Variant report

Variant	esv3406974
Chromosome Location	chr9:84898447-84923322
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:84917850..84920304-chr9:84921549..84923460,2	MCF-7	breast:
2	chr9:84888213..84889834-chr9:84897716..84899682,2	MCF-7	breast:
3	chr9:84917850..84920304-chr9:84921549..84923460,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM75D1-4	chr9:84912297-84912455	ENSG00000228430.4
2	lnc-FAM75D1-4	chr9:84912297-84912455	ENSG00000228430.4

Variant related genes	Relation type
ENSG00000228430	chromatin interactions

Extended variants
information (count: 174 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:174 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs568681886	chr9:84898453-84898454	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs146982838	chr9:84898472-84898473	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs112441756	chr9:84898510-84898511	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs565517303	chr9:84898581-84898582	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs138151472	chr9:84898584-84898585	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs113191563	chr9:84898587-84898588	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs368314346	chr9:84898588-84898589	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs143199561	chr9:84898612-84898613	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs543360336	chr9:84898682-84898683	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs189689272	chr9:84898687-84898688	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs573815177	chr9:84898688-84898689	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs541938559	chr9:84898725-84898726	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs560608424	chr9:84898733-84898734	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs113528349	chr9:84898764-84898765	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs182533106	chr9:84898772-84898773	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs564472641	chr9:84898780-84898781	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs35631969	chr9:84898816-84898817	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs397771220	chr9:84898817-84898818	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs386415277	chr9:84898818-84898819	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs112713855	chr9:84898879-84898880	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs78779530	chr9:84898948-84898949	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs141395101	chr9:84899042-84899043	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs189242324	chr9:84899046-84899047	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs150826450	chr9:84899132-84899133	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs111565926	chr9:84899195-84899196	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs117112233	chr9:84899197-84899198	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs550959523	chr9:84899220-84899221	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs73465472	chr9:84899291-84899292	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs536932792	chr9:84899320-84899321	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs138268923	chr9:84899329-84899330	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs543249354	chr9:84899332-84899333	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs142897692	chr9:84899387-84899388	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs567383552	chr9:84899411-84899412	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs146118541	chr9:84899562-84899563	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs78888943	chr9:84899578-84899579	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs193060592	chr9:84899590-84899591	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs564463119	chr9:84899591-84899592	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs28469416	chr9:84899599-84899600	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs543735973	chr9:84899615-84899616	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs562376944	chr9:84899625-84899626	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs113908394	chr9:84899692-84899693	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs529575663	chr9:84899700-84899701	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs112010614	chr9:84899746-84899747	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs74614582	chr9:84899760-84899761	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs549599030	chr9:84899808-84899809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs185432252	chr9:84899922-84899923	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs551096688	chr9:84899999-84900000	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs569289260	chr9:84900000-84900001	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs144822151	chr9:84900051-84900052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs548719999	chr9:84900055-84900056	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

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
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	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
Urothelial cell carcinoma	18451213	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Renal cell carcinoma	18765545	CNVD
Astrocytoma	22246337	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Epilepsy	20502679	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:84890600-84899600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:84890800-84899800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:84896400-84898600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:84896400-84898800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:84898600-84899400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:84898800-84899800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:84899600-84900200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:84899800-84900200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:84909800-84910200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr9:84909800-84911400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr9:84910200-84911200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:84910400-84910800	Enhancers	Colon Smooth Muscle	Colon
13	chr9:84911200-84911600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr9:84917800-84918200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:84918000-84918400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:84918000-84919000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:84918200-84918600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:84923000-84923600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr9:84923200-84923600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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