Variant report

Variant	nsv965366
Chromosome Location	chr3:162983278-163013954
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	ARID3A	chr3:163005669-163005678	K562	blood:	n/a	n/a
2	CEBPB	chr3:163004771-163005007	HepG2	liver:	n/a	chr3:163004841-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004839-163004852 chr3:163004839-163004850
3	CEBPB	chr3:163004712-163004916	K562	blood:	n/a	chr3:163004841-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004839-163004852 chr3:163004839-163004850
4	CEBPB	chr3:162995031-162995257	A549	lung:	n/a	chr3:162995163-162995176
5	CEBPB	chr3:163004791-163004858	H1-hESC	embryonic stem cell:	n/a	chr3:163004841-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004839-163004852 chr3:163004839-163004850
6	CEBPB	chr3:163004717-163004994	IMR90	lung:	n/a	chr3:163004841-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004841-163004850 chr3:163004841-163004850 chr3:163004839-163004852 chr3:163004839-163004852 chr3:163004839-163004850
7	CHD2	chr3:162984654-162984921	GM12878	blood:	n/a	n/a
8	CTCF	chr3:162991580-162991730	MCF-7	breast:	n/a	n/a
9	CTCF	chr3:162991565-162991788	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:162991541-162991829	GM12878	blood:	n/a	n/a
11	CTCF	chr3:163009617-163009656	GM10248	blood:	n/a	n/a
12	CTCF	chr3:162991660-162991810	HA-sp	spinal cord:	n/a	n/a
13	CTCF	chr3:162991660-162991810	RPTEC	kidney:	n/a	n/a
14	CTCF	chr3:162987299-162987376	Lung_OC	lung:	n/a	n/a
15	CTCF	chr3:162991580-162991730	A549	lung:	n/a	n/a
16	CTCF	chr3:162991675-162991692	HepG2	liver:	n/a	n/a
17	CTCF	chr3:162991630-162991752	LNCaP	prostate:	n/a	n/a
18	CTCF	chr3:163002704-163002730	GM20000	blood:	n/a	n/a
19	CTCF	chr3:162991580-162991730	HEEpiC	esophagus:	n/a	n/a
20	CTCF	chr3:162991447-162991896	MCF-7	breast:	n/a	n/a
21	CTCF	chr3:162991600-162991750	MCF-7	breast:	n/a	n/a
22	CTCF	chr3:162991579-162991765	MCF-7	breast:	n/a	n/a
23	CTCF	chr3:162991616-162991751	LNCaP	prostate:	n/a	n/a
24	CTCF	chr3:162991404-162991910	MCF-7	breast:	n/a	n/a
25	CTCF	chr3:162991580-162991730	BE2_C	brain:	n/a	n/a
26	CTCF	chr3:162991625-162991739	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr3:162991640-162991790	WERI-Rb-1	eye:	n/a	n/a
28	CTCF	chr3:162991540-162991690	Caco-2	colon:	n/a	n/a
29	CUX1	chr3:162989125-162989198	GM12878	blood:	n/a	n/a
30	E2F4	chr3:163006238-163006438	MCF10A-Er-Src	breast:	n/a	n/a
31	EP300	chr3:162984619-162984819	GM12878	blood:	n/a	n/a
32	EP300	chr3:162984631-162984870	GM12878	blood:	n/a	n/a
33	FAM48A	chr3:163011835-163011941	GM12878	blood:	n/a	n/a
34	FOS	chr3:163005723-163006103	HUVEC	blood vessel:	n/a	chr3:163005804-163005814 chr3:163005803-163005814 chr3:163005804-163005814
35	GATA3	chr3:162985651-162985821	SH-SY5Y	brain:	n/a	n/a
36	GATA3	chr3:162992326-162992474	SH-SY5Y	brain:	n/a	n/a
37	IRF1	chr3:162988545-162988744	K562	blood:	n/a	n/a
38	JUN	chr3:163004794-163004880	K562	blood:	n/a	n/a
39	JUN	chr3:162991959-162991982	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAFF	chr3:162987144-162987361	HepG2	liver:	n/a	n/a
41	MAFK	chr3:163003619-163003668	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAFK	chr3:162987233-162987447	HepG2	liver:	n/a	chr3:162987285-162987300
43	MAFK	chr3:162987173-162987368	HepG2	liver:	n/a	chr3:162987285-162987300
44	MXI1	chr3:162988607-162988666	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:162987501-162987586	MCF-7	breast:	n/a	n/a
46	POLR2A	chr3:163004715-163004915	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr3:162989185-162989282	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr3:162990054-162990094	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr3:163010676-163010732	ProgFib	skin:	n/a	n/a
50	POLR2A	chr3:163013784-163013856	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:163011480..163014323-chr3:163020834..163023758,2	MCF-7	breast:
2	chr3:162774576..162775267-chr3:162991199..162992106,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SI-4	chr3:162996298-162996391	ENSG00000241369
2	lnc-SI-4	chr3:162996298-162996391	ENSG00000241369
3	lnc-SI-4	chr3:162996298-162996361	ENSG00000241369
4	lnc-SI-4	chr3:162992984-162993107	ENSG00000241369
5	lnc-SI-4	chr3:162996298-162996391	ENSG00000241369
6	lnc-SI-4	chr3:162992984-162993107	ENSG00000241369
7	lnc-SI-4	chr3:162996298-162996391	ENSG00000241369
8	lnc-SI-4	chr3:162996298-162996391	ENSG00000241369
9	lnc-SI-4	chr3:162996298-162996391	ENSG00000241369
10	lnc-SI-4	chr3:162992984-162993107	ENSG00000241369
11	lnc-SI-4	chr3:162992984-162993107	ENSG00000241369

Variant related genes	Relation type
CT64	TF binding region
ENSG00000241369	chromatin interactions

Extended variants
information (count: 102 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:102 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6804797	chr3:162993012-162993013	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs140295187	chr3:162993040-162993041	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs545770618	chr3:162993080-162993081	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs535777135	chr3:162993103-162993104	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs1529366	chr3:162996318-162996319	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs367765403	chr3:162996386-162996387	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs145097998	chr3:163011622-163011623	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs199684730	chr3:163011629-163011630	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs569635358	chr3:163011632-163011633	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs535152207	chr3:163011635-163011636	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs548951071	chr3:163011642-163011643	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs1688525	chr3:163011679-163011680	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs116412569	chr3:163011695-163011696	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs528550825	chr3:163011703-163011704	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs548305459	chr3:163011743-163011744	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs189445109	chr3:163011754-163011755	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs537013891	chr3:163011755-163011756	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs34745202	chr3:163011757-163011758	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs148928982	chr3:163011770-163011771	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs116121730	chr3:163011779-163011780	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs145389648	chr3:163011829-163011830	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs529415627	chr3:163011858-163011859	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs558465196	chr3:163011859-163011860	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs572303060	chr3:163011896-163011897	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs181327078	chr3:163011947-163011948	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs534683202	chr3:163011968-163011969	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs554674187	chr3:163012011-163012012	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs375819466	chr3:163012025-163012026	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs547849667	chr3:163012031-163012032	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs543010452	chr3:163012052-163012053	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs7429715	chr3:163012082-163012083	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs200984078	chr3:163012087-163012088	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs114667715	chr3:163012155-163012156	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs1648986	chr3:163012225-163012226	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs369583755	chr3:163012226-163012227	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs559671243	chr3:163012227-163012228	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs528634756	chr3:163012228-163012229	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs548390791	chr3:163012229-163012230	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs111231327	chr3:163012237-163012238	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs561806994	chr3:163012254-163012255	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs530917428	chr3:163012258-163012259	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs3031300	chr3:163012259-163012260	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs550699839	chr3:163012301-163012302	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs375217638	chr3:163012314-163012315	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs570866899	chr3:163012349-163012350	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs538542563	chr3:163012356-163012357	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs552471211	chr3:163012367-163012368	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs35709571	chr3:163012392-163012393	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs183935425	chr3:163012420-163012421	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs189052439	chr3:163012431-163012432	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

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
small cell lung cancer	20016488	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
Breast cancer	21364760	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
Bladder cancer	21909424	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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