Variant report

Variant	esv16659
Chromosome Location	chr9:72762238-72763468
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72762270..72763345-chr9:72843683..72845020,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF9-1	chr9:72762897-72762994	ENSG00000204706.10

Extended variants
information (count: 30 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562639916	chr9:72762266-72762267	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs58169693	chr9:72762277-72762278	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs187650406	chr9:72762332-72762333	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs192439602	chr9:72762333-72762334	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs555249488	chr9:72762359-72762360	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs573552747	chr9:72762388-72762389	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs543850323	chr9:72762426-72762427	Strong transcription Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs556113989	chr9:72762442-72762443	Strong transcription Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs577697805	chr9:72762507-72762508	Strong transcription Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs142001990	chr9:72762548-72762549	Strong transcription Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs559958285	chr9:72762592-72762593	Strong transcription Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs77916042	chr9:72762622-72762623	Strong transcription Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs150262592	chr9:72762640-72762641	Strong transcription Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs562416872	chr9:72762691-72762692	Strong transcription Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs7022893	chr9:72762716-72762717	Strong transcription Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs10114215	chr9:72762776-72762777	Strong transcription Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs569215725	chr9:72762845-72762846	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs533143329	chr9:72762922-72762923	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
19	rs184935749	chr9:72762981-72762982	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
20	rs188918057	chr9:72762993-72762994	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
21	rs547891089	chr9:72763044-72763045	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs558965151	chr9:72763098-72763099	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs181745111	chr9:72763146-72763147	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs567894296	chr9:72763149-72763150	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs184075668	chr9:72763200-72763201	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs11141853	chr9:72763368-72763369	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs537732828	chr9:72763399-72763400	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs572503024	chr9:72763403-72763404	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs376169383	chr9:72763429-72763430	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs189971725	chr9:72763451-72763452	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Breast cancer	17133270	CNVD
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
Melanoma	22183965	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
Epilepsy	22083797	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	22522925	CNVD
Intellectual disability	21811512	CNVD
Autism	21484199	CNVD
Breast cancer	22737080	CNVD
Malignant peripheral nerve sheath tumor	22811580	CNVD
Leprosy	22719964	CNVD
Primary ovarian insufficiency	22879975	CNVD
Malignant melanoma	17260012	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72725800-72764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:72731200-72768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:72740600-72766400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:72741400-72765600	Weak transcription	Esophagus	oesophagus
7	chr9:72741600-72775400	Weak transcription	Adipose Nuclei	Adipose
8	chr9:72741600-72789400	Weak transcription	Spleen	Spleen
9	chr9:72746600-72762600	Weak transcription	Psoas Muscle	Psoas
10	chr9:72749800-72762600	Weak transcription	Fetal Stomach	stomach
11	chr9:72749800-72763000	Weak transcription	Lung	lung
12	chr9:72750400-72762600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:72750400-72771600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:72751000-72771800	Weak transcription	Aorta	Aorta
15	chr9:72752000-72779600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:72752400-72775200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:72752600-72771400	Weak transcription	NH-A	brain
18	chr9:72753800-72770000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:72754800-72764200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:72755400-72765800	Weak transcription	Left Ventricle	heart
21	chr9:72758800-72772200	Weak transcription	Colonic Mucosa	Colon
22	chr9:72759000-72763800	Strong transcription	Colon Smooth Muscle	Colon
23	chr9:72759200-72774400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:72759600-72800000	Weak transcription	Right Ventricle	heart
25	chr9:72759800-72774000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:72759800-72792200	Weak transcription	HMEC	breast
27	chr9:72760000-72768600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:72760000-72785200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:72760400-72765400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:72761000-72767400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:72761200-72768400	Weak transcription	HSMM	muscle
32	chr9:72761600-72762400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:72761600-72762400	Weak transcription	HSMMtube	muscle
34	chr9:72761600-72763000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:72761600-72766000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:72761800-72762800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:72762000-72763400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:72762200-72762800	Strong transcription	Ovary	ovary
39	chr9:72762200-72763200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:72762400-72762600	Active TSS	Monocytes-CD14+_RO01746	blood
41	chr9:72762400-72763200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr9:72762400-72764600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:72762400-72767400	Strong transcription	HSMMtube	muscle
44	chr9:72762600-72762800	Enhancers	Fetal Stomach	stomach
45	chr9:72762600-72763000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr9:72762600-72763200	Enhancers	Fetal Muscle Leg	muscle
47	chr9:72762600-72763200	Enhancers	Psoas Muscle	Psoas
48	chr9:72762800-72763000	Genic enhancers	Ovary	ovary
49	chr9:72762800-72763200	Weak transcription	Fetal Stomach	stomach
50	chr9:72762800-72770000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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