Variant report

Variant	nsv893588
Chromosome Location	chr9:96620419-96668352
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:36)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96627300..96630174-chr9:96631736..96634462,3	K562	blood:
2	chr9:96338791..96340611-chr9:96652934..96654583,2	MCF-7	breast:
3	chr9:96626497..96631168-chr9:96631736..96634980,4	K562	blood:
4	chr9:96652322..96655527-chr9:96667781..96670779,3	MCF-7	breast:
5	chr9:96618460..96620840-chr9:96622073..96624809,2	MCF-7	breast:
6	chr9:96621656..96622249-chr9:96722539..96723082,2	MCF-7	breast:
7	chr9:96665849..96668496-chr9:96668506..96670375,2	K562	blood:
8	chr9:96655426..96659394-chr9:96661426..96665501,6	MCF-7	breast:
9	chr9:96666033..96667879-chr9:96676753..96678543,2	MCF-7	breast:
10	chr9:96622372..96623312-chr9:96724925..96725807,3	MCF-7	breast:
11	chr9:96638083..96638756-chr9:127129759..127130596,2	MCF-7	breast:
12	chr9:96621785..96622572-chr9:96671016..96671565,2	MCF-7	breast:
13	chr9:96652322..96655527-chr9:96667781..96670779,3	MCF-7	breast:
14	chr9:96642929..96644771-chr9:96665466..96667734,2	MCF-7	breast:
15	chr9:96648101..96650436-chr9:96654606..96657253,2	MCF-7	breast:
16	chr9:96627771..96630715-chr9:96632328..96634346,2	MCF-7	breast:
17	chr9:96659943..96662280-chr9:96662528..96664579,2	K562	blood:
18	chr9:96627300..96630174-chr9:96631736..96634462,3	K562	blood:
19	chr9:96633328..96633896-chr9:96671075..96671772,2	MCF-7	breast:
20	chr9:96656015..96657684-chr9:96723768..96726547,2	MCF-7	breast:
21	chr9:96666065..96667806-chr9:96670157..96672697,2	MCF-7	breast:
22	chr9:96662639..96665282-chr9:96667242..96668877,2	K562	blood:
23	chr9:96438187..96440623-chr9:96628235..96630777,2	K562	blood:
24	chr9:96652972..96654970-chr9:96657253..96659540,2	MCF-7	breast:
25	chr9:96642929..96644771-chr9:96665466..96667734,2	MCF-7	breast:
26	chr9:96655426..96659394-chr9:96661426..96665501,6	MCF-7	breast:
27	chr9:96627771..96630715-chr9:96632328..96634346,2	MCF-7	breast:
28	chr9:96652972..96654970-chr9:96657253..96659540,2	MCF-7	breast:
29	chr9:96626497..96631168-chr9:96631736..96634980,4	K562	blood:
30	chr9:96662639..96665282-chr9:96667242..96668877,2	K562	blood:
31	chr9:96659943..96662280-chr9:96662528..96664579,2	K562	blood:
32	chr9:96619287..96621506-chr9:96664361..96666949,2	MCF-7	breast:
33	chr9:96648101..96650436-chr9:96654606..96657253,2	MCF-7	breast:
34	chr9:96651911..96654186-chr9:96654605..96657124,2	MCF-7	breast:
35	chr9:96664499..96666537-chr9:96711318..96713769,2	MCF-7	breast:
36	chr9:96651911..96654186-chr9:96654605..96657124,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPDC1-2	chr9:96620393-96620615	XLOC_007465
2	lnc-PTPDC1-2	chr9:96620393-96620609	NONHSAT133279

No data

Variant related genes	Relation type
ENSG00000231990	chromatin interactions
ENSG00000197724	chromatin interactions

Extended variants
information (count: 1136 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:1136 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3209003	chr9:96620419-96620420	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs186564517	chr9:96620439-96620440	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs117929255	chr9:96620450-96620451	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs10992929	chr9:96620495-96620496	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs373623141	chr9:96620504-96620505	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs72751417	chr9:96620536-96620537	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs576048329	chr9:96620546-96620547	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs559378597	chr9:96620554-96620555	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs367748124	chr9:96620570-96620571	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs558939921	chr9:96620578-96620579	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs371982285	chr9:96620591-96620592	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs10821239	chr9:96620652-96620653	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs7855547	chr9:96620673-96620674	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs559826829	chr9:96620707-96620708	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs59641089	chr9:96620709-96620710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs554932589	chr9:96620712-96620713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs532059688	chr9:96620713-96620714	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs78571228	chr9:96620716-96620717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs550074608	chr9:96620720-96620721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs571474962	chr9:96620752-96620753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs538805096	chr9:96620803-96620804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs547624186	chr9:96620804-96620805	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs181606481	chr9:96620832-96620833	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs140370186	chr9:96620844-96620845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs554597740	chr9:96620858-96620859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs576023082	chr9:96620863-96620864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs537323206	chr9:96620905-96620906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs559170175	chr9:96620910-96620911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs577477408	chr9:96620912-96620913	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs10992930	chr9:96620971-96620972	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs115380715	chr9:96621017-96621018	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs574580672	chr9:96621033-96621034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs541953153	chr9:96621050-96621051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs563509342	chr9:96621051-96621052	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs186640710	chr9:96621055-96621056	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs552307938	chr9:96621129-96621130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191488338	chr9:96621222-96621223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532453357	chr9:96621223-96621224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs547613078	chr9:96621226-96621227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs368276533	chr9:96621405-96621406	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs117512429	chr9:96621408-96621409	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs34268879	chr9:96621414-96621415	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs548294351	chr9:96621416-96621417	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs569665523	chr9:96621451-96621452	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs559432403	chr9:96621469-96621470	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs558269539	chr9:96621517-96621518	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs373038510	chr9:96621551-96621552	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs532840496	chr9:96621562-96621563	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs577462110	chr9:96621573-96621574	Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs3996240	chr9:96621608-96621609	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:75)

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
Breast cancer	22522925	CNVD
Effusion lymphoma	18079361	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:237 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96619400-96622800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:96619800-96626000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:96621400-96621600	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
4	chr9:96621800-96622400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:96622400-96622800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:96622800-96623000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr9:96622800-96623000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:96622800-96623000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:96622800-96623000	Bivalent/Poised TSS	Fetal Brain Female	brain
10	chr9:96622800-96623000	Bivalent Enhancer	Fetal Lung	lung
11	chr9:96622800-96623000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:96622800-96623200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:96622800-96623200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:96622800-96623400	Bivalent Enhancer	Fetal Stomach	stomach
15	chr9:96622800-96623600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:96622800-96623600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr9:96622800-96623600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:96622800-96623600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr9:96622800-96623600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr9:96622800-96623800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr9:96622800-96623800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr9:96623000-96623200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr9:96623000-96623200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:96623000-96623200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr9:96623000-96623200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:96623000-96623200	Bivalent Enhancer	Adipose Nuclei	Adipose
27	chr9:96623000-96623200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr9:96623000-96623200	Bivalent Enhancer	Lung	lung
29	chr9:96623000-96623200	Flanking Bivalent TSS/Enh	Spleen	Spleen
30	chr9:96623000-96623400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:96623000-96623400	Bivalent/Poised TSS	Psoas Muscle	Psoas
32	chr9:96623000-96623600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:96623000-96623600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
34	chr9:96623000-96623600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:96623000-96623600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr9:96623000-96623600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
37	chr9:96623000-96623600	Bivalent/Poised TSS	Right Ventricle	heart
38	chr9:96623000-96623800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:96623000-96624200	Bivalent Enhancer	Fetal Brain Male	brain
40	chr9:96623200-96623400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr9:96623200-96623400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr9:96623200-96623400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr9:96623200-96623400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:96623200-96623400	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
45	chr9:96623200-96623400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:96623200-96623400	Bivalent Enhancer	Brain Hippocampus Middle	brain
47	chr9:96623200-96623400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr9:96623200-96623600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:96623200-96623600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:96623400-96623600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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