Variant report

Variant	nsv970129
Chromosome Location	chr6:58214732-58243303
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	ATF2	chr6:58225246-58225574	GM12878	blood:	n/a	n/a
2	ATF2	chr6:58226933-58227385	GM12878	blood:	n/a	n/a
3	ATF2	chr6:58226948-58227297	GM12878	blood:	n/a	n/a
4	BATF	chr6:58241686-58241892	GM12878	blood:	n/a	chr6:58241758-58241769
5	BATF	chr6:58225176-58225639	GM12878	blood:	n/a	n/a
6	BATF	chr6:58241206-58241440	GM12878	blood:	n/a	chr6:58241313-58241322 chr6:58241337-58241348
7	BATF	chr6:58226995-58227530	GM12878	blood:	n/a	n/a
8	BATF	chr6:58241654-58241917	GM12878	blood:	n/a	chr6:58241758-58241769
9	BATF	chr6:58225149-58225723	GM12878	blood:	n/a	n/a
10	BATF	chr6:58226989-58227547	GM12878	blood:	n/a	n/a
11	BCL11A	chr6:58227066-58227268	GM12878	blood:	n/a	n/a
12	BCL11A	chr6:58226962-58227383	GM12878	blood:	n/a	n/a
13	BCL11A	chr6:58225136-58225637	GM12878	blood:	n/a	n/a
14	CTCF	chr6:58216143-58216282	GM13976	blood:	n/a	n/a
15	CTCF	chr6:58231641-58231711	GM20000	blood:	n/a	n/a
16	CTCF	chr6:58238089-58238128	GM10248	blood:	n/a	n/a
17	CTCF	chr6:58230914-58230995	GM20000	blood:	n/a	n/a
18	CTCF	chr6:58220508-58220531	GM20000	blood:	n/a	n/a
19	CTCF	chr6:58240294-58240337	Kidney_OC	kidney:	n/a	n/a
20	CTCF	chr6:58232546-58232593	GM10266	blood:	n/a	n/a
21	EP300	chr6:58227043-58227281	GM12878	blood:	n/a	n/a
22	FOXA1	chr6:58230632-58230889	HepG2	liver:	n/a	n/a
23	FOXM1	chr6:58225036-58225638	GM12878	blood:	n/a	chr6:58225439-58225447
24	FOXM1	chr6:58226933-58227397	GM12878	blood:	n/a	n/a
25	GATA2	chr6:58230659-58230813	SH-SY5Y	brain:	n/a	n/a
26	IRF4	chr6:58225102-58225654	GM12878	blood:	n/a	n/a
27	IRF4	chr6:58226983-58227339	GM12878	blood:	n/a	n/a
28	IRF4	chr6:58225138-58225663	GM12878	blood:	n/a	n/a
29	IRF4	chr6:58226950-58227413	GM12878	blood:	n/a	n/a
30	JUND	chr6:58237676-58237859	HepG2	liver:	n/a	n/a
31	MEF2A	chr6:58225125-58225706	GM12878	blood:	n/a	chr6:58225293-58225304
32	MEF2A	chr6:58225134-58225601	GM12878	blood:	n/a	chr6:58225293-58225304
33	MEF2A	chr6:58226980-58227298	GM12878	blood:	n/a	n/a
34	MEF2C	chr6:58225222-58225708	GM12878	blood:	n/a	chr6:58225293-58225304
35	NFIC	chr6:58241531-58241991	GM12878	blood:	n/a	n/a
36	NFIC	chr6:58226950-58227444	GM12878	blood:	n/a	n/a
37	NFIC	chr6:58226805-58227569	GM12878	blood:	n/a	n/a
38	NFIC	chr6:58225020-58225878	GM12878	blood:	n/a	n/a
39	PBX3	chr6:58227408-58227563	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:58226261-58226490	ProgFib	skin:	n/a	n/a
41	POLR2A	chr6:58223451-58223478	ProgFib	skin:	n/a	n/a
42	POU2F2	chr6:58227056-58227217	GM12878	blood:	n/a	n/a
43	POU2F2	chr6:58220377-58220736	GM12878	blood:	n/a	n/a
44	POU2F2	chr6:58224989-58225663	GM12878	blood:	n/a	chr6:58225393-58225402 chr6:58225391-58225404 chr6:58225168-58225179 chr6:58225393-58225403 chr6:58225392-58225404 chr6:58225393-58225403 chr6:58225292-58225303 chr6:58225394-58225401 chr6:58225392-58225402 chr6:58225390-58225404
45	POU2F2	chr6:58227008-58227342	GM12878	blood:	n/a	chr6:58227268-58227279 chr6:58227270-58227278 chr6:58227267-58227282 chr6:58227263-58227284 chr6:58227263-58227285
46	POU2F2	chr6:58225297-58225485	GM12878	blood:	n/a	chr6:58225393-58225402 chr6:58225391-58225404 chr6:58225393-58225403 chr6:58225392-58225404 chr6:58225393-58225403 chr6:58225394-58225401 chr6:58225392-58225402 chr6:58225390-58225404
47	POU2F2	chr6:58225261-58225510	GM12878	blood:	n/a	chr6:58225393-58225402 chr6:58225391-58225404 chr6:58225393-58225403 chr6:58225392-58225404 chr6:58225393-58225403 chr6:58225292-58225303 chr6:58225394-58225401 chr6:58225392-58225402 chr6:58225390-58225404
48	RUNX3	chr6:58226962-58227377	GM12878	blood:	n/a	n/a
49	RUNX3	chr6:58227046-58227284	GM12878	blood:	n/a	n/a
50	RUNX3	chr6:58225034-58225584	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB23-3	chr6:58234838-58240189	ENSG00000272316.1
2	lnc-RAB23-3	chr6:58234692-58238642	XLOC_005753
3	lnc-RAB23-18	chr6:58228887-58229426	ENSG00000271761.1
4	lnc-RAB23-3	chr6:58239194-58239687	XLOC_005753

Variant related genes	Relation type
ENSG00000272316	TF binding region
ENSG00000271761	TF binding region

Extended variants
information (count: 304 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:304 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570466791	chr6:58226409-58226410	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs192445689	chr6:58226440-58226441	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs552983550	chr6:58226492-58226493	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs574605464	chr6:58226585-58226586	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs542405545	chr6:58226604-58226605	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs184997776	chr6:58226605-58226606	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs576007669	chr6:58226614-58226615	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs546518710	chr6:58226618-58226619	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs564637356	chr6:58226643-58226644	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs563792240	chr6:58226850-58226851	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs548419585	chr6:58226901-58226902	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs577372643	chr6:58226998-58226999	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs541768695	chr6:58227006-58227007	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs540290488	chr6:58227043-58227044	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs188926505	chr6:58227048-58227049	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs2982029	chr6:58227062-58227063	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs529382128	chr6:58227151-58227152	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs2475577	chr6:58227216-58227217	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs547959592	chr6:58227363-58227364	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs559928178	chr6:58227392-58227393	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs569559789	chr6:58227429-58227430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6926125	chr6:58227450-58227451	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs552407640	chr6:58227455-58227456	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs570656566	chr6:58227459-58227460	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs377143282	chr6:58227517-58227518	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs552708684	chr6:58227562-58227563	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs568143685	chr6:58227609-58227610	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs535594463	chr6:58227673-58227674	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs557581241	chr6:58227680-58227681	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs575870299	chr6:58227697-58227698	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs546087132	chr6:58227703-58227704	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs2758421	chr6:58227715-58227716	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs12662930	chr6:58227724-58227725	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs2472997	chr6:58227747-58227748	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs2475578	chr6:58227790-58227791	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs183977765	chr6:58227794-58227795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs2758422	chr6:58227809-58227810	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs3996679	chr6:58227893-58227894	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs374820902	chr6:58227913-58227914	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs3996680	chr6:58227954-58227955	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs3996681	chr6:58227968-58227969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs529343082	chr6:58227969-58227970	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs530777976	chr6:58227970-58227971	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs544340120	chr6:58228060-58228061	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs562651654	chr6:58228078-58228079	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs530681894	chr6:58228089-58228090	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs367838057	chr6:58228106-58228107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs552105833	chr6:58228114-58228115	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs477994	chr6:58228129-58228130	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs189550523	chr6:58228178-58228179	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Neuroblastoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	17603634	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
T-cell lymphomas	19863542	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Myelofibrosis	22110671	CNVD
small cell lung cancer	20016488	CNVD
Ovarian cancer	21720365	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:58226400-58228200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:58226800-58227000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:58227000-58227400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:58237800-58245200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:58237800-58253400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:58238000-58245000	Weak transcription	Fetal Stomach	stomach
7	chr6:58238000-58252600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:58238000-58252800	Weak transcription	Fetal Intestine Large	intestine
9	chr6:58240800-58245800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:58243000-58250200	Weak transcription	Liver	Liver
11	chr6:58243000-58272800	Weak transcription	Fetal Intestine Small	intestine

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