Variant report

Variant	esv3422153
Chromosome Location	chr9:139848831-139853429
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:139843163..139846708-chr9:139847303..139850951,4	MCF-7	breast:
2	chr9:139846781..139851560-chr9:139853266..139856441,7	MCF-7	breast:
3	chr9:139851916..139854622-chr9:139944503..139947387,2	K562	blood:
4	chr9:139849258..139851788-chr9:139867160..139869789,2	K562	blood:
5	chr9:139850465..139853578-chr9:139856402..139858921,3	K562	blood:
6	chr9:139849727..139851420-chr9:139864037..139866854,2	MCF-7	breast:
7	chr9:139842440..139845608-chr9:139845661..139851377,6	K562	blood:
8	chr9:139849578..139851272-chr9:139885199..139887273,2	MCF-7	breast:
9	chr9:139849027..139851788-chr9:139867721..139869789,2	K562	blood:
10	chr9:139835507..139852162-chr9:139884980..139895056,54	MCF-7	breast:
11	chr9:139850757..139852964-chr9:139867131..139869305,2	MCF-7	breast:
12	chr9:139850179..139852005-chr9:139888667..139891050,2	MCF-7	breast:
13	chr9:139847121..139851325-chr9:139867441..139871069,4	MCF-7	breast:
14	chr9:139687375..139689603-chr9:139852507..139855187,2	MCF-7	breast:
15	chr9:139842940..139845914-chr9:139851022..139854030,3	MCF-7	breast:
16	chr9:139850061..139852190-chr9:139857168..139859196,2	MCF-7	breast:
17	chr9:139852373..139854470-chr9:139885232..139887782,2	MCF-7	breast:
18	chr9:139842646..139845128-chr9:139852171..139853785,2	MCF-7	breast:
19	chr9:139851302..139852999-chr9:139912265..139914788,2	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCN12-1	chr9:139849823-139849878	NONHSAT135634
2	lnc-LCN12-1	chr9:139849176-139849278	NONHSAT135634
3	lnc-LCN12-1	chr9:139849823-139849948	NONHSAT135628
4	lnc-LCN12-1	chr9:139849176-139849278	NONHSAT135633
5	lnc-LCN12-1	chr9:139849823-139849949	NONHSAT135633

No data

Variant related genes	Relation type
ENSG00000238268	chromatin interactions
ENSG00000184925	chromatin interactions
ENSG00000169583	chromatin interactions
ENSG00000236394	chromatin interactions
ENSG00000148362	chromatin interactions
ENSG00000107331	chromatin interactions

Extended variants
information (count: 201 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:201 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571321977	chr9:139848844-139848845	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs188774343	chr9:139848882-139848883	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs375395558	chr9:139848889-139848890	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs535645175	chr9:139848893-139848894	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs550631266	chr9:139848921-139848922	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs113279411	chr9:139848938-139848939	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs567565708	chr9:139848956-139848957	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs536682489	chr9:139848957-139848958	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs553358962	chr9:139848964-139848965	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs7041368	chr9:139848988-139848989	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs34391952	chr9:139849007-139849008	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs556034099	chr9:139849010-139849011	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs559120793	chr9:139849020-139849021	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs575782191	chr9:139849039-139849040	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs116454430	chr9:139849040-139849041	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs554884984	chr9:139849054-139849055	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs574752199	chr9:139849087-139849088	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs542220055	chr9:139849088-139849089	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs566196498	chr9:139849126-139849127	Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs535041679	chr9:139849231-139849232	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
21	rs148579371	chr9:139849241-139849242	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
22	rs4880081	chr9:139849285-139849286	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	mRNA abundance
23	rs530667144	chr9:139849291-139849292	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs112301461	chr9:139849296-139849297	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs369851461	chr9:139849351-139849352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs144424549	chr9:139849369-139849370	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs567573684	chr9:139849380-139849381	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs529967317	chr9:139849381-139849382	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs578060051	chr9:139849388-139849389	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs547036563	chr9:139849393-139849394	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs566718214	chr9:139849443-139849444	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs539005968	chr9:139849453-139849454	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs558811258	chr9:139849454-139849455	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs372151378	chr9:139849473-139849474	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs569331004	chr9:139849489-139849490	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs536256202	chr9:139849498-139849499	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs55839042	chr9:139849513-139849514	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs554696932	chr9:139849517-139849518	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs574816574	chr9:139849527-139849528	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs35519119	chr9:139849571-139849572	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs181554418	chr9:139849588-139849589	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs2292921	chr9:139849624-139849625	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs557479447	chr9:139849641-139849642	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs549935675	chr9:139849735-139849736	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs199906774	chr9:139849774-139849775	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs202175310	chr9:139849777-139849778	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs546586766	chr9:139849788-139849789	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs371689884	chr9:139849796-139849797	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
49	rs375114941	chr9:139849802-139849803	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs116237185	chr9:139849803-139849804	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
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
Urothelial carcinoma	21177765	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	20435627	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
Lung cancer	18438408	CNVD
Breast cancer	17603634	CNVD
Oral cancer	21386901	CNVD
Cardiac fibroma	18329553	CNVD
Lung cancer	19147751	CNVD
Melanoma	18172304	CNVD
Cervical cancer	16585170	CNVD
Ependymoma	19289631	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Cervical cancer	17311676	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Breast cancer	16608533	CNVD
Metanephric adenoma	20802469	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Chordoma	18071362	CNVD
small cell lung cancer	20016488	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Kleefstra Syndrome	21538692	CNVD
Disorders of sex development	22290220	CNVD
Cancer	21183584	CNVD
Chronic myelomonocytic leukemia	16760666	CNVD
Abnormal phenotypes	18644119	CNVD
Ovarian cancer	21720365	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Sudden cardiac death	19188705	CNVD
Myoepithelioma	18604193	CNVD
Tuberous sclerosis	19566914	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Hepatocellular carcinoma	22174799	CNVD
Idiopathic chronic pancreatitis	21572526	CNVD
Kleefstra syndrome	22670141	CNVD
Schizophrenia	22241247	CNVD
9q deletion syndrome	16826528	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Non-small cell lung cancer	21829676	CNVD
Non-syndromic sensorineural hearing loss	19293338	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Mantle cell lymphoma	19029149	CNVD
Autism	20808228	CNVD
Epilepsy	22083797	CNVD
Cancer	20164920	CNVD
Breast cancer	21509527	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Autism	22495309	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:139845000-139853600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:139845200-139860200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:139845200-139860400	Weak transcription	Right Atrium	heart
4	chr9:139845400-139849200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:139845400-139852800	Weak transcription	Thymus	Thymus
6	chr9:139845400-139853000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:139845400-139855400	Weak transcription	Gastric	stomach
8	chr9:139845400-139860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:139845600-139849400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:139845600-139854000	Weak transcription	Pancreas	Pancrea
11	chr9:139846200-139852600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr9:139846200-139860200	Weak transcription	Liver	Liver
13	chr9:139846600-139852000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:139847000-139851000	Strong transcription	Fetal Intestine Small	intestine
15	chr9:139847200-139853400	Weak transcription	Spleen	Spleen
16	chr9:139847600-139849400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:139847800-139855600	Weak transcription	Right Ventricle	heart
18	chr9:139848200-139849400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:139848200-139857400	Weak transcription	Fetal Heart	heart
20	chr9:139848400-139849800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr9:139848600-139850800	Weak transcription	Fetal Intestine Large	intestine
22	chr9:139848800-139849200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:139849200-139849400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:139849200-139849600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:139849400-139849600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:139849400-139849600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:139849400-139849600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:139849400-139849600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:139849400-139850200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:139849600-139849800	Enhancers	HSMMtube	muscle
31	chr9:139849600-139852400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:139849600-139852800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:139849600-139854000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:139849800-139850000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr9:139850000-139850200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr9:139850200-139854000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:139850800-139851000	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr9:139851000-139851200	Bivalent Enhancer	Fetal Stomach	stomach
39	chr9:139851000-139858600	Weak transcription	Fetal Intestine Small	intestine
40	chr9:139852000-139852200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr9:139852000-139862000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:139852200-139857600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr9:139852200-139860200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr9:139852400-139852800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:139852400-139856200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr9:139852400-139858200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr9:139852400-139860200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:139852600-139856400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr9:139852600-139857600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr9:139852800-139853000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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