Variant report

Variant	nsv969753
Chromosome Location	chr9:15873053-15877009
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr9:15873620-15873926	HepG2	liver:	n/a	n/a
2	CEBPB	chr9:15875974-15876186	A549	lung:	n/a	n/a
3	CTCF	chr9:15873688-15873857	GM13976	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
4	CTCF	chr9:15873660-15873810	GM12864	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
5	CTCF	chr9:15873580-15873730	GM12878	blood:	n/a	n/a
6	CTCF	chr9:15873700-15873850	HCFaa	heart:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
7	CTCF	chr9:15873700-15873850	AG04450	lung:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
8	CTCF	chr9:15873700-15873850	HCPEpiC	choroid plexus:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
9	CTCF	chr9:15873660-15873810	NB4	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
10	CTCF	chr9:15873680-15873830	HRPEpiC	eye:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
11	CTCF	chr9:15873720-15873870	HBMEC	blood vessel:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
12	CTCF	chr9:15873712-15873833	GM20000	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
13	CTCF	chr9:15873680-15873830	K562	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
14	CTCF	chr9:15873740-15873890	GM12869	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
15	CTCF	chr9:15873680-15873830	SK-N-SH_RA	brain:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
16	CTCF	chr9:15873585-15873983	IMR90	lung:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
17	CTCF	chr9:15873700-15873850	AoAF	blood vessel:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
18	CTCF	chr9:15873820-15873970	HFF-Myc	foreskin:	n/a	n/a
19	CTCF	chr9:15873740-15873890	GM12872	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
20	CTCF	chr9:15873640-15873790	HA-sp	spinal cord:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
21	CTCF	chr9:15873740-15873890	K562	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
22	CTCF	chr9:15873700-15873850	AG09309	skin:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
23	CTCF	chr9:15874020-15874170	GM12872	blood:	n/a	n/a
24	CTCF	chr9:15873700-15873850	GM12875	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
25	CTCF	chr9:15873720-15873870	AG04449	skin:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
26	CTCF	chr9:15873740-15873890	HAc	cerebellar:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
27	CTCF	chr9:15873633-15873917	HUVEC	blood vessel:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
28	CTCF	chr9:15873591-15873942	K562	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
29	CTCF	chr9:15873645-15873863	Pancreas_OC	pancreas:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
30	CTCF	chr9:15873688-15873884	A549	lung:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
31	CTCF	chr9:15873652-15873877	GM13977	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
32	CTCF	chr9:15873680-15873830	NHDF-neo	bronchial:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
33	CTCF	chr9:15873740-15873890	AG04450	lung:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
34	CTCF	chr9:15873680-15873830	MCF-7	breast:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
35	CTCF	chr9:15873720-15873870	AG09319	gingival:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
36	CTCF	chr9:15873720-15873870	HCT-116	colon:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
37	CTCF	chr9:15873677-15873867	K562	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
38	CTCF	chr9:15873720-15873870	HPAF	blood vessel:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
39	CTCF	chr9:15873720-15873870	GM12871	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
40	CTCF	chr9:15873680-15873830	Caco-2	colon:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
41	CTCF	chr9:15873571-15873980	GM12878	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
42	CTCF	chr9:15873720-15873870	GM12801	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
43	CTCF	chr9:15873631-15873889	Spleen_OC	spleen:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
44	CTCF	chr9:15873720-15873870	MCF-7	breast:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
45	CTCF	chr9:15873680-15873830	GM12868	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
46	CTCF	chr9:15873760-15873910	HMEC	breast:	n/a	n/a
47	CTCF	chr9:15873620-15873770	BE2_C	brain:	n/a	chr9:15873757-15873770
48	CTCF	chr9:15873680-15873830	HRE	kidney:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
49	CTCF	chr9:15873528-15873952	A549	lung:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770
50	CTCF	chr9:15873680-15873830	GM12874	blood:	n/a	chr9:15873756-15873777 chr9:15873754-15873772 chr9:15873757-15873770

No.	Distal block	Cell Line	Cell type
1	chr9:15873337..15874253-chr9:16131080..16131915,3	MCF-7	breast:
2	chr9:15876069..15878996-chr9:15881161..15882668,2	MCF-7	breast:
3	chr9:15873671..15874276-chr9:16131035..16131676,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAPC3-1	chr9:15874539-15874661	NONHSAT130279

Variant related genes	Relation type
CCDC171	TF binding region

Extended variants
information (count: 184 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:184 , 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	rs529201978	chr9:15873123-15873124	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs550869690	chr9:15873150-15873151	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs139887906	chr9:15873176-15873177	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs533593108	chr9:15873219-15873220	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs571199035	chr9:15873220-15873221	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs373080042	chr9:15873231-15873232	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs551713680	chr9:15873285-15873286	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs56325008	chr9:15873328-15873329	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs537027162	chr9:15873332-15873333	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs200561506	chr9:15873354-15873355	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs556928769	chr9:15873439-15873440	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs534468383	chr9:15873456-15873457	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs117259103	chr9:15873466-15873467	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs568074560	chr9:15873472-15873473	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs535407063	chr9:15873482-15873483	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs188755408	chr9:15873524-15873525	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs575638784	chr9:15873550-15873551	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs191871231	chr9:15873587-15873588	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs557708740	chr9:15873598-15873599	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs184852507	chr9:15873609-15873610	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs115280572	chr9:15873619-15873620	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs561804349	chr9:15873622-15873623	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs189316458	chr9:15873632-15873633	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs557867593	chr9:15873639-15873640	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs562518174	chr9:15873647-15873648	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs559127172	chr9:15873688-15873689	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs533499058	chr9:15873704-15873705	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs376864071	chr9:15873725-15873726	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs2769714	chr9:15873734-15873735	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs560525058	chr9:15873740-15873741	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs180814562	chr9:15873829-15873830	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs546733788	chr9:15873843-15873844	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs372323774	chr9:15873845-15873846	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs568135274	chr9:15873856-15873857	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs535521211	chr9:15873910-15873911	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs550630202	chr9:15873922-15873923	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs568824455	chr9:15873957-15873958	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs185850049	chr9:15873991-15873992	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs557983515	chr9:15874022-15874023	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs369153872	chr9:15874088-15874089	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs377113275	chr9:15874121-15874122	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs189536294	chr9:15874141-15874142	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs181807887	chr9:15874167-15874168	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs573822137	chr9:15874194-15874195	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs544281118	chr9:15874246-15874247	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs555949242	chr9:15874270-15874271	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs562592972	chr9:15874299-15874300	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs577925919	chr9:15874302-15874303	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs76263132	chr9:15874303-15874304	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs527903196	chr9:15874310-15874311	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	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
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21611746	CNVD
Glycine encephalopathy	21572526	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Glioblastoma multiforme	18628472	CNVD
Ovarian cancer	19835627	CNVD
Breast cancer	22522925	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15849000-15873800	Weak transcription	Fetal Lung	lung
2	chr9:15857800-15885400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:15863600-15878200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:15867000-15874400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:15873800-15874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:15873800-15874400	Enhancers	Fetal Lung	lung
7	chr9:15873800-15874400	Enhancers	A549	lung
8	chr9:15873800-15874600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:15873800-15874600	Enhancers	HSMMtube	muscle
10	chr9:15873800-15874600	Enhancers	NH-A	brain
11	chr9:15873800-15875000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr9:15874000-15874400	Enhancers	NHDF-Ad	bronchial
13	chr9:15874000-15874600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:15874000-15874600	Enhancers	NHLF	lung
15	chr9:15874200-15874600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:15874200-15874600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:15874200-15874600	Enhancers	HSMM	muscle
18	chr9:15874200-15874800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:15874400-15874800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:15874400-15874800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:15874400-15876600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:15874600-15876600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:15874600-15876800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:15874600-15878400	Weak transcription	HSMMtube	muscle
25	chr9:15874800-15876400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:15876400-15877400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:15876600-15877000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:15876600-15877200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:15876600-15877400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:15876800-15877000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:15876800-15877200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:15877000-15877200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:15877000-15903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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