Variant report

Variant	esv3385334
Chromosome Location	chr9:116935501-116935751
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116933656..116936282-chr9:116947384..116950321,2	MCF-7	breast:
2	chr9:116878648..116881578-chr9:116935106..116937121,2	MCF-7	breast:
3	chr9:116930014..116932339-chr9:116933734..116935674,2	MCF-7	breast:
4	chr9:116932183..116936074-chr9:116938591..116942808,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF618-2	chr9:116933576-116935890	NONHSAT134370

Variant related genes	Relation type
ENSG00000196739	chromatin interactions

Extended variants
information (count: 18 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553124083	chr9:116935508-116935509	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs566536565	chr9:116935520-116935521	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs111755490	chr9:116935523-116935524	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs188422062	chr9:116935533-116935534	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs373819659	chr9:116935561-116935562	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs377212380	chr9:116935576-116935577	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs539925627	chr9:116935586-116935587	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs558480637	chr9:116935587-116935588	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs575894102	chr9:116935598-116935599	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs145947178	chr9:116935610-116935611	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs139803212	chr9:116935643-116935644	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs142042026	chr9:116935659-116935660	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs4978568	chr9:116935660-116935661	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs150750466	chr9:116935682-116935683	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
15	rs532600276	chr9:116935684-116935685	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
16	rs7023173	chr9:116935688-116935689	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs7023177	chr9:116935696-116935697	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs534758969	chr9:116935737-116935738	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

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
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	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
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
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Lung cancer	19147751	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16272173	CNVD
Bladder cancer	21909424	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	21509527	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Cervical cancer	16585170	CNVD
Ependymoma	19289631	CNVD
Melanoma	17363583	CNVD

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919000-116936600	Weak transcription	Brain Hippocampus Middle	brain
2	chr9:116919000-116937600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:116919600-116939600	Weak transcription	Hela-S3	cervix
5	chr9:116926000-116937200	Weak transcription	Gastric	stomach
6	chr9:116926200-116937400	Weak transcription	Right Ventricle	heart
7	chr9:116926200-116943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:116926400-116937000	Weak transcription	Stomach Mucosa	stomach
9	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:116926600-116939400	Weak transcription	Fetal Kidney	kidney
12	chr9:116926800-116937000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:116928800-116935600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr9:116929000-116937000	Weak transcription	HSMM	muscle
15	chr9:116929200-116937800	Weak transcription	HUVEC	blood vessel
16	chr9:116929400-116937200	Weak transcription	HSMMtube	muscle
17	chr9:116929800-116936000	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr9:116930000-116938800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr9:116930400-116936200	Strong transcription	A549	lung
20	chr9:116930400-116937200	Weak transcription	Lung	lung
21	chr9:116930600-116937000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:116930600-116937200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:116930600-116954400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:116931000-116946400	Genic enhancers	Fetal Stomach	stomach
25	chr9:116931000-116971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:116932200-116938600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:116932600-116936800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:116932600-116938000	Enhancers	Fetal Thymus	thymus
29	chr9:116932800-116935800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:116932800-116939200	Weak transcription	Osteobl	bone
31	chr9:116932800-116943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:116932800-116971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:116933000-116935600	Weak transcription	Colonic Mucosa	Colon
34	chr9:116933000-116939400	Weak transcription	Fetal Lung	lung
35	chr9:116933200-116938200	Genic enhancers	Fetal Intestine Small	intestine
36	chr9:116933200-116939000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:116933200-116939200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:116933200-116940400	Weak transcription	Spleen	Spleen
39	chr9:116933400-116937200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:116933600-116936600	Enhancers	HepG2	liver
41	chr9:116933800-116937000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:116934000-116936000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:116934400-116936000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:116934400-116940600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr9:116934400-116942800	Enhancers	Colon Smooth Muscle	Colon
46	chr9:116934600-116935800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr9:116934600-116935800	Enhancers	Adipose Nuclei	Adipose
48	chr9:116934600-116936000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:116934600-116936000	Enhancers	Placenta	Placenta
50	chr9:116934600-116936200	Enhancers	HMEC	breast

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