Variant report

Variant	esv3345842
Chromosome Location	chr9:79260247-79263783
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	chr9:79261397-79261562	K562	blood:	n/a	n/a
2	CEBPB	chr9:79263372-79263537	IMR90	lung:	n/a	n/a
3	CEBPB	chr9:79262721-79262967	A549	lung:	n/a	chr9:79262828-79262839
4	CEBPB	chr9:79262670-79263000	MCF-7	breast:	n/a	chr9:79262828-79262839
5	CEBPB	chr9:79262777-79262976	IMR90	lung:	n/a	chr9:79262828-79262839
6	CEBPB	chr9:79262785-79262947	HepG2	liver:	n/a	chr9:79262828-79262839
7	CTCF	chr9:79261240-79261390	HCPEpiC	choroid plexus:	n/a	n/a
8	CTCF	chr9:79263686-79263727	K562	blood:	n/a	n/a
9	E2F6	chr9:79261322-79261490	K562	blood:	n/a	n/a
10	EP300	chr9:79260989-79261791	ECC-1	luminal epithelium:	n/a	n/a
11	GATA1	chr9:79261231-79261673	PBDE	blood:	n/a	chr9:79261505-79261515
12	GATA2	chr9:79261173-79261681	HUVEC	blood vessel:	n/a	chr9:79261505-79261515
13	GATA2	chr9:79261280-79261557	SH-SY5Y	brain:	n/a	chr9:79261505-79261515
14	GATA3	chr9:79261073-79261707	SK-N-SH	brain:	n/a	chr9:79261505-79261515
15	GATA3	chr9:79261108-79261738	SK-N-SH	brain:	n/a	chr9:79261505-79261515
16	HCFC1	chr9:79261416-79261567	K562	blood:	n/a	n/a
17	KAP1	chr9:79261266-79261595	HEK293	kidney:	n/a	n/a
18	MAX	chr9:79261279-79261492	K562	blood:	n/a	n/a
19	MYC	chr9:79263759-79263809	NB4	blood:	n/a	n/a
20	MYC	chr9:79261280-79261395	K562	blood:	n/a	n/a
21	NFIC	chr9:79261006-79261774	ECC-1	luminal epithelium:	n/a	chr9:79261449-79261466 chr9:79261450-79261466
22	NFIC	chr9:79260785-79261840	ECC-1	luminal epithelium:	n/a	chr9:79261449-79261466 chr9:79261450-79261466
23	NR3C1	chr9:79261236-79261525	ECC-1	luminal epithelium:	n/a	n/a
24	NR3C1	chr9:79261149-79261562	ECC-1	luminal epithelium:	n/a	n/a
25	RCOR1	chr9:79261365-79261501	K562	blood:	n/a	n/a
26	STAT3	chr9:79261626-79261826	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr9:79261059-79261237	MCF10A-Er-Src	breast:	n/a	chr9:79261195-79261204 chr9:79261192-79261206 chr9:79261194-79261203 chr9:79261189-79261209 chr9:79261189-79261209
28	TCF12	chr9:79261132-79261693	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:79255042..79257003-chr9:79260887..79262943,2	K562	blood:
2	chr9:79073732..79077462-chr9:79257559..79261400,5	MCF-7	breast:
3	chr9:79260136..79261869-chr9:79266939..79269421,2	MCF-7	breast:
4	chr9:79262793..79264432-chr9:79264865..79266558,2	MCF-7	breast:
5	chr9:79254567..79257524-chr9:79261863..79264861,3	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000187210	chromatin interactions
ENSG00000106772	chromatin interactions

Extended variants
information (count: 121 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:121 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs368679890	chr9:79260284-79260285	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs544018900	chr9:79260345-79260346	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs536342821	chr9:79260369-79260370	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs11144990	chr9:79260416-79260417	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs577873370	chr9:79260417-79260418	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs539844918	chr9:79260420-79260421	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs566956752	chr9:79260428-79260429	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs184091100	chr9:79260472-79260473	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs189026219	chr9:79260487-79260488	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs73456048	chr9:79260495-79260496	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs546076143	chr9:79260553-79260554	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs116829801	chr9:79260559-79260560	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs531085183	chr9:79260576-79260577	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs551197637	chr9:79260588-79260589	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs534856168	chr9:79260649-79260650	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs529173814	chr9:79260812-79260813	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs192466938	chr9:79260844-79260845	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs533718503	chr9:79260897-79260898	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs573242944	chr9:79260911-79260912	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs7867080	chr9:79260953-79260954	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs7849094	chr9:79260994-79260995	Weak transcription Genic enhancers Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs7849112	chr9:79261055-79261056	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs200964646	chr9:79261073-79261074	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs7864228	chr9:79261081-79261082	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs535477872	chr9:79261134-79261135	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs7848339	chr9:79261140-79261141	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs555405465	chr9:79261189-79261190	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs369135913	chr9:79261206-79261207	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs7864369	chr9:79261223-79261224	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs7848570	chr9:79261274-79261275	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs569020866	chr9:79261311-79261312	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs148786820	chr9:79261317-79261318	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs79413499	chr9:79261359-79261360	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs372840665	chr9:79261387-79261388	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs10117779	chr9:79261396-79261397	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs11144991	chr9:79261414-79261415	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs573653930	chr9:79261416-79261417	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs7848716	chr9:79261467-79261468	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs7852547	chr9:79261522-79261523	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs531477952	chr9:79261624-79261625	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs370695583	chr9:79261671-79261672	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs183693772	chr9:79261697-79261698	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs564733332	chr9:79261712-79261713	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs533436472	chr9:79261745-79261746	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs556945487	chr9:79261760-79261761	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs146408026	chr9:79261786-79261787	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs529211342	chr9:79261792-79261793	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs374350312	chr9:79261804-79261805	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs548969031	chr9:79261809-79261810	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs13298720	chr9:79261825-79261826	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

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
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute myeloid leukemia	20729466	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Oral cancer	21386901	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Intellectual disability	22102821	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Melanoma	17363583	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:143 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79225400-79265600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:79232800-79261400	Weak transcription	Colonic Mucosa	Colon
3	chr9:79238600-79261200	Strong transcription	HSMM	muscle
4	chr9:79240000-79260800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:79241000-79260800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:79249600-79261000	Weak transcription	NH-A	brain
7	chr9:79249600-79265400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:79249600-79265600	Weak transcription	NHDF-Ad	bronchial
9	chr9:79249600-79265600	Weak transcription	NHLF	lung
10	chr9:79252000-79261200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:79252600-79278000	Weak transcription	Gastric	stomach
12	chr9:79254000-79263000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:79255800-79265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:79257800-79261200	Weak transcription	Osteobl	bone
15	chr9:79258000-79261600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr9:79258000-79262600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:79258000-79265600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:79258000-79270000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:79258200-79261000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:79258200-79265600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:79258200-79265600	Weak transcription	Adipose Nuclei	Adipose
22	chr9:79258200-79265800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:79258200-79267800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:79258400-79261000	Weak transcription	HUVEC	blood vessel
25	chr9:79259000-79261600	Genic enhancers	Fetal Intestine Small	intestine
26	chr9:79259000-79262600	Weak transcription	Brain Anterior Caudate	brain
27	chr9:79259000-79269200	Weak transcription	Brain Substantia Nigra	brain
28	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
29	chr9:79259200-79262400	Weak transcription	Fetal Stomach	stomach
30	chr9:79259200-79265600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:79259200-79265600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:79259400-79261400	Weak transcription	Fetal Thymus	thymus
33	chr9:79259400-79264800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:79259400-79264800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:79259400-79265200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:79259400-79265600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:79259400-79265600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:79259800-79260400	Enhancers	Small Intestine	intestine
39	chr9:79259800-79260600	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:79259800-79261000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:79259800-79261000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:79259800-79262600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:79259800-79263200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:79259800-79263400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:79259800-79264800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:79259800-79264800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:79259800-79265600	Weak transcription	Primary B cells from cord blood	blood
48	chr9:79259800-79265600	Weak transcription	Stomach Mucosa	stomach
49	chr9:79260000-79260400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:79260000-79261000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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