Variant report

Variant	esv3370785
Chromosome Location	chr2:98339370-98341868
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:366)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:98341820-98341970	WERI-Rb-1	eye:	n/a	n/a
2	CTCF	chr2:98341853-98342092	K562	blood:	n/a	n/a
3	CTCF	chr2:98341860-98342010	WERI-Rb-1	eye:	n/a	n/a
4	CTCF	chr2:98341840-98341990	HepG2	liver:	n/a	n/a
5	CTCF	chr2:98341794-98342177	K562	blood:	n/a	n/a
6	CTCF	chr2:98341850-98342054	HepG2	liver:	n/a	n/a
7	CTCF	chr2:98341821-98342010	K562	blood:	n/a	n/a
8	CTCF	chr2:98341856-98342040	H1-hESC	embryonic stem cell:	n/a	n/a
9	HMGN3	chr2:98340647-98340945	K562	blood:	n/a	n/a
10	RAD21	chr2:98341712-98342110	H1-hESC	embryonic stem cell:	n/a	n/a

(count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:98340073-98340123	NHBE	bronchial:	n/a
2	chr2:98341557-98341607	H1-hESC	embryonic stem cell:	embryo
3	chr2:98340655-98340705	AG09319	gingival:	n/a
4	chr2:98340425-98340475	GM12878	blood:	n/a
5	chr2:98340425-98340475	U87	brain:	n/a
6	chr2:98340511-98340561	GM12878	blood:	n/a
7	chr2:98340425-98340475	MCF10A-Er-Src	breast:	n/a
8	chr2:98341557-98341607	HEK293	kidney:	embryo
9	chr2:98340073-98340123	BE2_C	brain:	n/a
10	chr2:98340921-98340971	AG04449	skin:	fetal
11	chr2:98340921-98340971	GM06990	blood:	n/a
12	chr2:98340655-98340705	HIPEpiC	eye:	n/a
13	chr2:98340655-98340705	Caco-2	colon:	n/a
14	chr2:98340511-98340561	PrEC	prostate:	n/a
15	chr2:98341557-98341607	GM12892	blood:	n/a
16	chr2:98340921-98340971	NHBE	bronchial:	n/a
17	chr2:98340921-98340971	ProgFib	skin:	n/a
18	chr2:98340921-98340971	K562	blood:	n/a
19	chr2:98340655-98340705	HMEC	breast:	n/a
20	chr2:98340655-98340705	T-47D	breast:	n/a
21	chr2:98340073-98340123	HUVEC	blood vessel:	n/a
22	chr2:98340511-98340561	Hepatocyte	liver:	n/a
23	chr2:98340425-98340475	ProgFib	skin:	n/a
24	chr2:98340511-98340561	K562	blood:	n/a
25	chr2:98340425-98340475	NHBE	bronchial:	n/a
26	chr2:98340511-98340561	AG04449	skin:	fetal
27	chr2:98340425-98340475	GM06990	blood:	n/a
28	chr2:98341557-98341607	NT2-D1	testis:	n/a
29	chr2:98340921-98340971	HL-60	blood:	n/a
30	chr2:98340655-98340705	NB4	blood:	n/a
31	chr2:98340511-98340561	PFSK-1	brain:	n/a
32	chr2:98341557-98341607	HCT-116	colon:	n/a
33	chr2:98340073-98340123	NH-A	brain:	n/a
34	chr2:98340921-98340971	GM12891	blood:	n/a
35	chr2:98340921-98340971	PFSK-1	brain:	n/a
36	chr2:98340425-98340475	HCT-116	colon:	n/a
37	chr2:98340921-98340971	A549	lung:	n/a
38	chr2:98340511-98340561	HRPEpiC	eye:	n/a
39	chr2:98340921-98340971	HEEpiC	esophagus:	n/a
40	chr2:98340425-98340475	PANC-1	pancreas:	n/a
41	chr2:98340511-98340561	NHBE	bronchial:	n/a
42	chr2:98340425-98340475	PFSK-1	brain:	n/a
43	chr2:98340655-98340705	ECC-1	luminal epithelium:	n/a
44	chr2:98340921-98340971	CMK	blood:	n/a
45	chr2:98340073-98340123	IMR90	lung:	fetal
46	chr2:98341557-98341607	HRPEpiC	eye:	n/a
47	chr2:98340921-98340971	HCPEpiC	choroid plexus:	n/a
48	chr2:98340073-98340123	ECC-1	luminal epithelium:	n/a
49	chr2:98340073-98340123	RPTEC	kidney:	n/a
50	chr2:98340921-98340971	HRCEpiC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr2:98340167..98342272-chr2:98350738..98353485,2	MCF-7	breast:
2	chr2:98207043..98207962-chr2:98341661..98342410,2	MCF-7	breast:
3	chr2:98326581..98329549-chr2:98337971..98340144,2	MCF-7	breast:
4	chr2:98331870..98333821-chr2:98339114..98340858,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZAP70	TF binding region
ZAP70	CpG island
ENSG00000115085	chromatin interactions

Extended variants
information (count: 122 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:122 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192303396	chr2:98339405-98339406	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs568158430	chr2:98339418-98339419	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs527435848	chr2:98339444-98339445	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs60433076	chr2:98339462-98339463	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs13033383	chr2:98339513-98339514	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs539366843	chr2:98339592-98339593	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs555861595	chr2:98339611-98339612	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs141524200	chr2:98339631-98339632	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs535188762	chr2:98339636-98339637	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs57831860	chr2:98339664-98339665	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs572177808	chr2:98339708-98339709	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs541600255	chr2:98339777-98339778	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs74495591	chr2:98339781-98339782	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs578243075	chr2:98339783-98339784	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs558650107	chr2:98339847-98339848	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs574631320	chr2:98339851-98339852	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs544124607	chr2:98339857-98339858	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs577146097	chr2:98339859-98339860	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs544535047	chr2:98339882-98339883	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs563518982	chr2:98339886-98339887	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs562830979	chr2:98339977-98339978	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs542657096	chr2:98340073-98340074	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	CpG island	1 gene(s)	Overlapped CNVs	n/a
23	rs559380486	chr2:98340078-98340079	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	CpG island	1 gene(s)	Overlapped CNVs	n/a
24	rs184647250	chr2:98340095-98340096	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	CpG island	1 gene(s)	Overlapped CNVs	n/a
25	rs75699372	chr2:98340109-98340110	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	CpG island	1 gene(s)	Overlapped CNVs	n/a
26	rs75096652	chr2:98340124-98340125	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs60173117	chr2:98340145-98340146	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs550087075	chr2:98340154-98340155	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs569550149	chr2:98340219-98340220	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs535384729	chr2:98340245-98340246	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs555080416	chr2:98340330-98340331	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs6712517	chr2:98340364-98340365	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs559852316	chr2:98340398-98340399	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs201916152	chr2:98340436-98340437	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs200098110	chr2:98340462-98340463	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs572934153	chr2:98340463-98340464	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs189212561	chr2:98340482-98340483	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs201403055	chr2:98340483-98340484	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs199904922	chr2:98340484-98340485	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs531121007	chr2:98340499-98340500	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs201017088	chr2:98340503-98340504	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs202216858	chr2:98340520-98340521	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs200425356	chr2:98340526-98340527	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs36014221	chr2:98340545-98340546	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs201125862	chr2:98340578-98340579	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs373708142	chr2:98340579-98340580	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs201941891	chr2:98340588-98340589	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs200409156	chr2:98340601-98340602	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs56127120	chr2:98340604-98340605	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs56077145	chr2:98340605-98340606	Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	17483303	CNVD
Medulloblastoma	20607354	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Lung cancer	18438408	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	21509527	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Glioblastoma multiforme	21138945	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Tetralogy of Fallot	22912587	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98332000-98340000	Weak transcription	Esophagus	oesophagus
2	chr2:98333600-98341800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:98335000-98344800	Weak transcription	Right Atrium	heart
4	chr2:98336000-98339600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:98336000-98339800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr2:98336000-98340400	Weak transcription	Spleen	Spleen
7	chr2:98336000-98344400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:98336000-98346000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:98336200-98345000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr2:98336200-98345600	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr2:98336200-98345800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr2:98336200-98351200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:98336400-98340200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:98336400-98345000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:98336400-98346000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:98336400-98361400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:98336600-98346200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:98336600-98346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:98336600-98358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:98337400-98343800	Strong transcription	Fetal Thymus	thymus
21	chr2:98337400-98346600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:98337600-98339600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:98337800-98340000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:98337800-98343200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:98337800-98357400	Strong transcription	Dnd41	blood
26	chr2:98338000-98339800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:98338600-98339800	Genic enhancers	Primary T cells from cord blood	blood
28	chr2:98338600-98340400	Enhancers	Placenta	Placenta
29	chr2:98338600-98341000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:98338800-98358800	Strong transcription	Thymus	Thymus
31	chr2:98339200-98339400	Enhancers	Fetal Heart	heart
32	chr2:98339200-98341400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:98339200-98345800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:98339400-98342800	Weak transcription	HSMMtube	muscle
35	chr2:98339600-98339800	Enhancers	Fetal Muscle Trunk	muscle
36	chr2:98339600-98340200	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr2:98339600-98340800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:98339600-98357200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:98339800-98341800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:98339800-98341800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:98339800-98342000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr2:98339800-98342200	Strong transcription	Primary T cells from cord blood	blood
43	chr2:98340000-98340600	ZNF genes & repeats	Esophagus	oesophagus
44	chr2:98340000-98341600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:98340200-98341000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:98340400-98340600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr2:98340400-98340800	Bivalent Enhancer	Placenta	Placenta
48	chr2:98340400-98341000	ZNF genes & repeats	Lung	lung
49	chr2:98340400-98341000	Enhancers	Pancreas	Pancrea
50	chr2:98340400-98341000	ZNF genes & repeats	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links