Variant report

Variant	nsv598461
Chromosome Location	chr5:68878051-68911161
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:89)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:1)

(count:89 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr5:68897794-68898185	GM12878	blood:	n/a	n/a
2	BATF	chr5:68897780-68898118	GM12878	blood:	n/a	n/a
3	BCL11A	chr5:68897862-68898148	GM12878	blood:	n/a	n/a
4	BCL11A	chr5:68897742-68898263	GM12878	blood:	n/a	n/a
5	CTCF	chr5:68883919-68883967	Medullo	brain:	n/a	n/a
6	CTCF	chr5:68890705-68890753	Medullo	brain:	n/a	n/a
7	CTCF	chr5:68890437-68890536	LNCaP	prostate:	n/a	n/a
8	CTCF	chr5:68908378-68908428	Lung_OC	lung:	n/a	n/a
9	EBF1	chr5:68879258-68879506	GM12878	blood:	n/a	n/a
10	EBF1	chr5:68904882-68905202	GM12878	blood:	n/a	n/a
11	EBF1	chr5:68897874-68898259	GM12878	blood:	n/a	n/a
12	EBF1	chr5:68879238-68879448	GM12878	blood:	n/a	n/a
13	ESR1	chr5:68899863-68900234	T-47D	breast:	n/a	n/a
14	ESR1	chr5:68899849-68900262	T-47D	breast:	n/a	n/a
15	FOSL2	chr5:68910668-68911104	HepG2	liver:	n/a	n/a
16	FOXA1	chr5:68890145-68890685	HepG2	liver:	n/a	n/a
17	FOXA1	chr5:68899908-68900311	HepG2	liver:	n/a	n/a
18	GATA2	chr5:68890239-68890673	K562	blood:	n/a	n/a
19	IRF4	chr5:68897692-68898345	GM12878	blood:	n/a	n/a
20	IRF4	chr5:68904825-68905228	GM12878	blood:	n/a	n/a
21	IRF4	chr5:68897648-68898539	GM12878	blood:	n/a	n/a
22	NFIC	chr5:68897705-68898242	GM12878	blood:	n/a	n/a
23	PAX5	chr5:68897852-68898166	GM12878	blood:	n/a	chr5:68897992-68898001
24	PAX5	chr5:68893698-68894079	GM12878	blood:	n/a	n/a
25	PAX5	chr5:68897894-68898171	GM12878	blood:	n/a	chr5:68897992-68898001
26	PAX5	chr5:68897903-68898085	GM12878	blood:	n/a	chr5:68897992-68898001
27	PAX5	chr5:68893616-68894118	GM12878	blood:	n/a	n/a
28	PAX5	chr5:68904902-68905274	GM12878	blood:	n/a	n/a
29	PAX5	chr5:68897664-68898374	GM12878	blood:	n/a	chr5:68897992-68898001
30	PAX5	chr5:68893776-68894058	GM12878	blood:	n/a	n/a
31	PAX5	chr5:68893841-68894044	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:68884161-68884488	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:68891700-68893164	GM12892	blood:	n/a	n/a
34	POLR2A	chr5:68904987-68905203	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr5:68891756-68892660	GM12892	blood:	n/a	n/a
36	POLR2A	chr5:68891787-68893166	GM12892	blood:	n/a	n/a
37	POLR2A	chr5:68897581-68898436	GM12892	blood:	n/a	n/a
38	POLR2A	chr5:68897545-68898259	GM12878	blood:	n/a	n/a
39	POLR2A	chr5:68892679-68893165	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:68891791-68892232	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr5:68892713-68893156	GM12891	blood:	n/a	n/a
42	POLR2A	chr5:68892676-68893105	GM12891	blood:	n/a	n/a
43	POLR2A	chr5:68898789-68899106	GM12878	blood:	n/a	n/a
44	POLR2A	chr5:68891742-68892643	GM12878	blood:	n/a	n/a
45	POLR2A	chr5:68892817-68893077	GM12878	blood:	n/a	n/a
46	POLR2A	chr5:68890206-68890580	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr5:68897616-68898096	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:68894404-68894609	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:68879064-68879548	GM12878	blood:	n/a	n/a
50	POLR2A	chr5:68891828-68893113	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTF2H2C-1	chr5:68889300-68889532	NONHSAT101931
2	lnc-GTF2H2C-1	chr5:68890071-68890550	NONHSAT101931

No data

(count:1 , 50 per page) page: 1

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	GTF2H2D	hsa-miR-30a-5p	chr5:68888221-68888242

Variant related genes	Relation type
GTF2H2C	TF binding region
ENSG00000248477	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 114 )

Variant overlapped rSNPs/rCNVs (count:79 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs199857838	chr5:68878277-68878278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs113108396	chr5:68878284-68878285	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs528252649	chr5:68878285-68878286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs539957586	chr5:68878286-68878287	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs113076805	chr5:68878768-68878769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs564967144	chr5:68880512-68880513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs532042612	chr5:68880571-68880572	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs5012305	chr5:68880729-68880730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs483294	chr5:68880827-68880828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs377112207	chr5:68882560-68882561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs532793916	chr5:68882889-68882890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs550572147	chr5:68882934-68882935	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs527407623	chr5:68883457-68883458	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs79758696	chr5:68883552-68883553	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs569614317	chr5:68883553-68883554	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs530406116	chr5:68883573-68883574	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs201041583	chr5:68883633-68883634	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs547436933	chr5:68884142-68884143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs62374266	chr5:68885014-68885015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs62374267	chr5:68885316-68885317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs372547184	chr5:68885617-68885618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs78119549	chr5:68885670-68885671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs548858608	chr5:68885868-68885869	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs566955387	chr5:68885870-68885871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs377235391	chr5:68885958-68885959	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs369193750	chr5:68890095-68890096	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs367939611	chr5:68890263-68890264	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs376785524	chr5:68890264-68890265	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs549792536	chr5:68890266-68890267	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs154415	chr5:68892137-68892138	Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs368078879	chr5:68892251-68892252	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs2856277	chr5:68896890-68896891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs572977107	chr5:68897381-68897382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs540403636	chr5:68897961-68897962	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs376947395	chr5:68897977-68897978	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs564857072	chr5:68898005-68898006	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs375325174	chr5:68898095-68898096	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs577007168	chr5:68898337-68898338	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs200541864	chr5:68898433-68898434	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs201296716	chr5:68898568-68898569	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs544262222	chr5:68898757-68898758	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs562475771	chr5:68898759-68898760	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs529666443	chr5:68898792-68898793	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs548919357	chr5:68898806-68898807	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs560802257	chr5:68898856-68898857	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs527915475	chr5:68898857-68898858	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs552717867	chr5:68898870-68898871	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs371577427	chr5:68898894-68898895	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs537940316	chr5:68899383-68899384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs549825182	chr5:68899385-68899386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:114)

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
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ovarian cancer	21781307	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
Intellectual disability	22102821	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Breast cancer	22032731	CNVD
Prostate cancer	21965145	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
Non-small cell lung cancer	21829676	CNVD
adenomatous polyposis	22470819	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
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Retinoblastoma	22278416	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
abnormal development	18461090	CNVD
Merkel cell carcinoma	19020549	CNVD
Squamous cell cancer	20885788	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21045282	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Myelodysplastic syndrome	18663149	CNVD
Spinal muscular atrophy	15981080	CNVD
Spinal muscular atrophy	18839960	CNVD
Spinal muscular atrophy	19716110	CNVD
Sezary syndrome	18413736	CNVD
Ewing''s sarcoma	17952124	CNVD
Breast cancer	21990379	CNVD
Hirschsprung''s Disease	21712996	CNVD
Apoptosis	19488400	CNVD
Breast cancer	22048815	CNVD
Myelofibrosis	22110671	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Acute monocytic leukemia	16498392	CNVD
Colorectal cancer	20459617	CNVD
Gastric adenocarcinoma	19115996	CNVD
Spinal muscular atrophy	17160897	CNVD
Spinal muscular atrophy	17668391	CNVD
Spinal muscular atrophy	17668395	CNVD
Glioblastoma multiforme	22286061	CNVD
craniofacial dysmorphism	21918468	CNVD
Multiple myeloma	16616336	CNVD
Prostate cancer	16461572	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pseudo-TORCH syndrome	20727516	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Autism	21865298	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Obesity	21131291	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68857000-68878200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:68857000-68883400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:68869200-68879000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:68883400-68883800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:68883800-68886000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:68892000-68892200	Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr5:68892200-68892400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr5:68892600-68894000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:68896200-68901400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:68897800-68898200	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:68897800-68899000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:68898200-68902000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr5:68899000-68901400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:68901400-68902200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:68901400-68903000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr5:68902000-68902200	Enhancers	Primary B cells from peripheral blood	blood
17	chr5:68902000-68902200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr5:68902200-68902600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:68902200-68903000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr5:68902200-68906400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:68902600-68903000	Enhancers	Primary B cells from peripheral blood	blood
22	chr5:68902800-68903000	Enhancers	Primary B cells from cord blood	blood
23	chr5:68906400-68906600	Enhancers	Monocytes-CD14+_RO01746	blood

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