	chr5:52373000-52387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:52373400-52382600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:52373800-52386200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:52374200-52382600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:52375000-52382400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:52375800-52384000	Strong transcription	NHLF	lung

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