Variant report

Variant	nsv961481
Chromosome Location	chr2:110733765-110751303
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	chr2:110733954-110734198	GM12878	blood:	n/a	n/a
2	BATF	chr2:110738365-110738645	GM12878	blood:	n/a	n/a
3	BCL11A	chr2:110738261-110738582	GM12878	blood:	n/a	n/a
4	BHLHE40	chr2:110745383-110745582	HepG2	liver:	n/a	n/a
5	CBX3	chr2:110738340-110738572	K562	blood:	n/a	n/a
6	CTCF	chr2:110745229-110745247	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr2:110744382-110744494	GM12892	blood:	n/a	chr2:110744453-110744466
8	CTCF	chr2:110745245-110745776	A549	lung:	n/a	n/a
9	CTCF	chr2:110745400-110745600	K562	blood:	n/a	n/a
10	CTCF	chr2:110744249-110744647	A549	lung:	n/a	chr2:110744453-110744466
11	CTCF	chr2:110733916-110734284	K562	blood:	n/a	chr2:110734108-110734126
12	CTCF	chr2:110734068-110734205	Kidney_OC	kidney:	n/a	chr2:110734108-110734126
13	CTCF	chr2:110738238-110738763	A549	lung:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
14	CTCF	chr2:110745275-110745574	A549	lung:	n/a	n/a
15	CTCF	chr2:110745316-110745583	A549	lung:	n/a	n/a
16	CTCF	chr2:110734007-110734181	GM19239	blood:	n/a	chr2:110734108-110734126
17	CTCF	chr2:110738786-110738856	GM19239	blood:	n/a	n/a
18	CTCF	chr2:110738415-110738669	LNCaP	prostate:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
19	CTCF	chr2:110738360-110738644	MCF-7	breast:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
20	CTCF	chr2:110733973-110734254	LNCaP	prostate:	n/a	chr2:110734108-110734126
21	CTCF	chr2:110733958-110734240	GM19238	blood:	n/a	chr2:110734108-110734126
22	CTCF	chr2:110744324-110744704	MCF-7	breast:	n/a	chr2:110744453-110744466
23	CTCF	chr2:110738312-110738620	K562	blood:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
24	CTCF	chr2:110744401-110744529	GM12891	blood:	n/a	chr2:110744453-110744466
25	CTCF	chr2:110738395-110738722	Pancreas_OC	pancreas:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
26	CTCF	chr2:110745267-110745661	Fibrobl	skin:	n/a	n/a
27	CTCF	chr2:110733992-110734201	GM12878	blood:	n/a	chr2:110734108-110734126
28	CTCF	chr2:110734043-110734203	GM10248	blood:	n/a	chr2:110734108-110734126
29	CTCF	chr2:110738338-110738730	GM12892	blood:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
30	CTCF	chr2:110745348-110745630	Medullo	brain:	n/a	n/a
31	CTCF	chr2:110745306-110745847	GM19238	blood:	n/a	n/a
32	CTCF	chr2:110738750-110738896	GM12892	blood:	n/a	n/a
33	CTCF	chr2:110733912-110734233	K562	blood:	n/a	chr2:110734108-110734126
34	CTCF	chr2:110739171-110739196	GM10248	blood:	n/a	n/a
35	CTCF	chr2:110744363-110744579	Pancreas_OC	pancreas:	n/a	chr2:110744453-110744466
36	CTCF	chr2:110745324-110745668	GM19239	blood:	n/a	n/a
37	CTCF	chr2:110744371-110744566	LNCaP	prostate:	n/a	chr2:110744453-110744466
38	CTCF	chr2:110734084-110734158	GM13976	blood:	n/a	chr2:110734108-110734126
39	CTCF	chr2:110738390-110738685	LNCaP	prostate:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
40	CTCF	chr2:110745342-110745641	Kidney_OC	kidney:	n/a	n/a
41	CTCF	chr2:110744310-110744724	NHEK	skin:	n/a	chr2:110744453-110744466
42	CTCF	chr2:110744728-110744928	LNCaP	prostate:	n/a	n/a
43	CTCF	chr2:110738371-110738647	A549	lung:	n/a	chr2:110738522-110738540 chr2:110738517-110738538 chr2:110738528-110738537 chr2:110738525-110738535
44	CTCF	chr2:110745722-110745727	MCF-7	breast:	n/a	n/a
45	CTCF	chr2:110745132-110745279	GM19238	blood:	n/a	n/a
46	CTCF	chr2:110745302-110745604	Lung_OC	lung:	n/a	n/a
47	CTCF	chr2:110745316-110745651	GM12878	blood:	n/a	n/a
48	CTCF	chr2:110745361-110745653	K562	blood:	n/a	n/a
49	CTCF	chr2:110744446-110744530	Spleen_OC	spleen:	n/a	chr2:110744453-110744466
50	CTCF	chr2:110744322-110744568	H1-hESC	embryonic stem cell:	n/a	chr2:110744453-110744466

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIMS3-1	chr2:110746130-110746278	NONHSAT073165
2	lnc-LIMS3-1	chr2:110744703-110744767	NONHSAT073165
3	lnc-LIMS3-1	chr2:110745849-110746379	ENSG00000204588
4	lnc-LIMS3-1	chr2:110746317-110746379	NONHSAT073165
5	lnc-LIMS3-1	chr2:110745138-110745187	NONHSAT073165

Variant related genes	Relation type
LINC01123	TF binding region
ZBTB45P1	TF binding region
GPAA1P1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540625662	chr2:110738259-110738260	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs336701	chr2:110738305-110738306	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs369269722	chr2:110738327-110738328	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs560727210	chr2:110738391-110738392	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs529603276	chr2:110738494-110738495	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs549743418	chr2:110738737-110738738	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs185889550	chr2:110738774-110738775	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs531964331	chr2:110738777-110738778	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs199500468	chr2:110738798-110738799	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs550367611	chr2:110738812-110738813	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs367985110	chr2:110738843-110738844	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs538696574	chr2:110738844-110738845	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs539014538	chr2:110738899-110738900	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs546569449	chr2:110738931-110738932	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs2124961	chr2:110739130-110739131	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs563189274	chr2:110739678-110739679	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
17	rs571399457	chr2:110742211-110742212	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs339196	chr2:110742626-110742627	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs373152667	chr2:110743667-110743668	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs336709	chr2:110743690-110743691	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs533992791	chr2:110743774-110743775	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs554277122	chr2:110743814-110743815	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs565138343	chr2:110743840-110743841	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs200875767	chr2:110743841-110743842	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs388398	chr2:110743852-110743853	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs142252171	chr2:110743856-110743857	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs62159145	chr2:110744420-110744421	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs377420291	chr2:110745996-110745997	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs188552360	chr2:110746170-110746171	Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs539306421	chr2:110746193-110746194	Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs67932826	chr2:110746204-110746205	Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs572573222	chr2:110746240-110746241	Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs542732988	chr2:110746576-110746577	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs370823008	chr2:110749174-110749175	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs559776662	chr2:110749659-110749660	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs376647021	chr2:110749833-110749834	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs567909426	chr2:110750038-110750039	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs564090933	chr2:110750041-110750042	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

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
Colorectal cancer	16912164	CNVD
Ischaemic stroke	16980335	CNVD
Acute myeloid leukemia	18000384	CNVD
Nephronophthisis	17901113	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD
Disease	19212409	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110746000-110746400	Active TSS	Fetal Intestine Small	intestine

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