Variant report

Variant	esv3415864
Chromosome Location	chr9:43126656-43133154
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	BATF	chr9:43127672-43127998	GM12878	blood:	n/a	n/a
2	BATF	chr9:43127650-43128051	GM12878	blood:	n/a	n/a
3	BCL11A	chr9:43127700-43127994	GM12878	blood:	n/a	chr9:43127900-43127909 chr9:43127967-43127976
4	BCL11A	chr9:43127637-43128031	GM12878	blood:	n/a	chr9:43127900-43127909 chr9:43127967-43127976
5	BCL11A	chr9:43129760-43130001	GM12878	blood:	n/a	n/a
6	EP300	chr9:43128362-43128839	GM12878	blood:	n/a	n/a
7	EP300	chr9:43127675-43127978	GM12878	blood:	n/a	n/a
8	EP300	chr9:43133153-43133308	GM12878	blood:	n/a	n/a
9	EP300	chr9:43129397-43129710	GM12878	blood:	n/a	n/a
10	FOSL2	chr9:43129388-43129652	HepG2	liver:	n/a	n/a
11	FOSL2	chr9:43132958-43135150	HepG2	liver:	n/a	chr9:43133948-43133957 chr9:43134391-43134400
12	FOXA1	chr9:43131127-43131415	HepG2	liver:	n/a	n/a
13	FOXA2	chr9:43133021-43134267	A549	lung:	n/a	n/a
14	GABPA	chr9:43129432-43129659	Hela-S3	cervix:	n/a	n/a
15	GABPA	chr9:43130306-43130524	Hela-S3	cervix:	n/a	n/a
16	GATA2	chr9:43129368-43129701	K562	blood:	n/a	n/a
17	GATA2	chr9:43128857-43129216	K562	blood:	n/a	chr9:43129120-43129130 chr9:43129147-43129157
18	GATA2	chr9:43128262-43128685	K562	blood:	n/a	chr9:43128625-43128634 chr9:43128625-43128632 chr9:43128523-43128531 chr9:43128624-43128634
19	HEY1	chr9:43129414-43129649	K562	blood:	n/a	n/a
20	HEY1	chr9:43133145-43133458	K562	blood:	n/a	n/a
21	IRF4	chr9:43133129-43133505	GM12878	blood:	n/a	n/a
22	IRF4	chr9:43127609-43128081	GM12878	blood:	n/a	n/a
23	IRF4	chr9:43127597-43128101	GM12878	blood:	n/a	n/a
24	JUND	chr9:43133019-43133155	HepG2	liver:	n/a	n/a
25	JUND	chr9:43133111-43134090	HepG2	liver:	n/a	chr9:43133948-43133957
26	NR3C1	chr9:43132959-43134725	A549	lung:	n/a	chr9:43134293-43134311 chr9:43134489-43134505 chr9:43134490-43134505 chr9:43134490-43134504
27	PAX5	chr9:43127764-43127923	GM12878	blood:	n/a	n/a
28	PAX5	chr9:43128601-43128873	GM12878	blood:	n/a	n/a
29	PAX5	chr9:43129373-43129778	GM12878	blood:	n/a	n/a
30	PAX5	chr9:43127024-43127201	GM12878	blood:	n/a	n/a
31	PAX5	chr9:43128560-43128808	GM12878	blood:	n/a	n/a
32	PAX5	chr9:43133019-43135192	GM12878	blood:	n/a	n/a
33	PAX5	chr9:43129963-43130408	GM12878	blood:	n/a	n/a
34	PAX5	chr9:43127725-43127923	GM12878	blood:	n/a	n/a
35	PBX3	chr9:43128629-43128759	GM12878	blood:	n/a	n/a
36	PBX3	chr9:43128682-43128821	GM12878	blood:	n/a	n/a
37	POU2F2	chr9:43132458-43132820	GM12878	blood:	n/a	n/a
38	POU2F2	chr9:43127669-43128095	GM12878	blood:	n/a	chr9:43127743-43127754
39	POU2F2	chr9:43128602-43128754	GM12878	blood:	n/a	n/a
40	POU2F2	chr9:43132958-43134647	GM12891	blood:	n/a	chr9:43134326-43134338
41	POU2F2	chr9:43129340-43129755	GM12878	blood:	n/a	chr9:43129718-43129733 chr9:43129719-43129732 chr9:43129721-43129731 chr9:43129363-43129370 chr9:43129719-43129730 chr9:43129738-43129749 chr9:43129361-43129371 chr9:43129359-43129374 chr9:43129721-43129731 chr9:43129720-43129730 chr9:43129350-43129372 chr9:43129361-43129371 chr9:43129362-43129371
42	POU2F2	chr9:43133061-43135339	GM12878	blood:	n/a	chr9:43134326-43134338 chr9:43135290-43135311
43	RXRA	chr9:43128192-43128612	HepG2	liver:	n/a	chr9:43128456-43128470
44	RXRA	chr9:43133094-43133513	HepG2	liver:	n/a	n/a
45	SIX5	chr9:43127711-43128080	GM12878	blood:	n/a	n/a
46	SIX5	chr9:43129431-43129681	K562	blood:	n/a	n/a
47	SP1	chr9:43128285-43128841	GM12878	blood:	n/a	n/a
48	SP1	chr9:43127707-43128051	GM12878	blood:	n/a	n/a
49	SPI1	chr9:43127846-43128074	GM12878	blood:	n/a	chr9:43127967-43127976
50	TCF12	chr9:43128199-43128347	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM75A6-10	chr9:43132625-43132735	NONHSAT131349
2	lnc-FAM75A6-10	chr9:43130533-43130803	NONHSAT131349

Variant related genes	Relation type
ENSG00000232866	TF binding region
RNU6-538P	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:47 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10909724	chr9:43127052-43127053	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs10909723	chr9:43127102-43127103	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs575037338	chr9:43127134-43127135	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs542061322	chr9:43127135-43127136	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs563955018	chr9:43127177-43127178	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs531004171	chr9:43127202-43127203	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs199845872	chr9:43127243-43127244	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs543578923	chr9:43127244-43127245	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs529951039	chr9:43127664-43127665	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs55787202	chr9:43127686-43127687	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs569871855	chr9:43127688-43127689	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs10125341	chr9:43127706-43127707	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs375720112	chr9:43127827-43127828	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs12553317	chr9:43127833-43127834	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs536833090	chr9:43127841-43127842	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs12555609	chr9:43127847-43127848	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs200865099	chr9:43127849-43127850	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs552281932	chr9:43127895-43127896	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs2633917	chr9:43130200-43130201	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs3091303	chr9:43130305-43130306	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs62553490	chr9:43130360-43130361	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs2633918	chr9:43130560-43130561	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs62553491	chr9:43130594-43130595	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs11262165	chr9:43130671-43130672	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs11262164	chr9:43130703-43130704	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs536186353	chr9:43131135-43131136	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs371700412	chr9:43131208-43131209	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs62553493	chr9:43131328-43131329	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs201332566	chr9:43132462-43132463	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs371518899	chr9:43132521-43132522	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs7035214	chr9:43132536-43132537	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs62553495	chr9:43132548-43132549	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs78608031	chr9:43132564-43132565	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs371746412	chr9:43132602-43132603	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs7038118	chr9:43132642-43132643	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs375199204	chr9:43132650-43132651	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs201932711	chr9:43132698-43132699	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs200082545	chr9:43132774-43132775	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs200821914	chr9:43132793-43132794	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs557356585	chr9:43132807-43132808	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs374684357	chr9:43133000-43133001	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs368878424	chr9:43133025-43133026	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs372632053	chr9:43133030-43133031	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs375952751	chr9:43133083-43133084	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs188121536	chr9:43133108-43133109	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs373019216	chr9:43133135-43133136	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs546394709	chr9:43133148-43133149	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
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
Oral squamous cell carcinoma	17134496	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	22183965	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Oral cancer	21386901	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Sezary syndrome	18413736	CNVD
Breast cancer	20409316	CNVD
early-passage human iPS cells	21368824	CNVD
Schizophrenia	21346763	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Breast cancer	21990379	CNVD
Astrocytoma	22246337	CNVD
Lung adenocarcinoma	17086460	CNVD
Barrett''s adenocarcinoma	18663352	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:43133000-43133200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:43133000-43133800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:43133000-43133800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:43133000-43134200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:43133000-43134200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:43133000-43134200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:43133000-43134800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:43133000-43135000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:43133000-43135000	Active TSS	Brain Germinal Matrix	brain

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