Variant report

Variant	nsv877234
Chromosome Location	chr3:102833131-102950695
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	chr3:102936808-102937519	GM12878	blood:	n/a	n/a
4	ATF2	chr3:102846504-102846873	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	chr3:102936940-102937450	GM12878	blood:	n/a	n/a
10	BCL11A	chr3:102846636-102846904	GM12878	blood:	n/a	chr3:102846753-102846762
11	BCL3	chr3:102936869-102937427	GM12878	blood:	n/a	n/a
12	BCL3	chr3:102936961-102937363	GM12878	blood:	n/a	n/a
13	BCLAF1	chr3:102936936-102937419	GM12878	blood:	n/a	n/a
14	BCLAF1	chr3:102936803-102937523	GM12878	blood:	n/a	n/a
15	BHLHE40	chr3:102936950-102937419	GM12878	blood:	n/a	n/a
16	BHLHE40	chr3:102892955-102893330	GM12878	blood:	n/a	n/a
17	BHLHE40	chr3:102889471-102889774	GM12878	blood:	n/a	n/a
18	CCNT2	chr3:102882271-102882471	K562	blood:	n/a	n/a
19	CEBPB	chr3:102844341-102844608	HepG2	liver:	n/a	chr3:102844494-102844505
20	CEBPB	chr3:102912630-102912880	HepG2	liver:	n/a	chr3:102912736-102912747
21	CEBPB	chr3:102837167-102837612	HepG2	liver:	n/a	chr3:102837245-102837256
22	CEBPB	chr3:102865958-102866305	Hela-S3	cervix:	n/a	chr3:102866124-102866135
23	CEBPB	chr3:102937102-102937413	GM12878	blood:	n/a	n/a
24	CEBPB	chr3:102845746-102845963	HepG2	liver:	n/a	chr3:102845854-102845865
25	CEBPB	chr3:102936875-102937548	GM12878	blood:	n/a	n/a
26	CEBPB	chr3:102912685-102912861	Hela-S3	cervix:	n/a	chr3:102912736-102912747
27	CEBPB	chr3:102899975-102900407	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr3:102877445-102877893	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr3:102837140-102837379	IMR90	lung:	n/a	chr3:102837245-102837256
30	CHD2	chr3:102889644-102889761	GM12878	blood:	n/a	n/a
31	CHD2	chr3:102936950-102937417	GM12878	blood:	n/a	n/a
32	CHD2	chr3:102892896-102893057	GM12878	blood:	n/a	n/a
33	CTCF	chr3:102846680-102846830	HMEC	breast:	n/a	n/a
34	CTCF	chr3:102924340-102924490	Caco-2	colon:	n/a	n/a
35	CTCF	chr3:102875864-102875896	Spleen_OC	spleen:	n/a	n/a
36	CTCF	chr3:102843486-102843837	GM12878	blood:	n/a	n/a
37	CTCF	chr3:102871674-102871709	Pancreas_OC	pancreas:	n/a	n/a
38	CTCF	chr3:102845220-102845370	GM12872	blood:	n/a	chr3:102845259-102845277 chr3:102845254-102845275
39	CTCF	chr3:102871556-102871583	Fibrobl	skin:	n/a	n/a
40	CTCF	chr3:102843560-102843710	HRE	kidney:	n/a	n/a
41	CTCF	chr3:102846500-102846650	RPTEC	kidney:	n/a	n/a
42	CTCF	chr3:102862258-102862286	Lung_OC	lung:	n/a	n/a
43	CTCF	chr3:102845189-102845408	Kidney_OC	kidney:	n/a	chr3:102845259-102845277 chr3:102845254-102845275
44	CTCF	chr3:102916820-102916970	WI-38	lung:	n/a	n/a
45	CTCF	chr3:102845212-102845317	MCF-7	breast:	n/a	chr3:102845259-102845277 chr3:102845254-102845275
46	CTCF	chr3:102903760-102903910	HRE	kidney:	n/a	n/a
47	CTCF	chr3:102845120-102845270	HRE	kidney:	n/a	n/a
48	CTCF	chr3:102845180-102845330	RPTEC	kidney:	n/a	chr3:102845259-102845277 chr3:102845254-102845275
49	CTCF	chr3:102843540-102843690	BE2_C	brain:	n/a	n/a
50	CTCF	chr3:102845180-102845330	HRE	kidney:	n/a	chr3:102845259-102845277 chr3:102845254-102845275

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

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

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

Extended variants
information (count: 1207 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1207 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs182615743	chr3:102846000-102846001	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs151327756	chr3:102846001-102846002	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs577092511	chr3:102846055-102846056	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs530131432	chr3:102846117-102846118	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs539008108	chr3:102846122-102846123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs554250358	chr3:102846124-102846125	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs571782303	chr3:102846126-102846127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs572570072	chr3:102846130-102846131	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs534734749	chr3:102846131-102846132	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs188853503	chr3:102846198-102846199	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs561429505	chr3:102846199-102846200	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs148617285	chr3:102846200-102846201	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs141190907	chr3:102846207-102846208	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs530565650	chr3:102846243-102846244	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs150753929	chr3:102846244-102846245	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs532732318	chr3:102846253-102846254	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs551835434	chr3:102846260-102846261	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs34265996	chr3:102846270-102846271	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs192352172	chr3:102846312-102846313	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs10511205	chr3:102846337-102846338	Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs529699942	chr3:102846351-102846352	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs184640060	chr3:102846387-102846388	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs534332768	chr3:102846400-102846401	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs546160425	chr3:102846422-102846423	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs562310450	chr3:102846428-102846429	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs386664029	chr3:102846429-102846430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs569485074	chr3:102846430-102846431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs537229074	chr3:102846437-102846438	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs552314051	chr3:102846455-102846456	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs552122240	chr3:102846517-102846518	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs571534631	chr3:102846521-102846522	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs570717735	chr3:102846592-102846593	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs4856126	chr3:102846658-102846659	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs139663346	chr3:102846800-102846801	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs192090646	chr3:102846839-102846840	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs184947754	chr3:102846863-102846864	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs115403649	chr3:102846869-102846870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs4241416	chr3:102846877-102846878	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs576492589	chr3:102846940-102846941	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs543984090	chr3:102846991-102846992	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs569405864	chr3:102849407-102849408	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs189622892	chr3:102849484-102849485	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs535822117	chr3:102849507-102849508	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs551239475	chr3:102849584-102849585	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs183449862	chr3:102849611-102849612	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs557779464	chr3:102849663-102849664	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs187736246	chr3:102849680-102849681	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs533851825	chr3:102849719-102849720	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs555475618	chr3:102849777-102849778	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs573796269	chr3:102849779-102849780	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
Renal cell carcinoma	18765545	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:102846000-102846200	Enhancers	GM12878-XiMat	blood
2	chr3:102846200-102846400	Flanking Active TSS	GM12878-XiMat	blood
3	chr3:102846400-102847000	Enhancers	GM12878-XiMat	blood
4	chr3:102849400-102850000	Enhancers	Dnd41	blood
5	chr3:102850000-102854200	Weak transcription	Dnd41	blood
6	chr3:102854200-102856800	Enhancers	Dnd41	blood
7	chr3:102855400-102855800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:102855400-102856000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:102855600-102856000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:102859200-102859800	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:102859200-102859800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:102859200-102859800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:102859200-102859800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:102859600-102860200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:102873200-102874600	Enhancers	Fetal Brain Male	brain
16	chr3:102876400-102877800	Enhancers	Hela-S3	cervix
17	chr3:102877000-102877400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:102887800-102888400	Enhancers	Hela-S3	cervix
19	chr3:102887800-102888400	Enhancers	HMEC	breast
20	chr3:102888200-102888600	Enhancers	NHEK	skin
21	chr3:102888400-102892000	Weak transcription	HMEC	breast
22	chr3:102892000-102892400	Active TSS	HMEC	breast
23	chr3:102892200-102892400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:102892400-102893200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:102899800-102900600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:102899800-102900600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:102899800-102900600	Enhancers	Hela-S3	cervix
28	chr3:102899800-102900600	Enhancers	HMEC	breast
29	chr3:102899800-102900600	Enhancers	NHEK	skin
30	chr3:102900600-102903800	Weak transcription	HMEC	breast
31	chr3:102900600-102904000	Weak transcription	Hela-S3	cervix
32	chr3:102903800-102904200	ZNF genes & repeats	Left Ventricle	heart
33	chr3:102903800-102904200	Enhancers	HMEC	breast
34	chr3:102904000-102904400	Enhancers	Hela-S3	cervix
35	chr3:102918400-102919000	Enhancers	Rectal Smooth Muscle	rectum
36	chr3:102919000-102919400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:102919400-102919800	Enhancers	Brain Germinal Matrix	brain
38	chr3:102919400-102919800	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:102920000-102920400	Enhancers	Stomach Mucosa	stomach
40	chr3:102927800-102928400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:102929000-102929800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:102936200-102937800	Enhancers	GM12878-XiMat	blood
43	chr3:102936600-102937800	Enhancers	Dnd41	blood
44	chr3:102937000-102937800	Enhancers	NH-A	brain
45	chr3:102938800-102939000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:102938800-102939000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:102939000-102939200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr3:102939000-102939400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:102939200-102939600	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links