Variant report

Variant	nsv537874
Chromosome Location	chr5:115508328-115563533
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	CBX3	chr5:115509774-115510264	HCT-116	colon:	n/a	n/a
2	CBX3	chr5:115511708-115512163	HCT-116	colon:	n/a	n/a
3	CEBPB	chr5:115511551-115511792	K562	blood:	n/a	chr5:115511652-115511663
4	CEBPB	chr5:115511524-115511726	HepG2	liver:	n/a	chr5:115511652-115511663
5	CEBPB	chr5:115511494-115511805	IMR90	lung:	n/a	chr5:115511652-115511663
6	CTCF	chr5:115514420-115514570	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr5:115527000-115527150	GM06990	blood:	n/a	n/a
8	CTCF	chr5:115563372-115563423	GM13976	blood:	n/a	n/a
9	CTCF	chr5:115545600-115545750	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr5:115546959-115547004	Spleen_OC	spleen:	n/a	n/a
11	CTCF	chr5:115514460-115514610	BE2_C	brain:	n/a	n/a
12	CTCF	chr5:115526780-115526930	HepG2	liver:	n/a	n/a
13	EBF1	chr5:115553101-115553358	GM12878	blood:	n/a	n/a
14	EP300	chr5:115562218-115562251	K562	blood:	n/a	n/a
15	FOS	chr5:115511949-115512080	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr5:115511882-115512082	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr5:115511876-115512190	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr5:115511871-115512146	MCF10A-Er-Src	breast:	n/a	n/a
19	FOXA1	chr5:115546868-115547069	T-47D	breast:	n/a	n/a
20	FOXA2	chr5:115546874-115547055	HepG2	liver:	n/a	n/a
21	GATA3	chr5:115532827-115533270	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr5:115540807-115540886	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr5:115555733-115556106	SH-SY5Y	brain:	n/a	n/a
24	GATA3	chr5:115532851-115533266	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr5:115532809-115533271	MCF-7	breast:	n/a	n/a
26	GATA3	chr5:115562600-115562894	SH-SY5Y	brain:	n/a	n/a
27	GTF2F1	chr5:115527179-115527209	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUN	chr5:115541691-115541827	HepG2	liver:	n/a	chr5:115541725-115541738
29	JUN	chr5:115560931-115560946	H1-hESC	embryonic stem cell:	n/a	n/a
30	JUND	chr5:115554589-115554765	HepG2	liver:	n/a	n/a
31	KAP1	chr5:115544780-115545020	K562	blood:	n/a	n/a
32	MAFF	chr5:115514640-115514985	HepG2	liver:	n/a	chr5:115514809-115514827 chr5:115514815-115514829
33	MAFF	chr5:115514692-115514972	K562	blood:	n/a	chr5:115514809-115514827 chr5:115514815-115514829
34	MAFK	chr5:115514716-115514894	H1-hESC	embryonic stem cell:	n/a	chr5:115514815-115514829 chr5:115514812-115514832 chr5:115514814-115514830
35	MAFK	chr5:115546142-115546411	HepG2	liver:	n/a	chr5:115546288-115546299 chr5:115546284-115546300 chr5:115546287-115546301 chr5:115546289-115546300 chr5:115546288-115546299 chr5:115546289-115546300
36	MAFK	chr5:115514697-115514996	IMR90	lung:	n/a	chr5:115514815-115514829 chr5:115514812-115514832 chr5:115514814-115514830
37	MAFK	chr5:115514662-115514973	K562	blood:	n/a	chr5:115514815-115514829 chr5:115514812-115514832 chr5:115514814-115514830
38	MAFK	chr5:115514642-115514986	HepG2	liver:	n/a	chr5:115514815-115514829 chr5:115514812-115514832 chr5:115514814-115514830
39	MAFK	chr5:115514650-115514979	HepG2	liver:	n/a	chr5:115514815-115514829 chr5:115514812-115514832 chr5:115514814-115514830
40	MAFK	chr5:115514702-115514970	Hela-S3	cervix:	n/a	chr5:115514815-115514829 chr5:115514812-115514832 chr5:115514814-115514830
41	MAFK	chr5:115546140-115546435	IMR90	lung:	n/a	chr5:115546288-115546299 chr5:115546284-115546300 chr5:115546287-115546301 chr5:115546289-115546300 chr5:115546288-115546299 chr5:115546289-115546300
42	MAFK	chr5:115555495-115555627	HepG2	liver:	n/a	n/a
43	MYC	chr5:115511920-115512140	MCF10A-Er-Src	breast:	n/a	n/a
44	MYC	chr5:115548513-115548606	H1-hESC	embryonic stem cell:	n/a	chr5:115548588-115548599 chr5:115548588-115548599
45	NFYA	chr5:115547516-115547716	GM12878	blood:	n/a	n/a
46	NFYB	chr5:115514339-115514539	GM12878	blood:	n/a	n/a
47	POLR2A	chr5:115544329-115544356	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr5:115510284-115510294	ProgFib	skin:	n/a	n/a
49	POLR2A	chr5:115527331-115527464	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr5:115542870-115543154	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:115523919..115526832-chr5:115553749..115555427,2	MCF-7	breast:
2	chr5:115512590..115515778-chr5:115516651..115520258,3	MCF-7	breast:
3	chr5:115523919..115526832-chr5:115553749..115555427,2	MCF-7	breast:
4	chr5:115512590..115515778-chr5:115516651..115520258,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-3	chr5:115549572-115550152	NONHSAT103355
2	lnc-SEMA6A-7	chr5:115553723-115553992	NONHSAT103356

Variant related genes	Relation type
HMGN2P27	TF binding region
RNU6-644P	TF binding region
ENSG00000232916	chromatin interactions
ENSG00000212457	chromatin interactions

Extended variants
information (count: 2887 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:2887 , 50 per page) page: 1 2 3 4 5 6 7 ... 58

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2416434	chr5:115508352-115508353	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs556060376	chr5:115508363-115508364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs189653207	chr5:115508368-115508369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs555465739	chr5:115508370-115508371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs371556757	chr5:115508372-115508373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs568959257	chr5:115508378-115508379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs537871681	chr5:115508411-115508412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs7736793	chr5:115508441-115508442	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs577911966	chr5:115508459-115508460	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs28536184	chr5:115508471-115508472	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs553938652	chr5:115508484-115508485	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs573476145	chr5:115508487-115508488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs542729641	chr5:115508492-115508493	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs556486903	chr5:115508506-115508507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs183345197	chr5:115508550-115508551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs187839098	chr5:115508562-115508563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs545423336	chr5:115508570-115508571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs565089743	chr5:115508572-115508573	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs6594956	chr5:115508582-115508583	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs578181205	chr5:115508600-115508601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs547745245	chr5:115508622-115508623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs151062422	chr5:115508681-115508682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs192878206	chr5:115508719-115508720	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs530354007	chr5:115508738-115508739	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs376489772	chr5:115508748-115508749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs545309094	chr5:115508754-115508755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs560200238	chr5:115508794-115508795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs7719318	chr5:115508819-115508820	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs183563401	chr5:115508852-115508853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs79053054	chr5:115508891-115508892	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs58502196	chr5:115508894-115508895	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs187361956	chr5:115508895-115508896	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs142383656	chr5:115508906-115508907	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs553617801	chr5:115508929-115508930	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs573575485	chr5:115508930-115508931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs192677735	chr5:115508946-115508947	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs7703661	chr5:115508989-115508990	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs78393097	chr5:115509039-115509040	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs117989139	chr5:115509078-115509079	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs200194420	chr5:115509139-115509140	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs144729728	chr5:115509194-115509195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs147867355	chr5:115509198-115509199	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs114492206	chr5:115509217-115509218	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs561597566	chr5:115509251-115509252	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs530415011	chr5:115509266-115509267	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs114587545	chr5:115509318-115509319	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs563832553	chr5:115509355-115509356	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs76750425	chr5:115509359-115509360	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs184561580	chr5:115509366-115509367	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs10073199	chr5:115509419-115509420	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:76)

Disease	PMID	Source
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
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Cancer	16751803	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	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
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
Urothelial carcinoma	21177765	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
Lung cancer	18438408	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Breast cancer	21785460	CNVD
Squamous cell cancer	20885788	CNVD
Hepatocellular carcinoma	16750200	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	17133270	CNVD
Acute myeloid leukemia	20729466	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
lymphocytic leukemia	21291569	CNVD
Cancer	20164920	CNVD
Myelodysplastic syndrome	21251322	CNVD
Colorectal cancer	16272173	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	17550852	CNVD
Ovarian cancer	21720365	CNVD
Salivary gland tumor	18059337	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	19377443	CNVD
Prostate cancer	16461572	CNVD
Myelofibrosis	22110671	CNVD
Sezary syndrome	18413736	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Glaucoma	21310917	CNVD
Glioblastoma multiforme	22286061	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Prostate cancer	22341455	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Ependymoma	20639864	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD

Chromatin state (count:273 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115471600-115521600	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:115481400-115536000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr5:115484400-115510000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:115484400-115521400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:115489200-115526800	Weak transcription	Pancreas	Pancrea
6	chr5:115489800-115528600	Weak transcription	Ovary	ovary
7	chr5:115490000-115524400	Weak transcription	Left Ventricle	heart
8	chr5:115494600-115522200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:115495200-115521600	Weak transcription	Adipose Nuclei	Adipose
10	chr5:115495200-115524400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:115497400-115528800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:115499200-115527400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:115501200-115511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:115502200-115508800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:115502400-115524400	Weak transcription	Fetal Intestine Large	intestine
16	chr5:115502400-115526400	Weak transcription	Lung	lung
17	chr5:115502800-115521600	Weak transcription	Primary T cells from cord blood	blood
18	chr5:115503000-115509200	Weak transcription	Primary B cells from cord blood	blood
19	chr5:115508000-115509600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:115508200-115518400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:115508400-115517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:115508800-115509200	Enhancers	Rectal Smooth Muscle	rectum
23	chr5:115508800-115529200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:115509200-115509400	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr5:115509200-115528400	Weak transcription	A549	lung
26	chr5:115509400-115510200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr5:115509400-115510800	Strong transcription	Primary B cells from cord blood	blood
28	chr5:115509400-115511800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr5:115509600-115510200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:115509600-115510400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:115509600-115533400	Weak transcription	HSMM	muscle
32	chr5:115509800-115510200	ZNF genes & repeats	Liver	Liver
33	chr5:115509800-115510200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr5:115509800-115510400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr5:115509800-115510600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
36	chr5:115510000-115510400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:115510200-115511400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:115510200-115521400	Weak transcription	Liver	Liver
39	chr5:115510200-115521600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:115510200-115522000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:115510400-115522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:115510400-115524600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:115510400-115526200	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:115510400-115526800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:115510600-115514200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr5:115510800-115511800	Weak transcription	Primary B cells from cord blood	blood
47	chr5:115511400-115511800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:115511600-115512000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr5:115511600-115512000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:115511800-115512200	Strong transcription	Primary B cells from cord blood	blood

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