Variant report

Variant	nsv525902
Chromosome Location	chr9:3014254-3022906
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	FAM48A	chr9:3016491-3016563	GM12878	blood:	n/a	n/a
2	FOXA1	chr9:3018034-3018343	HepG2	liver:	n/a	n/a
3	MAFK	chr9:3017925-3017956	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:3014116-3014560	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr9:3017055-3017096	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr9:3014180-3014538	H1-neurons	neurons:	n/a	n/a
7	REST	chr9:3013896-3014856	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CARM1P1	TF binding region

Extended variants
information (count: 445 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:445 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4543592	chr9:3014254-3014255	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs531942796	chr9:3014277-3014278	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs552266518	chr9:3014301-3014302	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs112897058	chr9:3014308-3014309	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs58404695	chr9:3014310-3014311	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs565611781	chr9:3014311-3014312	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs534846712	chr9:3014319-3014320	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs577057158	chr9:3014327-3014328	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs568384065	chr9:3014328-3014329	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs537338683	chr9:3014349-3014350	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs556488552	chr9:3014391-3014392	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs557244856	chr9:3014429-3014430	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs2327698	chr9:3014477-3014478	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs148029136	chr9:3014491-3014492	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs118053578	chr9:3014500-3014501	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs200074611	chr9:3014526-3014527	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs555885559	chr9:3014537-3014538	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs572424995	chr9:3014540-3014541	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs541642180	chr9:3014567-3014568	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs572615364	chr9:3014569-3014570	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs191684576	chr9:3014570-3014571	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs530188868	chr9:3014600-3014601	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs543716986	chr9:3014607-3014608	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs374199285	chr9:3014611-3014612	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs376212102	chr9:3014618-3014619	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs200334493	chr9:3014642-3014643	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs574520956	chr9:3014656-3014657	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs2327699	chr9:3014702-3014703	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs141753712	chr9:3014731-3014732	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs551866828	chr9:3014800-3014801	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs565802573	chr9:3014808-3014809	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs2327700	chr9:3014813-3014814	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs59763936	chr9:3014819-3014820	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs568265449	chr9:3014826-3014827	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs537201872	chr9:3014895-3014896	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs147196091	chr9:3014903-3014904	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs570728856	chr9:3014930-3014931	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs138705553	chr9:3014956-3014957	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs577030520	chr9:3014957-3014958	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs372350689	chr9:3014966-3014967	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs184238045	chr9:3014970-3014971	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs142752903	chr9:3014988-3014989	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs147341205	chr9:3015030-3015031	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs555008718	chr9:3015034-3015035	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs574711256	chr9:3015038-3015039	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs545798613	chr9:3015106-3015107	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs28485138	chr9:3015158-3015159	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs369479935	chr9:3015213-3015214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs545840573	chr9:3015214-3015215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs190185632	chr9:3015222-3015223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	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
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Ovarian cancer	22355333	CNVD
Autism	20808228	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3007200-3018200	Weak transcription	Fetal Brain Male	brain
2	chr9:3011600-3015000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr9:3013200-3018400	Weak transcription	Adipose Nuclei	Adipose
4	chr9:3013800-3015200	Enhancers	Stomach Mucosa	stomach
5	chr9:3014200-3018200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:3015000-3018200	Weak transcription	Fetal Lung	lung
7	chr9:3018000-3018200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:3018200-3018600	Enhancers	Fetal Lung	lung
9	chr9:3018200-3019200	Enhancers	Stomach Smooth Muscle	stomach
10	chr9:3018200-3019800	Enhancers	Fetal Brain Male	brain
11	chr9:3018400-3019200	Enhancers	Adipose Nuclei	Adipose
12	chr9:3018400-3019600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:3018600-3018800	Weak transcription	Fetal Lung	lung
14	chr9:3018600-3019600	Enhancers	Fetal Brain Female	brain
15	chr9:3018800-3019000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:3018800-3019000	Enhancers	Ovary	ovary
17	chr9:3018800-3019200	Enhancers	Brain Cingulate Gyrus	brain
18	chr9:3018800-3019200	Enhancers	Fetal Lung	lung
19	chr9:3018800-3019200	Enhancers	Fetal Muscle Leg	muscle
20	chr9:3018800-3020000	Enhancers	Psoas Muscle	Psoas
21	chr9:3019200-3028000	Weak transcription	Adipose Nuclei	Adipose
22	chr9:3019200-3028600	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:3019600-3020400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr9:3019800-3020600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:3020000-3020400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr9:3020000-3020400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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