Variant report

Variant	nsv980121
Chromosome Location	chr4:15976687-15978027
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	CTCF	chr4:15976740-15976890	BJ	skin:	n/a	n/a
2	POLR2A	chr4:15977425-15977444	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15976147..15979142-chr4:16221984..16223628,2	MCF-7	breast:
2	chr4:15695760..15698048-chr4:15975957..15978418,2	MCF-7	breast:

Variant related genes	Relation type
PROM1	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 48 )

Variant overlapped rSNPs/rCNVs (count:51 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372339815	chr4:15976689-15976690	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs6855282	chr4:15976760-15976761	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs78268329	chr4:15976807-15976808	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs577674390	chr4:15976821-15976822	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs62288712	chr4:15976828-15976829	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs116835240	chr4:15976865-15976866	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs143681884	chr4:15976866-15976867	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs369002319	chr4:15976868-15976869	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs532812988	chr4:15976886-15976887	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs549331981	chr4:15976905-15976906	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs187627979	chr4:15976906-15976907	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs531476840	chr4:15976930-15976931	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs551398114	chr4:15976935-15976936	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs371918179	chr4:15976936-15976937	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs192797764	chr4:15976945-15976946	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs546680410	chr4:15977020-15977021	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs566561657	chr4:15977056-15977057	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs183867734	chr4:15977071-15977072	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs534165273	chr4:15977166-15977167	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs555451602	chr4:15977188-15977189	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs62288713	chr4:15977198-15977199	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs538117407	chr4:15977272-15977273	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs147221098	chr4:15977336-15977337	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs567649516	chr4:15977392-15977393	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs188010727	chr4:15977438-15977439	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs540367619	chr4:15977443-15977444	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs117779229	chr4:15977470-15977471	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs192102067	chr4:15977494-15977495	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs138818693	chr4:15977495-15977496	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs3796862	chr4:15977523-15977524	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs531639071	chr4:15977531-15977532	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs11734657	chr4:15977572-15977573	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs565129673	chr4:15977585-15977586	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs533411571	chr4:15977603-15977604	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs575196826	chr4:15977623-15977624	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs559035593	chr4:15977630-15977631	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs184603184	chr4:15977643-15977644	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs570878193	chr4:15977676-15977677	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs529315903	chr4:15977690-15977691	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12511293	chr4:15977719-15977720	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs3796861	chr4:15977731-15977732	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs569107838	chr4:15977781-15977782	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs538574387	chr4:15977805-15977806	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs558156928	chr4:15977808-15977809	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs3796860	chr4:15977823-15977824	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs3796859	chr4:15977828-15977829	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs149309971	chr4:15977877-15977878	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs573796091	chr4:15977952-15977953	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144484120	chr4:15977970-15977971	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs3796858	chr4:15977980-15977981	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:48)

Disease	PMID	Source
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	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
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15940200-15983600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:15965200-15983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:15965400-15979000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:15965600-15984000	Weak transcription	Colonic Mucosa	Colon
6	chr4:15967800-15983600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:15968000-16002600	Weak transcription	Left Ventricle	heart
8	chr4:15968200-15978200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:15968600-15979600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:15968600-15993600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:15968800-15983600	Weak transcription	Pancreas	Pancrea
12	chr4:15968800-15992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:15969600-15990000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:15969600-16011600	Weak transcription	Fetal Lung	lung
15	chr4:15969800-15986200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:15971000-15978200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:15971000-15983200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:15971000-15992200	Weak transcription	Fetal Brain Male	brain
19	chr4:15971000-16008000	Weak transcription	Aorta	Aorta
20	chr4:15971200-15979600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:15973200-15980000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:15973200-15993800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:15973600-15978200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:15973800-15978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:15973800-15979000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:15974000-15977800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:15974000-15991800	Weak transcription	Fetal Intestine Small	intestine
28	chr4:15974400-15978200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:15974400-15979600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:15974600-15980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:15974800-15977200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:15974800-15977600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:15975000-15978200	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:15975000-15978200	Weak transcription	Fetal Stomach	stomach
35	chr4:15975600-15978400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:15976400-15982000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr4:15976400-15985800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:15976600-15984400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:15976800-16002600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:15977000-16007400	Weak transcription	Gastric	stomach
41	chr4:15977200-15981000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr4:15977600-15982200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:15977800-15978600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:15978000-15978600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr4:15978000-15979200	Enhancers	Adipose Nuclei	Adipose
46	chr4:15978000-15996800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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