Variant report

Variant	nsv877233
Chromosome Location	chr3:102787456-102956925
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	chr3:102936818-102937806	GM12878	blood:	n/a	n/a
2	ATF2	chr3:102846474-102847000	GM12878	blood:	n/a	n/a
3	ATF2	chr3:102846504-102846873	GM12878	blood:	n/a	n/a
4	ATF2	chr3:102936808-102937519	GM12878	blood:	n/a	n/a
5	BATF	chr3:102936907-102937418	GM12878	blood:	n/a	n/a
6	BATF	chr3:102846641-102846881	GM12878	blood:	n/a	n/a
7	BATF	chr3:102936937-102937408	GM12878	blood:	n/a	n/a
8	BCL11A	chr3:102936945-102937388	GM12878	blood:	n/a	n/a
9	BCL11A	chr3:102846636-102846904	GM12878	blood:	n/a	chr3:102846753-102846762
10	BCL11A	chr3:102936940-102937450	GM12878	blood:	n/a	n/a
11	BCL3	chr3:102936869-102937427	GM12878	blood:	n/a	n/a
12	BCL3	chr3:102936961-102937363	GM12878	blood:	n/a	n/a
13	BCLAF1	chr3:102936803-102937523	GM12878	blood:	n/a	n/a
14	BCLAF1	chr3:102936936-102937419	GM12878	blood:	n/a	n/a
15	BHLHE40	chr3:102892955-102893330	GM12878	blood:	n/a	n/a
16	BHLHE40	chr3:102804471-102804525	GM12878	blood:	n/a	n/a
17	BHLHE40	chr3:102889471-102889774	GM12878	blood:	n/a	n/a
18	BHLHE40	chr3:102936950-102937419	GM12878	blood:	n/a	n/a
19	CCNT2	chr3:102882271-102882471	K562	blood:	n/a	n/a
20	CEBPB	chr3:102865958-102866305	Hela-S3	cervix:	n/a	chr3:102866124-102866135
21	CEBPB	chr3:102805733-102806117	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr3:102877445-102877893	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr3:102837167-102837612	HepG2	liver:	n/a	chr3:102837245-102837256
24	CEBPB	chr3:102845746-102845963	HepG2	liver:	n/a	chr3:102845854-102845865
25	CEBPB	chr3:102824103-102824368	IMR90	lung:	n/a	chr3:102824235-102824246 chr3:102824236-102824245 chr3:102824234-102824245
26	CEBPB	chr3:102837140-102837379	IMR90	lung:	n/a	chr3:102837245-102837256
27	CEBPB	chr3:102815579-102815882	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr3:102824090-102824419	HepG2	liver:	n/a	chr3:102824235-102824246 chr3:102824236-102824245 chr3:102824234-102824245
29	CEBPB	chr3:102912630-102912880	HepG2	liver:	n/a	chr3:102912736-102912747
30	CEBPB	chr3:102912685-102912861	Hela-S3	cervix:	n/a	chr3:102912736-102912747
31	CEBPB	chr3:102936875-102937548	GM12878	blood:	n/a	n/a
32	CEBPB	chr3:102899975-102900407	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr3:102824046-102824411	MCF-7	breast:	n/a	chr3:102824235-102824246 chr3:102824236-102824245 chr3:102824234-102824245
34	CEBPB	chr3:102844341-102844608	HepG2	liver:	n/a	chr3:102844494-102844505
35	CEBPB	chr3:102937102-102937413	GM12878	blood:	n/a	n/a
36	CHD2	chr3:102889644-102889761	GM12878	blood:	n/a	n/a
37	CHD2	chr3:102892896-102893057	GM12878	blood:	n/a	n/a
38	CHD2	chr3:102936950-102937417	GM12878	blood:	n/a	n/a
39	CTCF	chr3:102831740-102831890	GM12875	blood:	n/a	n/a
40	CTCF	chr3:102952983-102953139	GM10248	blood:	n/a	n/a
41	CTCF	chr3:102846760-102846910	RPTEC	kidney:	n/a	n/a
42	CTCF	chr3:102845100-102845416	GM12878	blood:	n/a	chr3:102845259-102845277 chr3:102845254-102845275
43	CTCF	chr3:102846500-102846650	RPTEC	kidney:	n/a	n/a
44	CTCF	chr3:102843620-102843770	RPTEC	kidney:	n/a	n/a
45	CTCF	chr3:102831526-102831641	Kidney_OC	kidney:	n/a	n/a
46	CTCF	chr3:102846680-102846830	HMEC	breast:	n/a	n/a
47	CTCF	chr3:102871556-102871583	Fibrobl	skin:	n/a	n/a
48	CTCF	chr3:102954489-102954521	GM10248	blood:	n/a	n/a
49	CTCF	chr3:102843486-102843837	GM12878	blood:	n/a	n/a
50	CTCF	chr3:102831460-102831610	GM12875	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:102879980..102881764-chr3:102891406..102893851,2	K562	blood:
2	chr3:102879980..102881764-chr3:102891406..102893851,2	K562	blood:
3	chr1:188479024..188479715-chr3:102939006..102939691,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZPLD1-2	chr3:102859657-102859798	XLOC_002743
2	lnc-ZPLD1-2	chr3:102865617-102865744	XLOC_002743
3	lnc-ZPLD1-2	chr3:102871138-102871281	XLOC_002743
4	lnc-ZPLD1-2	chr3:102817066-102817185	XLOC_002743
5	lnc-ZPLD1-6	chr3:102888748-102888923	l_2419_chr3:102888747-102894491_prostate
6	lnc-ZPLD1-2	chr3:102868713-102868835	XLOC_002743
7	lnc-ZPLD1-2	chr3:102863471-102863517	XLOC_002743
8	lnc-ZPLD1-6	chr3:102894427-102894491	l_2419_chr3:102888747-102894491_prostate

Variant related genes	Relation type
RNU1-43P	TF binding region
NDUFA4P2	TF binding region
SLC7A11	miRNA target sites
HOXA9	miRNA target sites
BTG3	miRNA target sites

Extended variants
information (count: 1753 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:1753 , 50 per page) page: 1 2 3 4 5 6 7 ... 36

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs80277555	chr3:102794411-102794412	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs116004599	chr3:102794440-102794441	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs573469614	chr3:102794462-102794463	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs540180911	chr3:102794485-102794486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs575859387	chr3:102794496-102794497	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs528923670	chr3:102794497-102794498	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs140323552	chr3:102794520-102794521	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs562273749	chr3:102794541-102794542	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs148383086	chr3:102794561-102794562	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs528659102	chr3:102795809-102795810	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs577281478	chr3:102795823-102795824	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs56672980	chr3:102795839-102795840	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs544761573	chr3:102795846-102795847	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs186591229	chr3:102795858-102795859	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs572144193	chr3:102795871-102795872	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs372553726	chr3:102795879-102795880	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs3860553	chr3:102796006-102796007	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs561126201	chr3:102796038-102796039	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs368844012	chr3:102796075-102796076	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs529335739	chr3:102796081-102796082	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs146297914	chr3:102796087-102796088	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs3914490	chr3:102796100-102796101	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs562888178	chr3:102796126-102796127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs533399867	chr3:102796195-102796196	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs550977231	chr3:102796206-102796207	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs551564954	chr3:102796218-102796219	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs75620388	chr3:102796219-102796220	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs544019380	chr3:102796257-102796258	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs142478467	chr3:102796342-102796343	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs534123865	chr3:102796365-102796366	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs549166918	chr3:102796380-102796381	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs190985961	chr3:102796402-102796403	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs116291658	chr3:102796474-102796475	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs6765316	chr3:102796499-102796500	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs556471000	chr3:102796502-102796503	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs550325351	chr3:102796530-102796531	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs182266239	chr3:102796567-102796568	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs186527879	chr3:102796623-102796624	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs60414141	chr3:102796624-102796625	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs377391180	chr3:102796638-102796639	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs143083486	chr3:102796639-102796640	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs144748325	chr3:102796706-102796707	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs113094070	chr3:102796762-102796763	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs561088855	chr3:102796772-102796773	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs148136454	chr3:102796792-102796793	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs542830772	chr3:102796821-102796822	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs117711140	chr3:102796861-102796862	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs565207959	chr3:102796887-102796888	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs189641937	chr3:102796924-102796925	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs551795277	chr3:102796958-102796959	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17431168	CNVD
Renal cell carcinoma	18765545	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Pancreatic cancer	17952125	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:102794400-102794600	Enhancers	Fetal Kidney	kidney
2	chr3:102795800-102797400	Enhancers	Fetal Intestine Large	intestine
3	chr3:102796000-102797400	Enhancers	Fetal Intestine Small	intestine
4	chr3:102796600-102796800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:102796600-102799000	Weak transcription	Fetal Kidney	kidney
6	chr3:102796800-102800800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:102797400-102797800	Weak transcription	Fetal Intestine Large	intestine
8	chr3:102797400-102799000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:102797800-102798000	Enhancers	Fetal Intestine Large	intestine
10	chr3:102798000-102799000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:102799000-102799400	Enhancers	Fetal Intestine Large	intestine
12	chr3:102799000-102799400	Enhancers	Fetal Intestine Small	intestine
13	chr3:102799000-102799600	Active TSS	Fetal Lung	lung
14	chr3:102799400-102802800	Weak transcription	Fetal Intestine Large	intestine
15	chr3:102799400-102802800	Weak transcription	Fetal Intestine Small	intestine
16	chr3:102800800-102801000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:102801000-102802000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:102802000-102802200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:102802800-102805400	Enhancers	Fetal Intestine Large	intestine
20	chr3:102802800-102805400	Enhancers	Fetal Intestine Small	intestine
21	chr3:102803400-102805600	Enhancers	Fetal Kidney	kidney
22	chr3:102804000-102805200	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:102805400-102806400	Weak transcription	Fetal Intestine Large	intestine
24	chr3:102805400-102806400	Weak transcription	Fetal Intestine Small	intestine
25	chr3:102805800-102806200	Enhancers	Hela-S3	cervix
26	chr3:102806400-102807200	Enhancers	Fetal Intestine Large	intestine
27	chr3:102806600-102806800	Enhancers	Fetal Intestine Small	intestine
28	chr3:102824400-102825000	Active TSS	Fetal Intestine Large	intestine
29	chr3:102830800-102831400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:102831000-102831400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:102831000-102831400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr3:102831000-102831600	Enhancers	H9 Cell Line	embryonic stem cell
33	chr3:102831000-102831600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:102831000-102831600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:102831000-102832000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:102831200-102831800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:102831400-102831800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:102846000-102846200	Enhancers	GM12878-XiMat	blood
39	chr3:102846200-102846400	Flanking Active TSS	GM12878-XiMat	blood
40	chr3:102846400-102847000	Enhancers	GM12878-XiMat	blood
41	chr3:102849400-102850000	Enhancers	Dnd41	blood
42	chr3:102850000-102854200	Weak transcription	Dnd41	blood
43	chr3:102854200-102856800	Enhancers	Dnd41	blood
44	chr3:102855400-102855800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:102855400-102856000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr3:102855600-102856000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:102859200-102859800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr3:102859200-102859800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr3:102859200-102859800	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:102859200-102859800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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