Variant report

Variant	nsv1021309
Chromosome Location	chr9:2336185-2506959
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:31)
LncRNA
region (count:25)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:2472769..2475226-chr9:2476541..2478535,2	MCF-7	breast:
2	chr9:2496935..2498735-chr9:2499361..2500948,2	MCF-7	breast:
3	chr9:2367757..2369969-chr9:2374700..2376724,2	K562	blood:
4	chr9:2335749..2336338-chr9:2727775..2728597,3	MCF-7	breast:
5	chr9:2486399..2488878-chr9:2490772..2493168,2	MCF-7	breast:
6	chr9:2367757..2369969-chr9:2374700..2376724,2	K562	blood:
7	chr9:2469587..2470552-chr9:2495208..2496164,11	MCF-7	breast:
8	chr9:2496935..2498735-chr9:2499361..2500948,2	MCF-7	breast:
9	chr9:2353709..2356767-chr9:2357162..2361529,4	K562	blood:
10	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
11	chr9:2335812..2338035-chr9:2341360..2343149,2	MCF-7	breast:
12	chr9:2469587..2470552-chr9:2495208..2496164,11	MCF-7	breast:
13	chr9:2469803..2470606-chr9:2495203..2496152,5	MCF-7	breast:
14	chr9:2332261..2334098-chr9:2335447..2337175,2	MCF-7	breast:
15	chr9:2422977..2424644-chr9:2426365..2429153,2	MCF-7	breast:
16	chr9:2377530..2380377-chr9:2380910..2383194,2	MCF-7	breast:
17	chr9:2422977..2424644-chr9:2426365..2429153,2	MCF-7	breast:
18	chr9:2353709..2355330-chr9:2357162..2359493,2	K562	blood:
19	chr9:2486399..2488878-chr9:2490772..2493168,2	MCF-7	breast:
20	chr9:2419060..2420979-chr9:2425024..2427147,2	K562	blood:
21	chr9:2353709..2356767-chr9:2357162..2361529,4	K562	blood:
22	chr9:2469664..2470582-chr9:2495207..2496164,12	MCF-7	breast:
23	chr9:2419060..2420979-chr9:2425024..2427147,2	K562	blood:
24	chr9:2334689..2336340-chr9:2621369..2623518,2	MCF-7	breast:
25	chr9:2377530..2380377-chr9:2380910..2383194,2	MCF-7	breast:
26	chr9:2333652..2336415-chr9:2621221..2622791,2	MCF-7	breast:
27	chr9:2469664..2470582-chr9:2495207..2496164,12	MCF-7	breast:
28	chr9:2472769..2475226-chr9:2476541..2478535,2	MCF-7	breast:
29	chr9:2353709..2355330-chr9:2357162..2359493,2	K562	blood:
30	chr9:2469321..2470077-chr9:2662127..2662743,2	MCF-7	breast:
31	chr9:2469803..2470606-chr9:2495203..2496152,5	MCF-7	breast:

(count:25 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0020-1	chr9:2484180-2484336	l_3727_chr9:2411588-2611526_ovary
2	lnc-KIAA0020-1	chr9:2503280-2503403	ENSG00000236404
3	lnc-KIAA0020-1	chr9:2506411-2506540	ENSG00000236404
4	lnc-KIAA0020-1	chr9:2486116-2486306	l_3727_chr9:2411588-2611526_ovary
5	lnc-KIAA0020-1	chr9:2425397-2425540	ENSG00000236404.4
6	lnc-KIAA0020-1	chr9:2493075-2493180	ENSG00000236404.4
7	lnc-VLDLR-2	chr9:2390027-2390054	XLOC_007266
8	lnc-KIAA0020-1	chr9:2425393-2425545	ENSG00000236404
9	lnc-KIAA0020-1	chr9:2415397-2415540	l_3727_chr9:2411588-2611526_ovary
10	lnc-KIAA0020-1	chr9:2423837-2423844	NONHSAT129995
11	lnc-KIAA0020-1	chr9:2496359-2496540	l_3727_chr9:2411588-2611526_ovary
12	lnc-KIAA0020-1	chr9:2493270-2493403	l_3727_chr9:2411588-2611526_ovary
13	lnc-KIAA0020-1	chr9:2422702-2424510	ENSG00000236404.4
14	lnc-VLDLR-2	chr9:2408820-2408888	XLOC_007266
15	lnc-KIAA0020-1	chr9:2494061-2494105	ENSG00000236404
16	lnc-KIAA0020-1	chr9:2411589-2414510	l_3727_chr9:2411588-2611526_ovary
17	lnc-KIAA0020-1	chr9:2506419-2506540	ENSG00000236404.4
18	lnc-KIAA0020-1	chr9:2486316-2486612	l_3727_chr9:2411588-2611526_ovary
19	lnc-KIAA0020-1	chr9:2483075-2483418	l_3727_chr9:2411588-2611526_ovary
20	lnc-KIAA0020-1	chr9:2423860-2427978	NONHSAT129995
21	lnc-KIAA0020-1	chr9:2494180-2494302	ENSG00000236404.4
22	lnc-KIAA0020-1	chr9:2493073-2493180	ENSG00000236404
23	lnc-KIAA0020-1	chr9:2506359-2506540	ENSG00000236404
24	lnc-KIAA0020-1	chr9:2422702-2424510	ENSG00000236404
25	lnc-VLDLR-2	chr9:2429811-2429986	XLOC_007266

No data

Variant related genes	Relation type
ENSG00000236404	chromatin interactions
ENSG00000147852	chromatin interactions
FBXW7	miRNA target sites
SP3	miRNA target sites

Extended variants
information (count: 8222 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:8222 , 50 per page) page: 1 2 3 4 5 6 7 ... 165

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs569252390	chr9:2336192-2336193	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs562606525	chr9:2336212-2336213	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs537375340	chr9:2336224-2336225	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs531413095	chr9:2336269-2336270	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs75507221	chr9:2336276-2336277	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs539042988	chr9:2336287-2336288	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs78631286	chr9:2336298-2336299	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs182079611	chr9:2336333-2336334	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs539268127	chr9:2336347-2336348	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs60981423	chr9:2336397-2336398	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs572900841	chr9:2336408-2336409	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs374008440	chr9:2336432-2336433	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs184839646	chr9:2336447-2336448	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs138410324	chr9:2336517-2336518	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs149419557	chr9:2336527-2336528	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs564443870	chr9:2336533-2336534	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs188083478	chr9:2336568-2336569	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs7040313	chr9:2336607-2336608	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs11788548	chr9:2336621-2336622	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs555145287	chr9:2336659-2336660	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs571869128	chr9:2336719-2336720	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs529396003	chr9:2336749-2336750	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs543089719	chr9:2336777-2336778	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs562932972	chr9:2336795-2336796	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs531759205	chr9:2336815-2336816	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs59550042	chr9:2336820-2336821	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs570802419	chr9:2336842-2336843	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs538868438	chr9:2336871-2336872	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs369748753	chr9:2336875-2336876	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs534806255	chr9:2336930-2336931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs180747388	chr9:2336965-2336966	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs138452668	chr9:2336973-2336974	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs557941260	chr9:2336991-2336992	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs566645925	chr9:2337015-2337016	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs59617066	chr9:2337040-2337041	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs555065441	chr9:2337064-2337065	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs7871010	chr9:2337135-2337136	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs537458413	chr9:2337144-2337145	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs557320160	chr9:2337154-2337155	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs577963804	chr9:2337202-2337203	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs144008631	chr9:2337234-2337235	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs147308232	chr9:2337235-2337236	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs375598037	chr9:2337241-2337242	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs542824363	chr9:2337282-2337283	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs55864252	chr9:2337306-2337307	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs531834976	chr9:2337374-2337375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs545466648	chr9:2337381-2337382	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs565260539	chr9:2337409-2337410	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs533112885	chr9:2337448-2337449	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs546889537	chr9:2337509-2337510	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:103)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Chordoma	21215367	CNVD
Ovarian cancer	22355333	CNVD
Renal cell carcinoma	21215367	CNVD

Chromatin state (count:951 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2334800-2339000	Enhancers	Adipose Nuclei	Adipose
2	chr9:2335400-2336200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:2335600-2337000	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:2335600-2337000	Weak transcription	Right Atrium	heart
5	chr9:2335600-2337400	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:2335600-2337600	Weak transcription	Psoas Muscle	Psoas
7	chr9:2335600-2337800	Weak transcription	Ovary	ovary
8	chr9:2335600-2346600	Weak transcription	Left Ventricle	heart
9	chr9:2336000-2337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:2336200-2336400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr9:2336200-2336800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:2336400-2337400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:2336600-2337200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:2337000-2337200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:2337000-2337200	Enhancers	Fetal Muscle Leg	muscle
16	chr9:2337000-2337400	Enhancers	Right Atrium	heart
17	chr9:2337000-2339000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:2337000-2340200	Enhancers	Fetal Lung	lung
19	chr9:2337200-2337400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr9:2337200-2337600	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:2337200-2338200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:2337200-2338600	Enhancers	Rectal Smooth Muscle	rectum
23	chr9:2337200-2338800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:2337200-2339200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:2337400-2338800	Enhancers	Colon Smooth Muscle	Colon
26	chr9:2337400-2346600	Weak transcription	Right Atrium	heart
27	chr9:2337600-2337800	Enhancers	Psoas Muscle	Psoas
28	chr9:2337600-2339600	Enhancers	Fetal Muscle Leg	muscle
29	chr9:2337600-2341400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:2337800-2338600	Enhancers	Ovary	ovary
31	chr9:2338200-2338600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:2338200-2341200	Enhancers	HMEC	breast
33	chr9:2338400-2341400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:2338600-2339000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:2338600-2339800	Enhancers	NHEK	skin
36	chr9:2338600-2340000	Weak transcription	Fetal Brain Male	brain
37	chr9:2338800-2339400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:2339200-2340400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:2339200-2341000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:2339800-2340200	Flanking Active TSS	NHEK	skin
41	chr9:2339800-2341200	Enhancers	Placenta	Placenta
42	chr9:2340200-2341200	Enhancers	NHEK	skin
43	chr9:2340400-2340600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:2341000-2342000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:2341400-2356200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:2342600-2342800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:2343600-2346400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:2344600-2345600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:2345200-2345400	Enhancers	Psoas Muscle	Psoas
50	chr9:2345200-2345400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links