Variant report

Variant	nsv428762
Chromosome Location	chr4:57261084-57261742
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	POLR2A	chr4:57261149-57261309	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:57261060-57261223	ProgFib	skin:	n/a	n/a
3	POLR2A	chr4:57261136-57261199	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:57261106-57261198	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:57261211-57261213	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57257925..57261959-chr4:57299598..57302953,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270147	TF binding region
ENSG00000128059	chromatin interactions
ENSG00000128050	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs550686805	chr4:57261124-57261125	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs567402783	chr4:57261176-57261177	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs536315832	chr4:57261202-57261203	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs138098736	chr4:57261216-57261217	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs566483988	chr4:57261226-57261227	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs3733326	chr4:57261234-57261235	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs559984575	chr4:57261240-57261241	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs527429338	chr4:57261346-57261347	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs184074077	chr4:57261356-57261357	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs199983276	chr4:57261370-57261371	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs554346726	chr4:57261372-57261373	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs34605681	chr4:57261373-57261374	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs199711867	chr4:57261396-57261397	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs3036860	chr4:57261400-57261401	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs186916603	chr4:57261408-57261409	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs113509123	chr4:57261449-57261450	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs200268394	chr4:57261524-57261525	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs371980582	chr4:57261527-57261528	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs144451574	chr4:57261568-57261569	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs375085596	chr4:57261605-57261606	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs2660744	chr4:57261610-57261611	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs147822472	chr4:57261646-57261647	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs3908150	chr4:57261652-57261653	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs76674380	chr4:57261656-57261657	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs2412738	chr4:57261665-57261666	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs527367886	chr4:57261679-57261680	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs560199458	chr4:57261713-57261714	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs375102221	chr4:57261717-57261718	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs201443229	chr4:57261729-57261730	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	19435819	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Ovarian neoplasms	16753589	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Glioblastoma	17504929	CNVD
Glioblastoma	16823502	CNVD
Melanoma	16908931	CNVD
Glioblastoma	20031968	CNVD
Medulloblastoma	19270706	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Olfactory neuroblastoma	18408657	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Rhabdomyosarcoma	16790082	CNVD
Gastrointestinal stromal cancer	17438095	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	22183965	CNVD
Breast cancer	21785460	CNVD
Medullary thyroid carcinoma	18765511	CNVD

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57268400	Weak transcription	Lung	lung
3	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
4	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57254600-57271600	Weak transcription	Ovary	ovary
6	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
7	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:57254800-57261800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:57254800-57262000	Weak transcription	Placenta	Placenta
10	chr4:57254800-57264000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:57254800-57264000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
18	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
19	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:57255000-57261200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:57255000-57262200	Weak transcription	A549	lung
22	chr4:57255000-57264400	Weak transcription	Brain Germinal Matrix	brain
23	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
26	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:57255000-57266200	Weak transcription	NH-A	brain
28	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:57255000-57266600	Weak transcription	HSMM	muscle
32	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:57255200-57262000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:57255200-57262200	Weak transcription	Fetal Lung	lung
37	chr4:57255200-57262200	Weak transcription	Osteobl	bone
38	chr4:57255200-57264000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:57255200-57264000	Weak transcription	Fetal Stomach	stomach
40	chr4:57255200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:57255200-57266200	Weak transcription	HUVEC	blood vessel
42	chr4:57255200-57266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr4:57255200-57266800	Weak transcription	Fetal Kidney	kidney
44	chr4:57255200-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:57255200-57267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:57255200-57267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:57255200-57271600	Weak transcription	NHEK	skin
48	chr4:57255200-57272200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:57255200-57275600	Weak transcription	NHLF	lung
50	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon

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