Variant report

Variant	nsv10449
Chromosome Location	chr4:9828789-9832770
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	BRCA1	chr4:9829608-9829617	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F4	chr4:9830042-9830666	MCF10A-Er-Src	breast:	n/a	n/a
3	EBF1	chr4:9830516-9830857	GM12878	blood:	n/a	chr4:9830672-9830682 chr4:9830670-9830683 chr4:9830672-9830681 chr4:9830670-9830681 chr4:9830672-9830681
4	EBF1	chr4:9830537-9830752	GM12878	blood:	n/a	chr4:9830672-9830682 chr4:9830670-9830683 chr4:9830672-9830681 chr4:9830670-9830681 chr4:9830672-9830681
5	ELK1	chr4:9829919-9829966	GM12878	blood:	n/a	n/a
6	MAFK	chr4:9832414-9832469	HepG2	liver:	n/a	chr4:9832422-9832439
7	MAFK	chr4:9832277-9832460	HepG2	liver:	n/a	chr4:9832422-9832439
8	POLR2A	chr4:9832409-9832744	HepG2	liver:	n/a	n/a
9	STAT1	chr4:9830744-9830757	GM12878	blood:	n/a	n/a
10	STAT3	chr4:9829459-9829562	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr4:9828622-9828837	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:9827283..9829135-chr4:9829200..9831465,2	K562	blood:

Variant related genes	Relation type
SLC2A9	TF binding region
ENSG00000109667	chromatin interactions

Extended variants
information (count: 179 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:179 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs368931977	chr4:9828838-9828839	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs145863940	chr4:9828862-9828863	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs138761199	chr4:9828930-9828931	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs548776293	chr4:9828995-9828996	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs566351734	chr4:9829010-9829011	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs6837273	chr4:9829086-9829087	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs367717615	chr4:9829155-9829156	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs558379310	chr4:9829209-9829210	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs570381143	chr4:9829251-9829252	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs143972797	chr4:9829278-9829279	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs150251636	chr4:9829321-9829322	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs574378024	chr4:9829344-9829345	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs535389660	chr4:9829400-9829401	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs547967735	chr4:9829417-9829418	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs556727168	chr4:9829433-9829434	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs371927101	chr4:9829434-9829435	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs555494407	chr4:9829441-9829442	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs543848669	chr4:9829445-9829446	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs565253491	chr4:9829459-9829460	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs182890204	chr4:9829465-9829466	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs7680554	chr4:9829481-9829482	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs187190467	chr4:9829487-9829488	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs559811939	chr4:9829527-9829528	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs530412414	chr4:9829528-9829529	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs542421823	chr4:9829627-9829628	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs138924648	chr4:9829657-9829658	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs62295672	chr4:9829658-9829659	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs531016157	chr4:9829666-9829667	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs192857942	chr4:9829672-9829673	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs570471806	chr4:9829695-9829696	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs534753540	chr4:9829718-9829719	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs182640648	chr4:9829733-9829734	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs575861504	chr4:9829755-9829756	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs73804391	chr4:9829784-9829785	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs556837766	chr4:9829785-9829786	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs550409510	chr4:9829795-9829796	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs11938866	chr4:9829799-9829800	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs539272094	chr4:9829810-9829811	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs557966793	chr4:9829827-9829828	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs532532214	chr4:9829865-9829866	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs144652081	chr4:9829882-9829883	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs148507678	chr4:9829920-9829921	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs372021642	chr4:9829956-9829957	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs559775057	chr4:9829958-9829959	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs574896082	chr4:9829981-9829982	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs35596118	chr4:9830009-9830010	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs28735365	chr4:9830036-9830037	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs112255785	chr4:9830039-9830040	Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs536850130	chr4:9830047-9830048	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs192240784	chr4:9830053-9830054	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Wilms tumour	21544195	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
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	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
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Schizophrenia	22241247	CNVD
Autosomal-dominant microtia	18179897	CNVD
Glioma	17123091	CNVD
Colorectal cancer	20459617	CNVD
Breast cancer	17133270	CNVD
Sezary syndrome	18413736	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Neuroblastoma	20406844	CNVD
early-passage human iPS cells	21368824	CNVD
Sinonasal adenocarcinoma	21360264	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Breast cancer	17142309	CNVD
Glioma	20126413	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Obesity	21131291	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9808200-9832000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:9808800-9834400	Weak transcription	NHEK	skin
3	chr4:9810000-9830600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:9820200-9842600	Weak transcription	HMEC	breast
5	chr4:9820400-9833400	Weak transcription	Esophagus	oesophagus
6	chr4:9821000-9832400	Weak transcription	Liver	Liver
7	chr4:9821600-9833200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:9823800-9836400	Weak transcription	Left Ventricle	heart
9	chr4:9824000-9832400	Weak transcription	Fetal Intestine Large	intestine
10	chr4:9825800-9835000	Weak transcription	Aorta	Aorta
11	chr4:9826400-9837600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:9827000-9832400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:9827600-9832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:9828400-9829800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr4:9828400-9829800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr4:9828600-9829000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:9828600-9832000	Weak transcription	HepG2	liver
18	chr4:9829800-9830400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr4:9829800-9839000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr4:9830400-9832200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:9830600-9836600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:9831600-9840600	Weak transcription	Pancreas	Pancrea
23	chr4:9832000-9833600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr4:9832000-9837200	Strong transcription	HepG2	liver
25	chr4:9832200-9835000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:9832200-9839600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:9832400-9833600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr4:9832400-9835000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:9832400-9836400	Strong transcription	Liver	Liver
30	chr4:9832400-9836600	Strong transcription	Fetal Intestine Large	intestine
31	chr4:9832600-9836400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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