Variant report

Variant	esv1174960
Chromosome Location	chr4:1339455-1339462
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:1339420-1339570	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr4:1339460-1339610	HBMEC	blood vessel:	n/a	n/a
3	CTCF	chr4:1339420-1339570	AoAF	blood vessel:	n/a	n/a
4	CTCF	chr4:1339460-1339610	AG10803	skin:	n/a	n/a
5	CTCF	chr4:1339440-1339590	HCFaa	heart:	n/a	n/a
6	CTCF	chr4:1339440-1339590	AG09319	gingival:	n/a	n/a
7	CTCF	chr4:1339460-1339610	HPF	lung:	n/a	n/a
8	CTCF	chr4:1339460-1339610	AG09309	skin:	n/a	n/a
9	CTCF	chr4:1339440-1339590	HMEC	breast:	n/a	n/a
10	CTCF	chr4:1339400-1339550	HPAF	blood vessel:	n/a	n/a
11	HEY1	chr4:1339458-1339599	HepG2	liver:	n/a	n/a
12	HEY1	chr4:1339307-1340040	HepG2	liver:	n/a	n/a
13	JUN	chr4:1339390-1341877	K562	blood:	n/a	n/a
14	MXI1	chr4:1339461-1341919	IMR90	lung:	n/a	n/a
15	POLR2A	chr4:1339387-1339694	U87	brain:	n/a	n/a
16	POLR2A	chr4:1339300-1340409	U87	brain:	n/a	n/a
17	POLR2A	chr4:1339364-1339689	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:1339448-1340104	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr4:1339300-1340374	U87	brain:	n/a	n/a
20	POLR2A	chr4:1339400-1339694	U87	brain:	n/a	n/a
21	POLR2A	chr4:1339437-1339998	HUVEC	blood vessel:	n/a	n/a
22	REST	chr4:1339379-1341798	H1-neurons	neurons:	n/a	chr4:1341595-1341604 chr4:1340917-1340930
23	ZNF384	chr4:1339274-1340166	K562	blood:	n/a	n/a
24	ZNF384	chr4:1339388-1339991	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:
2	chr4:1339011..1342367-chr4:1367715..1370691,3	MCF-7	breast:
3	chr4:1336558..1338149-chr4:1338227..1340765,3	MCF-7	breast:
4	chr4:1188846..1191354-chr4:1337880..1340557,2	MCF-7	breast:
5	chr4:679728..681770-chr4:1339441..1342302,2	K562	blood:
6	chr4:1313002..1315500-chr4:1338426..1340938,2	MCF-7	breast:
7	chr4:1295898..1297425-chr4:1338423..1340843,2	MCF-7	breast:
8	chr4:1280977..1287340-chr4:1335495..1344055,33	MCF-7	breast:
9	chr4:1292718..1295595-chr4:1336898..1340190,3	MCF-7	breast:
10	chr4:1338673..1343611-chr4:1344125..1350325,16	MCF-7	breast:
11	chr4:1239502..1245378-chr4:1336996..1344860,21	K562	blood:
12	chr4:1338699..1344021-chr4:1351274..1357737,7	MCF-7	breast:
13	chr4:1240883..1245378-chr4:1339091..1342291,13	K562	blood:
14	chr4:984860..987749-chr4:1337412..1341360,3	MCF-7	breast:
15	chr4:1280840..1286312-chr4:1338111..1343712,9	K562	blood:
16	chr4:1289122..1291329-chr4:1338444..1340407,2	MCF-7	breast:
17	chr4:1236808..1249320-chr4:1336333..1343819,66	MCF-7	breast:
18	chr4:1339048..1342461-chr4:1794240..1796574,3	MCF-7	breast:
19	chr4:1339117..1341001-chr4:1581105..1584040,2	K562	blood:
20	chr4:1336595..1339547-chr4:1340996..1343146,3	MCF-7	breast:
21	chr4:1323033..1328941-chr4:1337055..1342245,8	MCF-7	breast:
22	chr4:1282437..1287650-chr4:1338224..1344043,13	MCF-7	breast:
23	chr4:1280807..1287593-chr4:1339102..1342185,6	K562	blood:

No data

Variant related genes	Relation type
UVSSA	TF binding region
ENSG00000145217	chromatin interactions
ENSG00000068078	chromatin interactions
ENSG00000090316	chromatin interactions
ENSG00000253399	chromatin interactions
ENSG00000159674	chromatin interactions
ENSG00000244459	chromatin interactions
ENSG00000196810	chromatin interactions
ENSG00000127415	chromatin interactions
ENSG00000159692	chromatin interactions
ENSG00000163945	chromatin interactions
ENSG00000169026	chromatin interactions

Extended variants
information (count: 1 )
Associated
traits (count: 63 )

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs71168831	chr4:1339456-1339457	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	20932292	CNVD
Breast cancer	22522925	CNVD
Type 2 diabetes	21754918	CNVD

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1317800-1339600	Weak transcription	Right Atrium	heart
2	chr4:1334400-1339600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:1335200-1339600	Weak transcription	Small Intestine	intestine
4	chr4:1335400-1339600	Weak transcription	Ovary	ovary
5	chr4:1335400-1339600	Weak transcription	Psoas Muscle	Psoas
6	chr4:1335400-1339600	Weak transcription	Right Ventricle	heart
7	chr4:1335600-1339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:1335600-1339600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:1335600-1339600	Weak transcription	Left Ventricle	heart
10	chr4:1335600-1339600	Weak transcription	Lung	lung
11	chr4:1335600-1339600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:1338600-1339600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:1338600-1339600	Enhancers	Pancreas	Pancrea
14	chr4:1338800-1339600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:1338800-1339600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:1338800-1339600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr4:1338800-1342400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr4:1339000-1339600	Enhancers	Liver	Liver
19	chr4:1339000-1339600	Weak transcription	Gastric	stomach
20	chr4:1339000-1340000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:1339000-1341600	Active TSS	Osteobl	bone
22	chr4:1339000-1341800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:1339000-1342000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:1339000-1342000	Active TSS	HSMM	muscle
25	chr4:1339200-1339600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:1339200-1339600	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:1339200-1339600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:1339200-1339600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:1339200-1339600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:1339200-1339600	Enhancers	Colonic Mucosa	Colon
31	chr4:1339200-1339600	Enhancers	Fetal Brain Male	brain
32	chr4:1339200-1339800	Active TSS	Brain Germinal Matrix	brain
33	chr4:1339200-1339800	Flanking Active TSS	Fetal Brain Female	brain
34	chr4:1339200-1340000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:1339200-1340000	Flanking Active TSS	Fetal Lung	lung
36	chr4:1339200-1341400	Active TSS	HMEC	breast
37	chr4:1339200-1341400	Active TSS	NH-A	brain
38	chr4:1339200-1341600	Active TSS	Muscle Satellite Cultured Cells	--
39	chr4:1339200-1342000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr4:1339400-1339600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:1339400-1339600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:1339400-1339600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr4:1339400-1339600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:1339400-1339600	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr4:1339400-1339600	Active TSS	Brain Cingulate Gyrus	brain
46	chr4:1339400-1339600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:1339400-1339600	Enhancers	Fetal Heart	heart
48	chr4:1339400-1339600	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr4:1339400-1339600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr4:1339400-1339800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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