Variant report

Variant	esv13127
Chromosome Location	chr3:97899419-97939393
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:326)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:10)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:326 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr3:97915093-97915523	H1-hESC	embryonic stem cell:	n/a	n/a
2	BCL3	chr3:97916362-97916553	GM12878	blood:	n/a	n/a
3	BHLHE40	chr3:97907429-97907720	GM12878	blood:	n/a	n/a
4	BRCA1	chr3:97907317-97907430	GM12878	blood:	n/a	n/a
5	CEBPB	chr3:97922385-97922691	A549	lung:	n/a	chr3:97922556-97922567
6	CEBPB	chr3:97922385-97922736	HepG2	liver:	n/a	chr3:97922556-97922567
7	CHD1	chr3:97907603-97907803	GM12878	blood:	n/a	n/a
8	CHD2	chr3:97907426-97907647	GM12878	blood:	n/a	n/a
9	CTCF	chr3:97907485-97907636	ProgFib	skin:	n/a	n/a
10	CTCF	chr3:97907500-97907669	GM20000	blood:	n/a	n/a
11	CTCF	chr3:97904140-97904290	GM12870	blood:	n/a	n/a
12	CTCF	chr3:97907480-97907630	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr3:97907499-97907682	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr3:97907480-97907630	GM12873	blood:	n/a	n/a
15	CTCF	chr3:97907480-97907630	NHEK	skin:	n/a	n/a
16	CTCF	chr3:97907361-97907709	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr3:97907457-97907738	A549	lung:	n/a	n/a
18	CTCF	chr3:97907500-97907650	HepG2	liver:	n/a	n/a
19	CTCF	chr3:97904113-97904299	HepG2	liver:	n/a	n/a
20	CTCF	chr3:97907483-97907663	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr3:97904080-97904230	GM12870	blood:	n/a	n/a
22	CTCF	chr3:97907460-97907610	GM12869	blood:	n/a	n/a
23	CTCF	chr3:97904140-97904290	Caco-2	colon:	n/a	n/a
24	CTCF	chr3:97904160-97904310	NHEK	skin:	n/a	n/a
25	CTCF	chr3:97907820-97907970	GM12865	blood:	n/a	n/a
26	CTCF	chr3:97904140-97904290	HRE	kidney:	n/a	n/a
27	CTCF	chr3:97907480-97907630	AoAF	blood vessel:	n/a	n/a
28	CTCF	chr3:97907455-97907730	LNCaP	prostate:	n/a	n/a
29	CTCF	chr3:97907321-97907742	MCF-7	breast:	n/a	n/a
30	CTCF	chr3:97903808-97904617	HCT-116	colon:	n/a	n/a
31	CTCF	chr3:97907500-97907650	AG04449	skin:	n/a	n/a
32	CTCF	chr3:97907500-97907650	BE2_C	brain:	n/a	n/a
33	CTCF	chr3:97907600-97907750	NHDF-neo	bronchial:	n/a	n/a
34	CTCF	chr3:97904120-97904270	GM12875	blood:	n/a	n/a
35	CTCF	chr3:97904160-97904310	GM12873	blood:	n/a	n/a
36	CTCF	chr3:97907500-97907650	GM12867	blood:	n/a	n/a
37	CTCF	chr3:97907500-97907650	HL-60	blood:	n/a	n/a
38	CTCF	chr3:97904072-97904296	A549	lung:	n/a	n/a
39	CTCF	chr3:97904160-97904310	HCPEpiC	choroid plexus:	n/a	n/a
40	CTCF	chr3:97907560-97907710	BE2_C	brain:	n/a	n/a
41	CTCF	chr3:97904140-97904290	GM12878	blood:	n/a	n/a
42	CTCF	chr3:97904100-97904250	GM12865	blood:	n/a	n/a
43	CTCF	chr3:97907481-97907677	GM13977	blood:	n/a	n/a
44	CTCF	chr3:97904176-97904272	ProgFib	skin:	n/a	n/a
45	CTCF	chr3:97907540-97907690	GM12872	blood:	n/a	n/a
46	CTCF	chr3:97904029-97904420	GM12878	blood:	n/a	n/a
47	CTCF	chr3:97907405-97907670	A549	lung:	n/a	n/a
48	CTCF	chr3:97903930-97904436	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:97907520-97907670	GM12878	blood:	n/a	n/a
50	CTCF	chr3:97904115-97904305	GM19238	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:97907135..97908282-chr3:98048120..98049025,6	MCF-7	breast:
2	chr3:97907135..97908080-chr3:98062563..98063391,2	MCF-7	breast:
3	chr3:97904894..97907628-chr3:98045904..98048505,2	K562	blood:
4	chr3:97758293..97759189-chr3:97903652..97904697,9	MCF-7	breast:
5	chr3:97757849..97759434-chr3:97903672..97904727,17	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MINA-6	chr3:97904268-97904295	NONHSAT090787
2	lnc-MINA-6	chr3:97916789-97916922	NONHSAT090787
3	lnc-OR5H15-1	chr3:97915250-97915894	XLOC_002733
4	lnc-OR5H15-1	chr3:97915253-97915894	XLOC_002733
5	lnc-MINA-6	chr3:97925331-97925450	NONHSAT090787
6	lnc-OR5H15-1	chr3:97910049-97910454	XLOC_002733
7	lnc-OR5H15-1	chr3:97912268-97912342	XLOC_002733
8	lnc-OR5H15-1	chr3:97910049-97910454	XLOC_002733
9	lnc-MINA-6	chr3:97923366-97923509	NONHSAT090787
10	lnc-OR5H15-1	chr3:97912268-97912342	XLOC_002733

No data

Variant related genes	Relation type
OR5H5P	TF binding region
OR5H4P	TF binding region
OR5H3P	TF binding region
FAM46C	miRNA target sites
LYPD3	miRNA target sites
TGFB2	miRNA target sites

Extended variants
information (count: 2506 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:2506 , 50 per page) page: 1 2 3 4 5 6 7 ... 51

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9883962	chr3:97899419-97899420	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs573319984	chr3:97899425-97899426	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs143885387	chr3:97899427-97899428	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs112680495	chr3:97899428-97899429	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs199807242	chr3:97899430-97899431	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs66680941	chr3:97899432-97899433	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs199713557	chr3:97899433-97899434	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs560886389	chr3:97899438-97899439	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs114704834	chr3:97899442-97899443	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs147246325	chr3:97899476-97899477	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs76758153	chr3:97899505-97899506	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs9860699	chr3:97899535-97899536	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs551989509	chr3:97899540-97899541	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs571772798	chr3:97899550-97899551	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs188963200	chr3:97899557-97899558	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs369651182	chr3:97899569-97899570	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs556804808	chr3:97899590-97899591	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs72922822	chr3:97899603-97899604	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs193207805	chr3:97899604-97899605	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs545349238	chr3:97899629-97899630	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs9880245	chr3:97899634-97899635	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs9860882	chr3:97899648-97899649	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs182236314	chr3:97899651-97899652	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs186546499	chr3:97899655-97899656	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs142908835	chr3:97899676-97899677	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs575383623	chr3:97899681-97899682	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs544032997	chr3:97899687-97899688	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs370055038	chr3:97899707-97899708	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs529905522	chr3:97899762-97899763	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs9861160	chr3:97899769-97899770	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs144533223	chr3:97899818-97899819	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs377388918	chr3:97899828-97899829	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs532022006	chr3:97899890-97899891	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs552241510	chr3:97899902-97899903	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs9864963	chr3:97899914-97899915	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs531111395	chr3:97899915-97899916	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs191189043	chr3:97899921-97899922	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs56741748	chr3:97899922-97899923	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs184109534	chr3:97899954-97899955	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs189806025	chr3:97899963-97899964	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs566816294	chr3:97899991-97899992	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs538695057	chr3:97899994-97899995	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs559003393	chr3:97899996-97899997	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs192995332	chr3:97900002-97900003	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs544317808	chr3:97900005-97900006	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs79089286	chr3:97900009-97900010	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs9865124	chr3:97900012-97900013	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs9809399	chr3:97900047-97900048	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs79076455	chr3:97900060-97900061	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs532130449	chr3:97900078-97900079	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

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
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:97899400-97899800	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr3:97899400-97900000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr3:97899400-97900800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:97900000-97900200	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr3:97900400-97902000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:97900400-97902400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:97901000-97901800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:97901000-97902200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:97901400-97902000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:97901400-97902000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:97901400-97902200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:97902000-97907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:97902200-97906400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:97902200-97907200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:97902400-97907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:97906400-97906800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:97906800-97907000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:97906800-97907000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:97906800-97908000	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:97906800-97908400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:97907000-97907400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:97907000-97908000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:97907000-97908000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:97907000-97908200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:97907000-97910200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:97907200-97907600	Enhancers	Primary T cells from cord blood	blood
27	chr3:97907200-97907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:97907200-97907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:97907200-97907600	Enhancers	GM12878-XiMat	blood
30	chr3:97907200-97907800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:97907400-97908400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:97908200-97908600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:97908400-97910000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:97908600-97908800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:97908800-97910800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:97910000-97912200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr3:97910200-97910400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:97910200-97910800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:97910400-97913600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:97910800-97911400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:97910800-97913800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr3:97911400-97911600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:97911600-97912000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:97912000-97912600	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:97912200-97914600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr3:97912600-97916000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:97913600-97913800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:97913600-97914400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:97913800-97915400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:97914400-97917600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links