Variant report

Variant	nsv877153
Chromosome Location	chr3:88417316-88541582
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:259)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:10)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:259 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr3:88438892-88438979	K562	blood:	n/a	n/a
2	BACH1	chr3:88434387-88434629	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr3:88501523-88501717	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr3:88528668-88528894	A549	lung:	n/a	n/a
5	CEBPB	chr3:88528652-88528747	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr3:88427165-88427365	H1-hESC	embryonic stem cell:	n/a	chr3:88427292-88427305
7	CEBPB	chr3:88515855-88516126	HepG2	liver:	n/a	chr3:88515996-88516007 chr3:88515997-88516006
8	CEBPB	chr3:88528621-88528887	IMR90	lung:	n/a	n/a
9	CEBPB	chr3:88434165-88434583	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr3:88514020-88514170	HEEpiC	esophagus:	n/a	n/a
11	CTCF	chr3:88514078-88514170	MCF-7	breast:	n/a	n/a
12	CTCF	chr3:88428380-88428530	GM12865	blood:	n/a	chr3:88428421-88428434 chr3:88428419-88428437 chr3:88428414-88428435
13	CTCF	chr3:88516420-88516570	HBMEC	blood vessel:	n/a	n/a
14	CTCF	chr3:88514000-88514150	HBMEC	blood vessel:	n/a	n/a
15	CTCF	chr3:88514020-88514170	HMEC	breast:	n/a	n/a
16	CTCF	chr3:88516460-88516610	HepG2	liver:	n/a	n/a
17	CTCF	chr3:88449307-88449344	GM20000	blood:	n/a	n/a
18	CTCF	chr3:88516480-88516630	HepG2	liver:	n/a	n/a
19	CTCF	chr3:88516440-88516590	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr3:88516420-88516570	Caco-2	colon:	n/a	n/a
21	CTCF	chr3:88516500-88516650	HCPEpiC	choroid plexus:	n/a	n/a
22	CTCF	chr3:88516480-88516630	Caco-2	colon:	n/a	n/a
23	CTCF	chr3:88514060-88514210	RPTEC	kidney:	n/a	n/a
24	CTCF	chr3:88516500-88516650	HEK293	kidney:	n/a	n/a
25	CTCF	chr3:88519100-88519250	HAc	cerebellar:	n/a	n/a
26	CTCF	chr3:88516460-88516610	HBMEC	blood vessel:	n/a	n/a
27	CTCF	chr3:88514040-88514190	HAc	cerebellar:	n/a	n/a
28	CTCF	chr3:88428358-88428558	GM12878	blood:	n/a	chr3:88428421-88428434 chr3:88428419-88428437 chr3:88428414-88428435
29	CTCF	chr3:88514000-88514150	Caco-2	colon:	n/a	n/a
30	CTCF	chr3:88514067-88514164	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr3:88514060-88514210	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:88516512-88516566	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:88428300-88428450	MCF-7	breast:	n/a	chr3:88428421-88428434 chr3:88428419-88428437 chr3:88428414-88428435
34	CTCF	chr3:88514000-88514150	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr3:88468481-88468493	GM13976	blood:	n/a	n/a
36	CTCF	chr3:88514000-88514150	HCFaa	heart:	n/a	n/a
37	CTCF	chr3:88514075-88514176	MCF-7	breast:	n/a	n/a
38	CTCF	chr3:88514020-88514170	HCPEpiC	choroid plexus:	n/a	n/a
39	CTCF	chr3:88463612-88463648	GM20000	blood:	n/a	n/a
40	CTCF	chr3:88516460-88516610	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:88514100-88514250	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr3:88514020-88514170	HRPEpiC	eye:	n/a	n/a
43	CTCF	chr3:88514120-88514270	HRE	kidney:	n/a	n/a
44	CTCF	chr3:88514080-88514230	HMEC	breast:	n/a	n/a
45	CTCF	chr3:88514080-88514230	MCF-7	breast:	n/a	n/a
46	CTCF	chr3:88514492-88514520	MCF-7	breast:	n/a	chr3:88514499-88514515
47	CUX1	chr3:88527309-88527310	GM12878	blood:	n/a	n/a
48	CUX1	chr3:88482645-88483002	GM12878	blood:	n/a	n/a
49	E2F4	chr3:88473166-88473219	MCF10A-Er-Src	breast:	n/a	n/a
50	E2F4	chr3:88509770-88509804	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:88443258..88445795-chr3:88448224..88450369,2	K562	blood:
2	chr3:88526173..88527680-chr3:88528498..88531008,2	MCF-7	breast:
3	chr3:88526173..88527680-chr3:88528498..88531008,2	MCF-7	breast:
4	chr3:88443258..88445795-chr3:88448224..88450369,2	K562	blood:
5	chr20:7969749..7970528-chr3:88470088..88470821,2	MCF-7	breast:
6	chr3:88520234..88522396-chr3:88537772..88539509,2	K562	blood:
7	chr3:88520234..88522396-chr3:88537772..88539509,2	K562	blood:

(count:10 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf38-2	chr3:88514238-88517304	XLOC_002727
2	lnc-C3orf38-2	chr3:88418571-88418634	XLOC_002727
3	lnc-C3orf38-2	chr3:88431735-88431938	XLOC_002727
4	lnc-C3orf38-2	chr3:88514238-88517156	XLOC_002727
5	lnc-C3orf38-2	chr3:88514425-88514628	l_2409_chr3:88470262-88514628_testes
6	lnc-C3orf38-2	chr3:88501234-88501324	l_2409_chr3:88470262-88514628_testes
7	lnc-C3orf38-2	chr3:88431735-88431938	XLOC_002727
8	lnc-C3orf38-2	chr3:88470263-88470483	l_2409_chr3:88470262-88514628_testes
9	lnc-C3orf38-2	chr3:88474992-88475125	l_2409_chr3:88470262-88514628_testes
10	lnc-C3orf38-2	chr3:88431734-88431938	NONHSAT090703

No data

Variant related genes	Relation type
ENSG00000207316	TF binding region
ECE1	miRNA target sites
HCCS	miRNA target sites

Extended variants
information (count: 1774 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:1774 , 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	rs116066601	chr3:88418007-88418008	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs542530430	chr3:88418023-88418024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs570787343	chr3:88418030-88418031	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs572551323	chr3:88418053-88418054	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs545587888	chr3:88418059-88418060	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs564172362	chr3:88418064-88418065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs189582584	chr3:88418072-88418073	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs543050368	chr3:88418098-88418099	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs561339242	chr3:88418149-88418150	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs199546562	chr3:88418243-88418244	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs145634328	chr3:88418263-88418264	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs559887281	chr3:88418267-88418268	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs111372868	chr3:88418396-88418397	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs192373978	chr3:88418397-88418398	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs552412589	chr3:88418448-88418449	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs561331849	chr3:88418461-88418462	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs112959576	chr3:88418466-88418467	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs149070452	chr3:88418467-88418468	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs538325987	chr3:88418475-88418476	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs556634355	chr3:88418476-88418477	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs568462190	chr3:88418480-88418481	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs528581632	chr3:88418483-88418484	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs9857680	chr3:88418498-88418499	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs553380390	chr3:88418577-88418578	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs367789575	chr3:88418644-88418645	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs572564848	chr3:88418648-88418649	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs539993083	chr3:88418658-88418659	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs558044854	chr3:88418662-88418663	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs184793777	chr3:88418684-88418685	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs543113639	chr3:88418694-88418695	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs561353268	chr3:88418699-88418700	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs371659418	chr3:88418731-88418732	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs189478546	chr3:88418743-88418744	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs115032992	chr3:88418753-88418754	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs557560739	chr3:88418798-88418799	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs540983119	chr3:88418803-88418804	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs559570180	chr3:88418822-88418823	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs533056445	chr3:88418846-88418847	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs1870266	chr3:88418911-88418912	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs78188975	chr3:88418936-88418937	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs398091637	chr3:88418938-88418939	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs563462795	chr3:88418979-88418980	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs531887971	chr3:88419003-88419004	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs550251040	chr3:88419022-88419023	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs568470833	chr3:88419031-88419032	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs535804509	chr3:88419048-88419049	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs181463911	chr3:88419062-88419063	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs558169447	chr3:88419063-88419064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs566389631	chr3:88419086-88419087	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs539737389	chr3:88419096-88419097	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
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
Acute lymphoblastic leukemia	20435627	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
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Lung cancer	19547694	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88418000-88419200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:88428200-88428600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:88433600-88434400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:88434000-88434400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:88434000-88434400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:88434000-88434400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:88434000-88434600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:88447600-88448000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:88448600-88449000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:88448600-88449600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:88449000-88449400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:88452400-88452800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:88452800-88457800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:88453800-88455000	Enhancers	Primary T cells from cord blood	blood
15	chr3:88454600-88454800	Enhancers	Fetal Heart	heart
16	chr3:88454800-88455400	Weak transcription	Fetal Heart	heart
17	chr3:88455000-88457200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:88455400-88456200	Enhancers	Fetal Heart	heart
19	chr3:88456000-88456800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:88457200-88459200	Enhancers	Primary T cells from cord blood	blood
21	chr3:88457800-88458600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:88457800-88459400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:88458000-88458200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:88458200-88458400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:88459000-88460000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:88459000-88460000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:88459200-88459600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr3:88459200-88460200	Enhancers	Primary hematopoietic stem cells	blood
29	chr3:88459600-88460000	Active TSS	Primary T cells from cord blood	blood
30	chr3:88459800-88460200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:88460000-88460800	Enhancers	Primary T cells from cord blood	blood
32	chr3:88460800-88461200	Weak transcription	Primary T cells from cord blood	blood
33	chr3:88461200-88461600	Enhancers	Primary T cells from cord blood	blood
34	chr3:88461400-88461800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:88467400-88467800	Enhancers	Fetal Brain Male	brain
36	chr3:88476600-88482000	Weak transcription	Primary B cells from cord blood	blood
37	chr3:88482000-88482600	Enhancers	Primary B cells from cord blood	blood
38	chr3:88482600-88483000	Enhancers	GM12878-XiMat	blood
39	chr3:88482600-88483400	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr3:88482600-88483600	Enhancers	Dnd41	blood
41	chr3:88482800-88483200	Enhancers	Fetal Muscle Leg	muscle
42	chr3:88482800-88483800	Active TSS	NHDF-Ad	bronchial
43	chr3:88482800-88484800	Enhancers	Primary B cells from peripheral blood	blood
44	chr3:88483000-88483600	Flanking Active TSS	GM12878-XiMat	blood
45	chr3:88483400-88483800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:88483400-88485600	Enhancers	Primary B cells from cord blood	blood
47	chr3:88483600-88484000	Flanking Active TSS	Dnd41	blood
48	chr3:88483600-88484000	Active TSS	GM12878-XiMat	blood
49	chr3:88483800-88484200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr3:88484000-88484200	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links