Variant report

Variant	esv5236
Chromosome Location	chr9:98265957-98266462
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	ARID3A	chr9:98266249-98267286	HepG2	liver:	n/a	n/a
2	BATF	chr9:98266336-98266581	GM12878	blood:	n/a	n/a
3	BATF	chr9:98266338-98266593	GM12878	blood:	n/a	n/a
4	BHLHE40	chr9:98266333-98266803	HepG2	liver:	n/a	n/a
5	BHLHE40	chr9:98266455-98266622	GM12878	blood:	n/a	n/a
6	BHLHE40	chr9:98266288-98266595	HepG2	liver:	n/a	n/a
7	CEBPB	chr9:98266273-98266593	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr9:98266295-98266627	HepG2	liver:	n/a	n/a
9	CEBPB	chr9:98266328-98266594	A549	lung:	n/a	n/a
10	CEBPB	chr9:98266300-98266535	K562	blood:	n/a	n/a
11	CEBPB	chr9:98266243-98266642	IMR90	lung:	n/a	n/a
12	CEBPB	chr9:98266242-98266678	HepG2	liver:	n/a	n/a
13	CEBPB	chr9:98266277-98266613	HepG2	liver:	n/a	n/a
14	CEBPB	chr9:98266288-98266597	K562	blood:	n/a	n/a
15	CEBPB	chr9:98266257-98266610	A549	lung:	n/a	n/a
16	CEBPB	chr9:98266332-98266563	HepG2	liver:	n/a	n/a
17	CEBPB	chr9:98266282-98266664	A549	lung:	n/a	n/a
18	CEBPB	chr9:98266334-98266682	MCF-7	breast:	n/a	n/a
19	CEBPD	chr9:98266329-98266579	HepG2	liver:	n/a	n/a
20	CHD1	chr9:98266325-98275163	IMR90	lung:	n/a	chr9:98271086-98271096 chr9:98274530-98274540
21	EP300	chr9:98266239-98266661	HepG2	liver:	n/a	chr9:98266471-98266480
22	EP300	chr9:98266263-98266720	A549	lung:	n/a	chr9:98266471-98266480
23	EP300	chr9:98266335-98266666	HepG2	liver:	n/a	chr9:98266471-98266480
24	EP300	chr9:98266309-98266665	HepG2	liver:	n/a	chr9:98266471-98266480
25	FOS	chr9:98266340-98266664	HUVEC	blood vessel:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266470-98266481 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
26	FOS	chr9:98266293-98266672	MCF10A-Er-Src	breast:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266470-98266481 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
27	FOS	chr9:98266293-98266656	MCF10A-Er-Src	breast:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266470-98266481 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
28	FOS	chr9:98266299-98266626	MCF10A-Er-Src	breast:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266470-98266481 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
29	FOS	chr9:98266306-98266657	MCF10A-Er-Src	breast:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266470-98266481 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
30	FOSL2	chr9:98266314-98266659	A549	lung:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266471-98266482 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
31	FOSL2	chr9:98266254-98266734	A549	lung:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266471-98266482 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
32	FOSL2	chr9:98266219-98266773	HepG2	liver:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266471-98266482 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
33	FOSL2	chr9:98266326-98266696	HepG2	liver:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266471-98266482 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
34	FOSL2	chr9:98266335-98266714	MCF-7	breast:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266471-98266482 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
35	FOXA1	chr9:98266360-98266556	T-47D	breast:	n/a	n/a
36	FOXA1	chr9:98266300-98266676	HepG2	liver:	n/a	n/a
37	FOXA1	chr9:98266291-98266755	HepG2	liver:	n/a	n/a
38	FOXA1	chr9:98266255-98266758	HepG2	liver:	n/a	n/a
39	FOXA1	chr9:98266332-98266765	HepG2	liver:	n/a	n/a
40	FOXA2	chr9:98266328-98266971	HepG2	liver:	n/a	n/a
41	FOXA2	chr9:98266148-98266687	A549	lung:	n/a	n/a
42	FOXA2	chr9:98266144-98266828	A549	lung:	n/a	n/a
43	FOXA2	chr9:98266335-98266659	HepG2	liver:	n/a	n/a
44	GATA3	chr9:98266241-98266864	A549	lung:	n/a	n/a
45	HDAC2	chr9:98266302-98266684	HepG2	liver:	n/a	chr9:98266544-98266558
46	JUN	chr9:98266292-98266652	HepG2	liver:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
47	JUN	chr9:98266334-98267165	K562	blood:	n/a	chr9:98266473-98266480 chr9:98266471-98266480 chr9:98266936-98266945 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
48	JUND	chr9:98266316-98267086	K562	blood:	n/a	chr9:98266473-98266480 chr9:98266470-98266481 chr9:98266471-98266480 chr9:98266936-98266945 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
49	JUND	chr9:98266375-98266653	A549	lung:	n/a	chr9:98266473-98266480 chr9:98266470-98266481 chr9:98266471-98266480 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479
50	JUND	chr9:98266289-98266712	HepG2	liver:	n/a	chr9:98266473-98266480 chr9:98266470-98266481 chr9:98266471-98266480 chr9:98266656-98266665 chr9:98266475-98266487 chr9:98266470-98266481 chr9:98266471-98266481 chr9:98266468-98266479

No.	Distal block	Cell Line	Cell type
1	chr9:98210232..98214386-chr9:98264282..98269915,4	K562	blood:
2	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
3	chr9:98246124..98248586-chr9:98264978..98268110,3	K562	blood:
4	chr9:98187644..98190286-chr9:98266151..98268622,2	K562	blood:
5	chr9:98078830..98081414-chr9:98266391..98270806,3	MCF-7	breast:
6	chr9:98187278..98190652-chr9:98265637..98273315,6	K562	blood:
7	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271155	TF binding region
PTCH1	TF binding region
ENSG00000158169	chromatin interactions
ENSG00000237857	chromatin interactions
ENSG00000185920	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs550708169	chr9:98266065-98266066	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs569146737	chr9:98266210-98266211	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs539831210	chr9:98266225-98266226	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs3958435	chr9:98266338-98266339	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs2897049	chr9:98266343-98266344	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs58747037	chr9:98266344-98266345	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs551742294	chr9:98266347-98266348	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs4448343	chr9:98266370-98266371	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs184917308	chr9:98266384-98266385	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs555983850	chr9:98266421-98266422	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs557906633	chr9:98266442-98266443	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Biliary cancer	19435499	CNVD
small cell lung cancer	20016488	CNVD
Intracranial aneurysm	16715129	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Basal cell nevus syndrome	21572526	CNVD
Mental retardation	19951919	CNVD
Retinoblastoma	22278416	CNVD
9q22.3 microdeletion syndrome	22283845	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
overgrowth syndrome	16570072	CNVD
Effusion lymphoma	18079361	CNVD
Pancreatic cancer	17952125	CNVD
Neurodevelopmental disorder	22521361	CNVD
Basal cell carcinoma	21518781	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:142 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
4	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
5	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
6	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
7	chr9:98257400-98266600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
9	chr9:98258000-98266400	Enhancers	Ovary	ovary
10	chr9:98258600-98266400	Weak transcription	Esophagus	oesophagus
11	chr9:98259600-98266600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98260000-98266400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:98260000-98266600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:98260400-98266400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:98260400-98266400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:98260400-98266400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:98260800-98266400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:98260800-98266400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:98260800-98266400	Weak transcription	NHDF-Ad	bronchial
20	chr9:98260800-98266600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:98260800-98267000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:98261400-98266800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:98261600-98266400	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:98262200-98266800	Enhancers	Fetal Heart	heart
25	chr9:98262400-98266600	Weak transcription	Osteobl	bone
26	chr9:98262600-98266400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:98262600-98266400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:98262600-98266400	Weak transcription	HSMM	muscle
29	chr9:98262600-98266400	Weak transcription	NH-A	brain
30	chr9:98262600-98266600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:98262600-98266600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:98262800-98266400	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:98262800-98266400	Weak transcription	HMEC	breast
34	chr9:98262800-98267600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr9:98263000-98266400	Weak transcription	Fetal Intestine Small	intestine
36	chr9:98263000-98267800	Weak transcription	Placenta	Placenta
37	chr9:98263000-98267800	Weak transcription	Lung	lung
38	chr9:98263200-98266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:98263200-98266400	Weak transcription	Fetal Intestine Large	intestine
40	chr9:98263400-98266600	Enhancers	Brain Cingulate Gyrus	brain
41	chr9:98263400-98266600	Enhancers	Brain Substantia Nigra	brain
42	chr9:98264000-98266600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:98264000-98267000	Enhancers	Brain Angular Gyrus	brain
44	chr9:98264000-98267600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:98264200-98266000	Flanking Active TSS	GM12878-XiMat	blood
46	chr9:98264200-98266400	Enhancers	Brain Anterior Caudate	brain
47	chr9:98264200-98267200	Enhancers	Pancreas	Pancrea
48	chr9:98264400-98267200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr9:98264600-98266400	Weak transcription	Left Ventricle	heart
50	chr9:98264600-98266400	Weak transcription	Right Ventricle	heart

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