Variant report

Variant	nsv591062
Chromosome Location	chr3:97907553-97914008
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:188)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:188 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:97907429-97907720	GM12878	blood:	n/a	n/a
2	CHD1	chr3:97907603-97907803	GM12878	blood:	n/a	n/a
3	CHD2	chr3:97907426-97907647	GM12878	blood:	n/a	n/a
4	CTCF	chr3:97907560-97907710	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr3:97907505-97907660	GM13976	blood:	n/a	n/a
6	CTCF	chr3:97907620-97907770	NHLF	lung:	n/a	n/a
7	CTCF	chr3:97907500-97907650	BE2_C	brain:	n/a	n/a
8	CTCF	chr3:97907480-97907630	HMF	breast:	n/a	n/a
9	CTCF	chr3:97907420-97907570	GM12868	blood:	n/a	n/a
10	CTCF	chr3:97907460-97907610	GM06990	blood:	n/a	n/a
11	CTCF	chr3:97907414-97907737	A549	lung:	n/a	n/a
12	CTCF	chr3:97907540-97907690	GM06990	blood:	n/a	n/a
13	CTCF	chr3:97907405-97907670	A549	lung:	n/a	n/a
14	CTCF	chr3:97907500-97907650	HRE	kidney:	n/a	n/a
15	CTCF	chr3:97907500-97907650	AG04449	skin:	n/a	n/a
16	CTCF	chr3:97907540-97907690	HRE	kidney:	n/a	n/a
17	CTCF	chr3:97907500-97907650	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:97907540-97907690	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr3:97907520-97907670	GM12874	blood:	n/a	n/a
20	CTCF	chr3:97907496-97907695	GM10248	blood:	n/a	n/a
21	CTCF	chr3:97907491-97907685	A549	lung:	n/a	n/a
22	CTCF	chr3:97907540-97907690	GM12864	blood:	n/a	n/a
23	CTCF	chr3:97907480-97907630	HFF	foreskin:	n/a	n/a
24	CTCF	chr3:97907560-97907710	A549	lung:	n/a	n/a
25	CTCF	chr3:97907520-97907670	WERI-Rb-1	eye:	n/a	n/a
26	CTCF	chr3:97907548-97907635	Pancreas_OC	pancreas:	n/a	n/a
27	CTCF	chr3:97907540-97907690	GM12871	blood:	n/a	n/a
28	CTCF	chr3:97907460-97907610	GM12869	blood:	n/a	n/a
29	CTCF	chr3:97907457-97907738	A549	lung:	n/a	n/a
30	CTCF	chr3:97907480-97907630	GM12864	blood:	n/a	n/a
31	CTCF	chr3:97907520-97907670	BJ	skin:	n/a	n/a
32	CTCF	chr3:97907560-97907710	BE2_C	brain:	n/a	n/a
33	CTCF	chr3:97907325-97907855	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:97907460-97907610	NHEK	skin:	n/a	n/a
35	CTCF	chr3:97907500-97907650	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr3:97907500-97907650	HepG2	liver:	n/a	n/a
37	CTCF	chr3:97907465-97907743	IMR90	lung:	n/a	n/a
38	CTCF	chr3:97907464-97907674	MCF-7	breast:	n/a	n/a
39	CTCF	chr3:97907456-97907670	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr3:97907460-97907610	GM12870	blood:	n/a	n/a
41	CTCF	chr3:97907820-97907970	GM12865	blood:	n/a	n/a
42	CTCF	chr3:97907480-97907630	GM12870	blood:	n/a	n/a
43	CTCF	chr3:97907487-97907682	Medullo	brain:	n/a	n/a
44	CTCF	chr3:97907500-97907650	HCT-116	colon:	n/a	n/a
45	CTCF	chr3:97907500-97907650	HL-60	blood:	n/a	n/a
46	CTCF	chr3:97907480-97907630	GM12868	blood:	n/a	n/a
47	CTCF	chr3:97907520-97907670	HCFaa	heart:	n/a	n/a
48	CTCF	chr3:97907438-97907728	K562	blood:	n/a	n/a
49	CTCF	chr3:97907480-97907630	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr3:97907480-97907630	HBMEC	blood vessel:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:97907135..97908080-chr3:98062563..98063391,2	MCF-7	breast:
2	chr3:97907135..97908282-chr3:98048120..98049025,6	MCF-7	breast:
3	chr3:97904894..97907628-chr3:98045904..98048505,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR5H15-1	chr3:97910049-97910454	XLOC_002733
2	lnc-OR5H15-1	chr3:97912268-97912342	XLOC_002733
3	lnc-OR5H15-1	chr3:97910049-97910454	XLOC_002733
4	lnc-OR5H15-1	chr3:97912268-97912342	XLOC_002733

No data

Variant related genes	Relation type
OR5H5P	TF binding region
TGFB2	miRNA target sites
LYPD3	miRNA target sites

Extended variants
information (count: 449 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:449 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs35594582	chr3:97907553-97907554	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs147713802	chr3:97907574-97907575	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs35694938	chr3:97907581-97907582	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs142571335	chr3:97907586-97907587	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs68030363	chr3:97907587-97907588	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs530390218	chr3:97907611-97907612	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs201612501	chr3:97907667-97907668	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs386663680	chr3:97907668-97907669	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs73135361	chr3:97907669-97907670	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs552231119	chr3:97907682-97907683	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs550687118	chr3:97907695-97907696	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs144709872	chr3:97907727-97907728	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs13060486	chr3:97907728-97907729	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs115591675	chr3:97907799-97907800	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs192319548	chr3:97907809-97907810	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs533921740	chr3:97907825-97907826	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs139597911	chr3:97907838-97907839	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs570456993	chr3:97907844-97907845	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs13083770	chr3:97907849-97907850	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs556275645	chr3:97907857-97907858	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs573771437	chr3:97907874-97907875	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs13064891	chr3:97907908-97907909	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs570522283	chr3:97907965-97907966	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs386663681	chr3:97907974-97907975	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs13093005	chr3:97907982-97907983	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs13088324	chr3:97907997-97907998	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs13088327	chr3:97908001-97908002	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs200965240	chr3:97908008-97908009	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs386356138	chr3:97908009-97908010	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs141648200	chr3:97908030-97908031	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs576812700	chr3:97908039-97908040	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs184523427	chr3:97908051-97908052	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs562763946	chr3:97908062-97908063	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs13093180	chr3:97908065-97908066	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs187908580	chr3:97908071-97908072	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs13088529	chr3:97908123-97908124	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs527526816	chr3:97908142-97908143	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs13065259	chr3:97908143-97908144	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs570792134	chr3:97908157-97908158	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs192394261	chr3:97908164-97908165	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs35292867	chr3:97908209-97908210	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs62267772	chr3:97908235-97908236	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs184419094	chr3:97908244-97908245	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs555219217	chr3:97908253-97908254	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs574954344	chr3:97908258-97908259	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs34072146	chr3:97908304-97908305	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs189352549	chr3:97908307-97908308	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs75707234	chr3:97908314-97908315	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs150391181	chr3:97908343-97908344	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs560162904	chr3:97908344-97908345	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

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
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:97906800-97908000	Enhancers	Primary hematopoietic stem cells	blood
2	chr3:97906800-97908400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:97907000-97908000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:97907000-97908000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:97907000-97908200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:97907000-97910200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:97907200-97907600	Enhancers	Primary T cells from cord blood	blood
8	chr3:97907200-97907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:97907200-97907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:97907200-97907600	Enhancers	GM12878-XiMat	blood
11	chr3:97907200-97907800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:97907400-97908400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:97908200-97908600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:97908400-97910000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:97908600-97908800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:97908800-97910800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:97910000-97912200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:97910200-97910400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:97910200-97910800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:97910400-97913600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:97910800-97911400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:97910800-97913800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr3:97911400-97911600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:97911600-97912000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:97912000-97912600	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:97912200-97914600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr3:97912600-97916000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:97913600-97913800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:97913600-97914400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:97913800-97915400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links