Variant report

Variant	nsv880861
Chromosome Location	chr5:52347692-52362765
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52342580..52344559-chr5:52347867..52350544,2	K562	blood:
2	chr5:52352312..52354080-chr5:52355424..52357750,2	K562	blood:
3	chr5:52352312..52354080-chr5:52355424..52357750,2	K562	blood:
4	chr5:52351776..52352321-chr9:91925750..91926479,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123975	chromatin interactions

Extended variants
information (count: 588 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:588 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3212680	chr5:52347692-52347693	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs1316036	chr5:52347858-52347859	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs182626370	chr5:52347880-52347881	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs147033070	chr5:52347899-52347900	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs570361918	chr5:52347921-52347922	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534578479	chr5:52347967-52347968	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs552815268	chr5:52348029-52348030	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs139861312	chr5:52348032-52348033	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs535161611	chr5:52348041-52348042	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs2910973	chr5:52348051-52348052	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs2974979	chr5:52348068-52348069	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs556778281	chr5:52348079-52348080	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs2974980	chr5:52348093-52348094	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs2974981	chr5:52348102-52348103	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs575091707	chr5:52348108-52348109	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs34063116	chr5:52348112-52348113	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs3212508	chr5:52348124-52348125	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs188546908	chr5:52348214-52348215	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs2974982	chr5:52348250-52348251	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs3212509	chr5:52348256-52348257	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs540590645	chr5:52348282-52348283	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs2974983	chr5:52348302-52348303	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs2910972	chr5:52348333-52348334	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs141676954	chr5:52348354-52348355	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs3021373	chr5:52348367-52348368	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs544718092	chr5:52348381-52348382	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs144774040	chr5:52348391-52348392	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs533524490	chr5:52348470-52348471	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs2910971	chr5:52348486-52348487	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs3212510	chr5:52348651-52348652	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs2974984	chr5:52348698-52348699	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs2974985	chr5:52348704-52348705	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs2910970	chr5:52348732-52348733	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs192933062	chr5:52348748-52348749	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs148565057	chr5:52348789-52348790	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs3212681	chr5:52348821-52348822	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs375283111	chr5:52348837-52348838	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs142956266	chr5:52348853-52348854	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs577875278	chr5:52348880-52348881	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs369603598	chr5:52348885-52348886	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs568717080	chr5:52348931-52348932	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs13184866	chr5:52348935-52348936	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs151118248	chr5:52348963-52348964	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs3212511	chr5:52348983-52348984	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs542354445	chr5:52348994-52348995	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs540149234	chr5:52349007-52349008	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs555780061	chr5:52349014-52349015	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs2910969	chr5:52349034-52349035	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs1421932	chr5:52349065-52349066	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs3212512	chr5:52349072-52349073	Enhancers Weak transcription Strong transcription Genic 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:215 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
7	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
9	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:52334600-52348400	Weak transcription	Lung	lung
11	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
13	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:52337400-52348800	Weak transcription	A549	lung
17	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:52338000-52348200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:52341200-52396400	Strong transcription	HMEC	breast
22	chr5:52341400-52348600	Weak transcription	Dnd41	blood
23	chr5:52341400-52359000	Weak transcription	NHDF-Ad	bronchial
24	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:52341800-52347800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:52341800-52358800	Weak transcription	Osteobl	bone
27	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:52342600-52383800	Strong transcription	NHEK	skin
30	chr5:52343000-52348600	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:52343000-52359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:52343200-52350800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:52343200-52351800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:52343200-52361800	Strong transcription	HepG2	liver
35	chr5:52343400-52350000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:52343400-52357200	Strong transcription	HUVEC	blood vessel
37	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
38	chr5:52343600-52348000	Weak transcription	Spleen	Spleen
39	chr5:52344000-52348600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:52344000-52369200	Weak transcription	Pancreas	Pancrea
41	chr5:52344200-52356000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:52344400-52348000	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:52344400-52348200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:52344400-52356400	Weak transcription	Esophagus	oesophagus
45	chr5:52344400-52356400	Weak transcription	Gastric	stomach
46	chr5:52345600-52350800	Strong transcription	Hela-S3	cervix
47	chr5:52346200-52349000	Weak transcription	Fetal Brain Male	brain
48	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:52346400-52348000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:52346400-52349800	Strong transcription	Duodenum Mucosa	Duodenum

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