Variant report

Variant	nsv460968
Chromosome Location	chr3:164380029-164415209
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	BRCA1	chr3:164401316-164401654	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr3:164401328-164401794	MCF-7	breast:	n/a	chr3:164401507-164401524 chr3:164401512-164401523
3	CEBPB	chr3:164401266-164401790	Hela-S3	cervix:	n/a	chr3:164401507-164401524 chr3:164401512-164401523
4	CEBPB	chr3:164397276-164397628	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:164412763-164413091	Hela-S3	cervix:	n/a	chr3:164412919-164412930
6	CEBPB	chr3:164412753-164413107	HepG2	liver:	n/a	chr3:164412919-164412930
7	CEBPB	chr3:164401241-164401844	MCF-7	breast:	n/a	chr3:164401507-164401524 chr3:164401512-164401523
8	CEBPB	chr3:164412780-164413072	A549	lung:	n/a	chr3:164412919-164412930
9	CEBPB	chr3:164412719-164413128	MCF-7	breast:	n/a	chr3:164412919-164412930
10	CEBPB	chr3:164399826-164399926	HepG2	liver:	n/a	chr3:164399882-164399893
11	CHD2	chr3:164409943-164409953	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:164391568-164391875	GM12878	blood:	n/a	chr3:164391727-164391736
13	CTCF	chr3:164391660-164391810	HEEpiC	esophagus:	n/a	chr3:164391727-164391736
14	CTCF	chr3:164391620-164391770	SK-N-SH_RA	brain:	n/a	chr3:164391727-164391736
15	CTCF	chr3:164391641-164391798	Hela-S3	cervix:	n/a	chr3:164391727-164391736
16	CTCF	chr3:164391740-164391890	HRE	kidney:	n/a	n/a
17	CTCF	chr3:164391640-164391790	HEK293	kidney:	n/a	chr3:164391727-164391736
18	CTCF	chr3:164391680-164391830	HMEC	breast:	n/a	chr3:164391727-164391736
19	CTCF	chr3:164391700-164391850	Hela-S3	cervix:	n/a	chr3:164391727-164391736
20	CTCF	chr3:164391622-164391809	Medullo	brain:	n/a	chr3:164391727-164391736
21	CTCF	chr3:164391640-164391790	HCT-116	colon:	n/a	chr3:164391727-164391736
22	CTCF	chr3:164391660-164391803	HepG2	liver:	n/a	chr3:164391727-164391736
23	CTCF	chr3:164391620-164391770	HCT-116	colon:	n/a	chr3:164391727-164391736
24	CTCF	chr3:164391620-164391770	Hela-S3	cervix:	n/a	chr3:164391727-164391736
25	CTCF	chr3:164409900-164410050	GM12869	blood:	n/a	n/a
26	CTCF	chr3:164411695-164411744	Lung_OC	lung:	n/a	n/a
27	CTCF	chr3:164391670-164391769	HepG2	liver:	n/a	chr3:164391727-164391736
28	CTCF	chr3:164391487-164391917	MCF-7	breast:	n/a	chr3:164391727-164391736
29	CTCF	chr3:164391660-164391810	MCF-7	breast:	n/a	chr3:164391727-164391736
30	CTCF	chr3:164391680-164391830	MCF-7	breast:	n/a	chr3:164391727-164391736
31	CTCF	chr3:164391620-164391770	HMF	breast:	n/a	chr3:164391727-164391736
32	CTCF	chr3:164391600-164391750	HBMEC	blood vessel:	n/a	chr3:164391727-164391736
33	CTCF	chr3:164391635-164391817	MCF-7	breast:	n/a	chr3:164391727-164391736
34	CTCF	chr3:164391672-164391780	SK-N-SH_RA	brain:	n/a	chr3:164391727-164391736
35	CTCF	chr3:164391640-164391790	HepG2	liver:	n/a	chr3:164391727-164391736
36	CTCF	chr3:164391720-164391870	RPTEC	kidney:	n/a	chr3:164391727-164391736
37	CTCF	chr3:164391640-164391790	RPTEC	kidney:	n/a	chr3:164391727-164391736
38	CTCF	chr3:164391660-164391810	BE2_C	brain:	n/a	chr3:164391727-164391736
39	CTCF	chr3:164391560-164391886	MCF-7	breast:	n/a	chr3:164391727-164391736
40	CTCF	chr3:164391680-164391830	HRPEpiC	eye:	n/a	chr3:164391727-164391736
41	CTCF	chr3:164391580-164391730	GM12872	blood:	n/a	n/a
42	CTCF	chr3:164391540-164391690	HA-sp	spinal cord:	n/a	n/a
43	CTCF	chr3:164391600-164391750	Caco-2	colon:	n/a	chr3:164391727-164391736
44	CTCF	chr3:164391620-164391770	HepG2	liver:	n/a	chr3:164391727-164391736
45	CTCF	chr3:164391640-164391790	Caco-2	colon:	n/a	chr3:164391727-164391736
46	CTCF	chr3:164391664-164391791	MCF-7	breast:	n/a	chr3:164391727-164391736
47	CTCF	chr3:164391600-164391750	HMF	breast:	n/a	chr3:164391727-164391736
48	CTCF	chr3:164391658-164391757	GM13977	blood:	n/a	chr3:164391727-164391736
49	CTCF	chr3:164391660-164391810	HRE	kidney:	n/a	chr3:164391727-164391736
50	CTCF	chr3:164402258-164402305	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:164382723..164384365-chr3:164390839..164393550,2	MCF-7	breast:
2	chr3:164382723..164384365-chr3:164390839..164393550,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SI-2	chr3:164388666-164389019	XLOC_003313
2	lnc-SI-5	chr3:164400353-164400433	l_2521_chr3:164387549-164449856_testes
3	lnc-SI-5	chr3:164387550-164388087	l_2521_chr3:164387549-164449856_testes
4	lnc-SERPINI1-9	chr3:164405416-164405657	XLOC_002900
5	lnc-SI-5	chr3:164402020-164402099	l_2521_chr3:164387549-164449856_testes
6	lnc-SI-2	chr3:164401605-164401689	XLOC_003313
7	lnc-SI-5	chr3:164400110-164400236	l_2521_chr3:164387549-164449856_testes
8	lnc-SI-2	chr3:164403812-164403864	XLOC_003313
9	lnc-SI-2	chr3:164402987-164403070	XLOC_003313
10	lnc-SERPINI1-9	chr3:164405416-164405657	XLOC_002900
11	lnc-SERPINI1-9	chr3:164405416-164405798	XLOC_002900

Variant related genes	Relation type
ENSG00000241636	TF binding region
COL3A1	miRNA target sites
AKAP13	miRNA target sites
RORC	miRNA target sites
AKT1	miRNA target sites
C1D	miRNA target sites

Extended variants
information (count: 243 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:243 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2201473	chr3:164387568-164387569	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs561101043	chr3:164387569-164387570	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs556161343	chr3:164387585-164387586	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs564941422	chr3:164387595-164387596	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs181503247	chr3:164387614-164387615	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs78178604	chr3:164387641-164387642	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs543332307	chr3:164387648-164387649	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs185852859	chr3:164387670-164387671	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs138383485	chr3:164387677-164387678	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs144027123	chr3:164387679-164387680	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs527813016	chr3:164387691-164387692	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs561116570	chr3:164387698-164387699	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs373906932	chr3:164387716-164387717	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs372433232	chr3:164387728-164387729	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs77398628	chr3:164387763-164387764	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs567557404	chr3:164387766-164387767	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs2722630	chr3:164387777-164387778	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs549913127	chr3:164387790-164387791	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs570032466	chr3:164387868-164387869	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs538936935	chr3:164387869-164387870	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs148802419	chr3:164387876-164387877	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs373263342	chr3:164387899-164387900	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs571933984	chr3:164387934-164387935	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs534756036	chr3:164387940-164387941	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs141557267	chr3:164387941-164387942	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs190377427	chr3:164387954-164387955	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs181003212	chr3:164387962-164387963	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs185248099	chr3:164387977-164387978	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs79291805	chr3:164387997-164387998	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs577088096	chr3:164388044-164388045	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs545757613	chr3:164388048-164388049	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs139044051	chr3:164388055-164388056	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs2643169	chr3:164388677-164388678	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs73030874	chr3:164388693-164388694	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs533988819	chr3:164388747-164388748	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs183381066	chr3:164388751-164388752	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs189237784	chr3:164388754-164388755	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs149726666	chr3:164388764-164388765	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs528761425	chr3:164388790-164388791	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs548229729	chr3:164388842-164388843	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs568038752	chr3:164388844-164388845	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs537177457	chr3:164388855-164388856	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs552258574	chr3:164388880-164388881	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs570561271	chr3:164388882-164388883	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs570669662	chr3:164388887-164388888	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs191918905	chr3:164388888-164388889	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs553089908	chr3:164388891-164388892	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs148907675	chr3:164388892-164388893	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs541701636	chr3:164388903-164388904	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs2172819	chr3:164388951-164388952	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Sudden cardiac death	19188705	CNVD
Mantle cell lymphoma	19029149	CNVD
Malformation	19546859	CNVD
Schizophrenia	19546859	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164919	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
small cell lung cancer	20016488	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:164394600-164395000	Enhancers	Hela-S3	cervix
2	chr3:164395200-164395600	Enhancers	Hela-S3	cervix
3	chr3:164401200-164401600	Enhancers	Hela-S3	cervix
4	chr3:164404000-164404400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:164404400-164404800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:164404800-164405200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:164404800-164405200	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:164405000-164405600	Active TSS	Brain Anterior Caudate	brain
9	chr3:164405000-164405600	Enhancers	Brain Hippocampus Middle	brain
10	chr3:164405200-164405400	Enhancers	Brain Angular Gyrus	brain
11	chr3:164405200-164405400	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr3:164405200-164405600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:164405400-164405600	Active TSS	Brain Cingulate Gyrus	brain
14	chr3:164405600-164405800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:164407600-164407800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:164412800-164413200	Enhancers	Brain Substantia Nigra	brain
17	chr3:164413200-164413600	Active TSS	Brain Substantia Nigra	brain

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