Variant report

Variant	esv3334736
Chromosome Location	chr5:68259096-68263094
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	BCL3	chr5:68260450-68262189	GM12878	blood:	n/a	n/a
2	BCL3	chr5:68260303-68262196	GM12878	blood:	n/a	n/a
3	CTCF	chr5:68260697-68260754	GM19239	blood:	n/a	n/a
4	CTCF	chr5:68258532-68259209	HCT-116	colon:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
5	CTCF	chr5:68259140-68259290	AG04449	skin:	n/a	n/a
6	CTCF	chr5:68258689-68259111	T-47D	breast:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
7	CTCF	chr5:68258643-68259129	MCF-7	breast:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
8	CTCF	chr5:68259240-68259390	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr5:68258624-68259133	MCF-7	breast:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
10	CTCF	chr5:68261771-68261782	GM13976	blood:	n/a	n/a
11	CTCF	chr5:68258692-68259113	H1-hESC	embryonic stem cell:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
12	CTCF	chr5:68258648-68259200	HCT-116	colon:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
13	CTCF	chr5:68261862-68261988	GM19239	blood:	n/a	n/a
14	CTCF	chr5:68258288-68259284	A549	lung:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
15	CTCF	chr5:68261080-68261230	HCFaa	heart:	n/a	n/a
16	CTCF	chr5:68258681-68259188	IMR90	lung:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
17	CTCF	chr5:68258408-68259294	SK-N-SH	brain:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
18	CTCF	chr5:68258688-68259108	K562	blood:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
19	CTCF	chr5:68258687-68259114	GM12878	blood:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
20	CTCF	chr5:68259148-68259224	GM13977	blood:	n/a	n/a
21	CTCF	chr5:68258703-68259159	A549	lung:	n/a	chr5:68258888-68258906 chr5:68258890-68258903 chr5:68258883-68258904
22	MYC	chr5:68258766-68259140	K562	blood:	n/a	n/a
23	NFATC1	chr5:68260253-68261422	GM12878	blood:	n/a	n/a
24	NFATC1	chr5:68260454-68261635	GM12878	blood:	n/a	n/a
25	NFATC1	chr5:68261711-68262150	GM12878	blood:	n/a	n/a
26	NFATC1	chr5:68261608-68262132	GM12878	blood:	n/a	n/a
27	NR2C2	chr5:68260475-68261442	GM12878	blood:	n/a	n/a
28	PBX3	chr5:68260495-68260905	GM12878	blood:	n/a	n/a
29	PBX3	chr5:68260971-68261252	GM12878	blood:	n/a	n/a
30	PBX3	chr5:68261287-68262073	GM12878	blood:	n/a	n/a
31	POLR2A	chr5:68261821-68261826	Gliobla	brain:	n/a	n/a
32	POLR2A	chr5:68261772-68261775	Gliobla	brain:	n/a	n/a
33	RAD21	chr5:68258501-68259144	SK-N-SH_RA	brain:	n/a	chr5:68258886-68258905
34	RAD21	chr5:68258509-68259258	HCT-116	colon:	n/a	chr5:68258886-68258905
35	RAD21	chr5:68258624-68259155	ECC-1	luminal epithelium:	n/a	chr5:68258886-68258905
36	RAD21	chr5:68258627-68259127	HepG2	liver:	n/a	chr5:68258886-68258905
37	RAD21	chr5:68258567-68259198	H1-hESC	embryonic stem cell:	n/a	chr5:68258886-68258905
38	RAD21	chr5:68258632-68259124	H1-hESC	embryonic stem cell:	n/a	chr5:68258886-68258905
39	RAD21	chr5:68258636-68259124	H1-hESC	embryonic stem cell:	n/a	chr5:68258886-68258905
40	RAD21	chr5:68258531-68259144	A549	lung:	n/a	chr5:68258886-68258905
41	RAD21	chr5:68258502-68259232	A549	lung:	n/a	chr5:68258886-68258905
42	RAD21	chr5:68258634-68259107	IMR90	lung:	n/a	chr5:68258886-68258905
43	RAD21	chr5:68258600-68259231	HCT-116	colon:	n/a	chr5:68258886-68258905
44	RAD21	chr5:68258574-68259160	MCF-7	breast:	n/a	chr5:68258886-68258905
45	RAD21	chr5:68258542-68259245	MCF-7	breast:	n/a	chr5:68258886-68258905
46	RAD21	chr5:68258615-68259164	ECC-1	luminal epithelium:	n/a	chr5:68258886-68258905
47	RAD21	chr5:68258649-68259103	Hela-S3	cervix:	n/a	chr5:68258886-68258905
48	RAD21	chr5:68257867-68259608	SK-N-SH	brain:	n/a	chr5:68258886-68258905
49	RCOR1	chr5:68260691-68260805	K562	blood:	n/a	n/a
50	SMC3	chr5:68258401-68259431	SK-N-SH	brain:	n/a	chr5:68258890-68258904

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68258016..68260416-chr5:68261824..68264961,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC30A5-1	chr5:68259073-68259310	XLOC_004417

Variant related genes	Relation type
ENSG00000249335	TF binding region
ENSG00000250066	chromatin interactions

Extended variants
information (count: 237 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:237 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs182167655	chr5:68259123-68259124	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs36070419	chr5:68259198-68259199	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs74722263	chr5:68259208-68259209	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs372639931	chr5:68259264-68259265	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs114617357	chr5:68259270-68259271	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs138559559	chr5:68259302-68259303	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs529510723	chr5:68259320-68259321	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs572906926	chr5:68259354-68259355	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs372845609	chr5:68259361-68259362	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs533693740	chr5:68259381-68259382	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs372970272	chr5:68259390-68259391	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs539943792	chr5:68259463-68259464	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs551763659	chr5:68259475-68259476	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs570073889	chr5:68259514-68259515	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs201432612	chr5:68259520-68259521	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs76662607	chr5:68259533-68259534	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs184550358	chr5:68259563-68259564	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs189892824	chr5:68259601-68259602	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs558618841	chr5:68259607-68259608	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs568239999	chr5:68259624-68259625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs565958505	chr5:68259675-68259676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs553811117	chr5:68259721-68259722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs572019997	chr5:68259728-68259729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs180727737	chr5:68259744-68259745	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs548631045	chr5:68259818-68259819	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs185170516	chr5:68259879-68259880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs563986618	chr5:68259944-68259945	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs112861174	chr5:68259953-68259954	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs141750860	chr5:68259954-68259955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs150764119	chr5:68259999-68260000	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs529467148	chr5:68260024-68260025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs73771638	chr5:68260055-68260056	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs559910508	chr5:68260132-68260133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs575979459	chr5:68260150-68260151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs533226591	chr5:68260182-68260183	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs551905192	chr5:68260218-68260219	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs181832709	chr5:68260227-68260228	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs530966165	chr5:68260245-68260246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs113981184	chr5:68260329-68260330	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs4458534	chr5:68260388-68260389	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs62354488	chr5:68260430-68260431	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs528674783	chr5:68260463-68260464	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs553652827	chr5:68260481-68260482	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs565877866	chr5:68260482-68260483	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs539100816	chr5:68260556-68260557	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs114455375	chr5:68260564-68260565	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs200691999	chr5:68260568-68260569	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs558784163	chr5:68260572-68260573	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs575623525	chr5:68260577-68260578	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs534485797	chr5:68260584-68260585	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:102)

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
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	20729466	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
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Merkel cell carcinoma	19020549	CNVD
Squamous cell cancer	20885788	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Ovarian cancer	21720365	CNVD
Lung adenocarcinoma	17086460	CNVD
Breast cancer	21045282	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Lung cancer	17086460	CNVD
Prostate cancer	16461572	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

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68246200-68262200	Weak transcription	Esophagus	oesophagus
2	chr5:68256400-68259200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr5:68257800-68259200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:68257800-68259200	Enhancers	Liver	Liver
5	chr5:68258000-68259200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr5:68258000-68261800	Weak transcription	Spleen	Spleen
7	chr5:68258400-68259200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:68258400-68259200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:68258600-68259200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:68258600-68259200	Active TSS	Muscle Satellite Cultured Cells	--
11	chr5:68258600-68259200	Enhancers	Brain Angular Gyrus	brain
12	chr5:68258600-68259200	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:68258600-68259200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr5:68258600-68259200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:68258600-68259200	Enhancers	Fetal Intestine Small	intestine
16	chr5:68258800-68259200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:68258800-68259200	Enhancers	Adipose Nuclei	Adipose
18	chr5:68258800-68260000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:68258800-68260400	Weak transcription	Fetal Kidney	kidney
20	chr5:68258800-68260400	Weak transcription	Fetal Lung	lung
21	chr5:68258800-68262000	Weak transcription	Brain Substantia Nigra	brain
22	chr5:68258800-68262000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:68259000-68259200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:68259000-68259200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:68259000-68259200	Active TSS	Brain Hippocampus Middle	brain
26	chr5:68259000-68259200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr5:68259000-68259200	Flanking Active TSS	NHDF-Ad	bronchial
28	chr5:68259000-68259200	Enhancers	Osteobl	bone
29	chr5:68259200-68262200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:68260400-68260600	Enhancers	Fetal Lung	lung
31	chr5:68260400-68260800	Enhancers	Gastric	stomach
32	chr5:68260400-68260800	Enhancers	Pancreas	Pancrea
33	chr5:68260400-68261400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr5:68260400-68261600	ZNF genes & repeats	Fetal Kidney	kidney
35	chr5:68260600-68260800	ZNF genes & repeats	Fetal Lung	lung
36	chr5:68260600-68261400	ZNF genes & repeats	Fetal Brain Male	brain
37	chr5:68261400-68262400	Weak transcription	Fetal Brain Male	brain
38	chr5:68261800-68262000	Enhancers	Spleen	Spleen
39	chr5:68262000-68262600	Enhancers	Fetal Muscle Trunk	muscle
40	chr5:68262200-68262600	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links