Variant report

Variant	nsv979088
Chromosome Location	chr2:110547996-110627162
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1314)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:3)

(count:1314 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr2:110595079-110595276	GM12878	blood:	n/a	n/a
2	BATF	chr2:110555685-110555899	GM12878	blood:	n/a	n/a
3	BATF	chr2:110552518-110552811	GM12878	blood:	n/a	n/a
4	BATF	chr2:110594892-110595317	GM12878	blood:	n/a	n/a
5	BATF	chr2:110565195-110565489	GM12878	blood:	n/a	n/a
6	BATF	chr2:110591595-110591865	GM12878	blood:	n/a	n/a
7	BATF	chr2:110550261-110550597	GM12878	blood:	n/a	n/a
8	BATF	chr2:110596658-110596861	GM12878	blood:	n/a	n/a
9	BATF	chr2:110596705-110596958	GM12878	blood:	n/a	n/a
10	BATF	chr2:110592910-110593154	GM12878	blood:	n/a	n/a
11	BATF	chr2:110554663-110555199	GM12878	blood:	n/a	n/a
12	BATF	chr2:110554721-110555155	GM12878	blood:	n/a	n/a
13	BATF	chr2:110597287-110597588	GM12878	blood:	n/a	n/a
14	BATF	chr2:110551684-110552114	GM12878	blood:	n/a	n/a
15	BCL11A	chr2:110622746-110622931	GM12878	blood:	n/a	n/a
16	BCL11A	chr2:110554748-110555164	GM12878	blood:	n/a	n/a
17	BCL11A	chr2:110550280-110550534	GM12878	blood:	n/a	n/a
18	BCL11A	chr2:110605050-110605227	GM12878	blood:	n/a	n/a
19	BCL11A	chr2:110551708-110552101	GM12878	blood:	n/a	n/a
20	BCL11A	chr2:110552372-110552860	GM12878	blood:	n/a	chr2:110552563-110552572
21	BCL11A	chr2:110599243-110599681	GM12878	blood:	n/a	n/a
22	BCL11A	chr2:110552529-110552917	GM12878	blood:	n/a	chr2:110552563-110552572
23	BCL11A	chr2:110608683-110608858	GM12878	blood:	n/a	n/a
24	BCL11A	chr2:110551679-110552114	GM12878	blood:	n/a	n/a
25	BCL11A	chr2:110615296-110615523	GM12878	blood:	n/a	n/a
26	BCL11A	chr2:110602022-110602295	GM12878	blood:	n/a	n/a
27	BCL11A	chr2:110584727-110584955	GM12878	blood:	n/a	n/a
28	BCL11A	chr2:110555695-110555957	GM12878	blood:	n/a	n/a
29	BHLHE40	chr2:110608748-110608993	HepG2	liver:	n/a	n/a
30	BHLHE40	chr2:110618320-110618612	HepG2	liver:	n/a	n/a
31	BHLHE40	chr2:110560190-110560446	HepG2	liver:	n/a	n/a
32	BHLHE40	chr2:110596505-110596759	HepG2	liver:	n/a	n/a
33	BHLHE40	chr2:110611478-110611704	HepG2	liver:	n/a	n/a
34	BHLHE40	chr2:110563703-110563900	HepG2	liver:	n/a	n/a
35	BHLHE40	chr2:110575410-110575772	HepG2	liver:	n/a	n/a
36	BHLHE40	chr2:110599190-110599634	HepG2	liver:	n/a	n/a
37	BHLHE40	chr2:110599670-110599908	HepG2	liver:	n/a	n/a
38	BHLHE40	chr2:110598028-110598323	HepG2	liver:	n/a	n/a
39	BHLHE40	chr2:110551661-110552000	HepG2	liver:	n/a	n/a
40	BHLHE40	chr2:110550306-110550705	HepG2	liver:	n/a	n/a
41	BHLHE40	chr2:110603361-110603699	HepG2	liver:	n/a	n/a
42	CBX3	chr2:110551643-110551985	K562	blood:	n/a	n/a
43	CEBPB	chr2:110551720-110551948	GM12878	blood:	n/a	n/a
44	CEBPB	chr2:110573581-110573891	K562	blood:	n/a	n/a
45	CEBPB	chr2:110573639-110573790	K562	blood:	n/a	n/a
46	CEBPD	chr2:110551558-110551969	K562	blood:	n/a	n/a
47	CTCF	chr2:110550338-110550546	Kidney_OC	kidney:	n/a	n/a
48	CTCF	chr2:110585511-110585607	LNCaP	prostate:	n/a	n/a
49	CTCF	chr2:110550385-110550512	GM19240	blood:	n/a	n/a
50	CTCF	chr2:110551696-110551916	GM12891	blood:	n/a	chr2:110551791-110551804

No data

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIMS3.1-2	chr2:110595460-110595619	NONHSAT073153
2	lnc-LIMS3.1-2	chr2:110596511-110596570	NONHSAT073153
3	lnc-SEPT10-2	chr2:110615775-110615987	ucscGeneNc_uc010fjz_1
4	lnc-SEPT10-2	chr2:110598802-110598916	ucscGeneNc_uc010fjz_1
5	lnc-SEPT10-2	chr2:110595035-110595535	ucscGeneNc_uc010fjz_1

No data

(count:3 , 50 per page) page: 1

No.	miRNA target gene	miRNA name	Chromosome Location
1	RGPD6	hsa-miR-15a-5p	chr2:110615252-110615272
2	RGPD6	hsa-miR-15a-5p	chr2:110614843-110614864
3	RGPD5	hsa-miR-335-5p	chr2:110614364-110614387

Variant related genes	Relation type
RGPD5	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62151741	chr2:110551101-110551102	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs28478863	chr2:110552127-110552128	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs574513766	chr2:110552180-110552181	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs543726285	chr2:110552181-110552182	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs368194978	chr2:110552185-110552186	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs372016063	chr2:110556568-110556569	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs10191102	chr2:110556714-110556715	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs112178381	chr2:110564671-110564672	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs2918665	chr2:110572702-110572703	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs28589309	chr2:110572744-110572745	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs2918664	chr2:110572752-110572753	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs150007575	chr2:110572888-110572889	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs2438862	chr2:110572971-110572972	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs111968970	chr2:110574953-110574954	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs2673122	chr2:110574954-110574955	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs62163513	chr2:110591985-110591986	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs55711961	chr2:110595885-110595886	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	17483303	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Lung cancer	18438408	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Colorectal cancer	16272173	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
myoclonus epilepsy	18472482	CNVD
Benign familial neonatal-infantile seizures	18472482	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Astrocytoma	22246337	CNVD
Myelofibrosis	22110671	CNVD
Ocular motor apraxia	21572526	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Idiopathic chronic pancreatitis	21549014	CNVD
Mental retardation	21549014	CNVD
Maculopathy	20981449	CNVD
Nephronophthisis	22470819	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Colorectal cancer	16912164	CNVD
Ischaemic stroke	16980335	CNVD
Acute myeloid leukemia	18000384	CNVD
Nephronophthisis	17901113	CNVD
Autism	22549408	CNVD
Autism	21865298	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110552000-110552400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr2:110552000-110552400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:110552000-110552400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:110552000-110552400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:110552000-110552400	Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr2:110552000-110552400	Active TSS	Left Ventricle	heart
7	chr2:110552000-110552400	Active TSS	Ovary	ovary
8	chr2:110552000-110552400	Active TSS	Psoas Muscle	Psoas
9	chr2:110552000-110552400	Active TSS	Right Atrium	heart
10	chr2:110552000-110552400	Active TSS	Right Ventricle	heart
11	chr2:110552000-110552400	Active TSS	Thymus	Thymus
12	chr2:110552000-110552400	Active TSS	HMEC	breast
13	chr2:110552000-110552400	Active TSS	HSMM	muscle

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