Variant report

Variant	esv3350329
Chromosome Location	chr9:96194029-96194345
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	BHLHE40	chr9:96193930-96194262	HepG2	liver:	n/a	n/a
2	BHLHE40	chr9:96193824-96194318	K562	blood:	n/a	n/a
3	ELF1	chr9:96194075-96194389	K562	blood:	n/a	chr9:96194201-96194214 chr9:96194203-96194214 chr9:96194227-96194240
4	ELF1	chr9:96194080-96194356	HepG2	liver:	n/a	chr9:96194201-96194214 chr9:96194203-96194214 chr9:96194227-96194240
5	ELF1	chr9:96193719-96194492	MCF-7	breast:	n/a	chr9:96194201-96194214 chr9:96194203-96194214 chr9:96194227-96194240
6	ELF1	chr9:96194076-96194357	HepG2	liver:	n/a	chr9:96194201-96194214 chr9:96194203-96194214 chr9:96194227-96194240
7	FOXA1	chr9:96193708-96194114	T-47D	breast:	n/a	n/a
8	FOXA1	chr9:96193746-96194044	T-47D	breast:	n/a	n/a
9	FOXA1	chr9:96193646-96194077	HepG2	liver:	n/a	n/a
10	FOXA2	chr9:96193765-96194070	HepG2	liver:	n/a	n/a
11	FOXP2	chr9:96194092-96194337	SK-N-MC	brain:	n/a	n/a
12	GABPA	chr9:96194111-96194296	HepG2	liver:	n/a	n/a
13	GABPA	chr9:96194119-96194295	HepG2	liver:	n/a	n/a
14	GATA3	chr9:96193692-96194107	T-47D	breast:	n/a	n/a
15	GATA3	chr9:96193750-96194054	MCF-7	breast:	n/a	n/a
16	GATA3	chr9:96193834-96194110	MCF-7	breast:	n/a	n/a
17	GATA3	chr9:96193486-96194405	MCF-7	breast:	n/a	n/a
18	GATA3	chr9:96193711-96194071	T-47D	breast:	n/a	n/a
19	GATA3	chr9:96193665-96194316	MCF-7	breast:	n/a	n/a
20	HNF4A	chr9:96193771-96194075	HepG2	liver:	n/a	chr9:96193959-96193977 chr9:96193962-96193974 chr9:96193961-96193974 chr9:96193962-96193974 chr9:96193961-96193975 chr9:96193960-96193975 chr9:96193960-96193975 chr9:96193960-96193975
21	HNF4A	chr9:96193840-96194120	HepG2	liver:	n/a	chr9:96193959-96193977 chr9:96193962-96193974 chr9:96193961-96193974 chr9:96193962-96193974 chr9:96193961-96193975 chr9:96193960-96193975 chr9:96193960-96193975 chr9:96193960-96193975
22	JUND	chr9:96194170-96194353	K562	blood:	n/a	n/a
23	MAFF	chr9:96194055-96194255	K562	blood:	n/a	chr9:96194153-96194171
24	MAFF	chr9:96193973-96194636	HepG2	liver:	n/a	chr9:96194153-96194171
25	MAFK	chr9:96194019-96194301	IMR90	lung:	n/a	chr9:96194150-96194167 chr9:96194158-96194169 chr9:96194159-96194170 chr9:96194154-96194170 chr9:96194157-96194171 chr9:96194154-96194169 chr9:96194159-96194170
26	MAFK	chr9:96193865-96194772	HepG2	liver:	n/a	chr9:96194150-96194167 chr9:96194158-96194169 chr9:96194159-96194170 chr9:96194154-96194170 chr9:96194157-96194171 chr9:96194154-96194169 chr9:96194159-96194170
27	MAFK	chr9:96193882-96194318	K562	blood:	n/a	chr9:96194150-96194167 chr9:96194158-96194169 chr9:96194159-96194170 chr9:96194154-96194170 chr9:96194157-96194171 chr9:96194154-96194169 chr9:96194159-96194170
28	MAFK	chr9:96193992-96194704	HepG2	liver:	n/a	chr9:96194150-96194167 chr9:96194158-96194169 chr9:96194159-96194170 chr9:96194154-96194170 chr9:96194157-96194171 chr9:96194154-96194169 chr9:96194159-96194170
29	MAZ	chr9:96194211-96194219	K562	blood:	n/a	n/a
30	MYC	chr9:96193842-96194231	K562	blood:	n/a	n/a
31	POLR2A	chr9:96194142-96194337	HepG2	liver:	n/a	n/a
32	SIN3AK20	chr9:96193620-96194244	MCF-7	breast:	n/a	n/a
33	SPI1	chr9:96194071-96194298	K562	blood:	n/a	chr9:96194203-96194212
34	SPI1	chr9:96194039-96194383	HL-60	blood:	n/a	chr9:96194203-96194212
35	ZC3H11A	chr9:96194021-96194123	K562	blood:	n/a	n/a
36	ZNF217	chr9:96193805-96194115	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96193694..96195891-chr9:96211466..96214118,3	K562	blood:
2	chr9:96193866..96195671-chr9:96205217..96208189,2	K562	blood:
3	chr9:96054744..96057085-chr9:96193778..96195427,2	MCF-7	breast:
4	chr9:96194036..96195679-chr9:96195790..96198245,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM120A-2	chr9:96193447-96194991	NONHSAT133251

Variant related genes	Relation type
ENSG00000237385	TF binding region
ENSG00000048828	chromatin interactions
ENSG00000188938	chromatin interactions
ENSG00000165238	chromatin interactions

Extended variants
information (count: 10 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12339736	chr9:96194061-96194062	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs564635294	chr9:96194070-96194071	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
3	rs139487629	chr9:96194095-96194096	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
4	rs117734979	chr9:96194123-96194124	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
5	rs376000451	chr9:96194128-96194129	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
6	rs187029988	chr9:96194178-96194179	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
7	rs62574530	chr9:96194214-96194215	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
8	rs145012759	chr9:96194226-96194227	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
9	rs76514195	chr9:96194239-96194240	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
10	rs144955704	chr9:96194296-96194297	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:73)

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
Mental retardation	21693067	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
Microcephaly	18830227	CNVD
overgrowth syndrome	16570072	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96185800-96208200	Weak transcription	Gastric	stomach
2	chr9:96186000-96208200	Weak transcription	Pancreas	Pancrea
3	chr9:96186600-96208200	Weak transcription	Lung	lung
4	chr9:96190600-96196600	Weak transcription	Placenta	Placenta
5	chr9:96192600-96194200	Weak transcription	Spleen	Spleen
6	chr9:96193000-96196600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:96193200-96194400	Enhancers	Fetal Intestine Large	intestine
8	chr9:96193800-96194200	Enhancers	Duodenum Mucosa	Duodenum
9	chr9:96193800-96194400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:96193800-96194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:96193800-96194400	Enhancers	Fetal Intestine Small	intestine
12	chr9:96193800-96194400	Enhancers	Fetal Kidney	kidney
13	chr9:96193800-96194400	Enhancers	Small Intestine	intestine
14	chr9:96193800-96194400	Flanking Active TSS	HepG2	liver
15	chr9:96193800-96194400	Enhancers	K562	blood
16	chr9:96193800-96194800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:96194000-96194200	Enhancers	Primary T cells from cord blood	blood
18	chr9:96194000-96194400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:96194000-96194400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:96194000-96194400	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:96194000-96194400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr9:96194000-96194400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:96194000-96194400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr9:96194000-96207800	Weak transcription	Thymus	Thymus
25	chr9:96194200-96194400	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:96194200-96194400	Enhancers	Spleen	Spleen
27	chr9:96194200-96207600	Weak transcription	Primary T cells from cord blood	blood

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