Variant report

Variant	esv3404703
Chromosome Location	chr2:99087420-99091918
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99091313..99093056-chr2:99094548..99096331,2	MCF-7	breast:
2	chr2:99085620..99087469-chr2:99095244..99097109,2	MCF-7	breast:
3	chr2:99067851..99070035-chr2:99087756..99089685,2	MCF-7	breast:
4	chr2:99081238..99085183-chr2:99088495..99091939,4	MCF-7	breast:
5	chr2:99068438..99070988-chr2:99085301..99087852,2	MCF-7	breast:
6	chr2:99085593..99087784-chr2:99223919..99225454,2	K562	blood:
7	chr2:99087794..99090481-chr2:99092257..99095199,3	K562	blood:
8	chr2:99084143..99087030-chr2:99088678..99090271,2	K562	blood:
9	chr2:99091514..99094203-chr2:99098934..99100639,2	MCF-7	breast:
10	chr2:99089938..99092200-chr2:99129449..99131064,2	K562	blood:
11	chr2:99088177..99090481-chr2:99093421..99095199,2	K562	blood:
12	chr2:99080684..99083981-chr2:99090485..99094412,5	MCF-7	breast:
13	chr2:99061357..99062955-chr2:99088853..99091234,2	MCF-7	breast:
14	chr2:98994035..98996505-chr2:99085390..99088257,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNGA3-1	chr2:99089791-99090054	NONHSAT072704
2	lnc-CNGA3-1	chr2:99089196-99089730	NONHSAT072704

No data

Variant related genes	Relation type
ENSG00000144191	chromatin interactions
ENSG00000115446	chromatin interactions
ENSG00000183513	chromatin interactions
ENSG00000040933	chromatin interactions

Extended variants
information (count: 175 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:175 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534322142	chr2:99087476-99087477	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs557990868	chr2:99087526-99087527	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs138353926	chr2:99087534-99087535	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs185902761	chr2:99087565-99087566	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs371129468	chr2:99087590-99087591	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs142752733	chr2:99087605-99087606	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs574066634	chr2:99087623-99087624	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs542722344	chr2:99087647-99087648	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs553528322	chr2:99087663-99087664	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs573226232	chr2:99087673-99087674	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs146075193	chr2:99087675-99087676	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs563080527	chr2:99087676-99087677	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs533119290	chr2:99087754-99087755	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs139936265	chr2:99087758-99087759	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs563371388	chr2:99087759-99087760	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs530427244	chr2:99087783-99087784	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs529099780	chr2:99087834-99087835	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs548854253	chr2:99087859-99087860	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs548638850	chr2:99087873-99087874	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs565447259	chr2:99087895-99087896	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs192416789	chr2:99087941-99087942	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs551008880	chr2:99087950-99087951	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs183738490	chr2:99087956-99087957	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs537380501	chr2:99087978-99087979	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs557654036	chr2:99087994-99087995	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs567732696	chr2:99088005-99088006	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs3754891	chr2:99088018-99088019	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs553461056	chr2:99088053-99088054	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs187436797	chr2:99088068-99088069	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs149432619	chr2:99088072-99088073	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs559017296	chr2:99088074-99088075	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs527856646	chr2:99088091-99088092	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs144769836	chr2:99088093-99088094	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs190343896	chr2:99088100-99088101	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs563621197	chr2:99088129-99088130	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs573714169	chr2:99088218-99088219	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs372424377	chr2:99088279-99088280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs542455198	chr2:99088288-99088289	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs559020182	chr2:99088320-99088321	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs376481974	chr2:99088322-99088323	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs528201141	chr2:99088328-99088329	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs76939825	chr2:99088338-99088339	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs564694007	chr2:99088347-99088348	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs148566313	chr2:99088355-99088356	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs550948751	chr2:99088361-99088362	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs182872697	chr2:99088369-99088370	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs187162086	chr2:99088403-99088404	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs192656460	chr2:99088472-99088473	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs547259026	chr2:99088476-99088477	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs34632912	chr2:99088482-99088483	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	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
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:329 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99072400-99095000	Weak transcription	Fetal Intestine Large	intestine
2	chr2:99072600-99119600	Weak transcription	Aorta	Aorta
3	chr2:99075600-99091800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:99076400-99095400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:99078400-99095600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:99080200-99094200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:99080400-99091400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:99081400-99095800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:99081800-99091400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:99082200-99089800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:99082200-99091400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:99082400-99088600	Weak transcription	Psoas Muscle	Psoas
13	chr2:99082400-99090200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:99082600-99088200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:99082600-99088400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:99082600-99088400	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:99082600-99088400	Weak transcription	Fetal Lung	lung
18	chr2:99082600-99088600	Weak transcription	Gastric	stomach
19	chr2:99082600-99096200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:99083000-99087600	Weak transcription	Pancreas	Pancrea
21	chr2:99083000-99088400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:99083000-99088400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:99083000-99089600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:99083000-99091000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:99083200-99090000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr2:99083200-99091400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:99083200-99091400	Weak transcription	HMEC	breast
28	chr2:99083200-99091800	Weak transcription	NHEK	skin
29	chr2:99083200-99093000	Weak transcription	Fetal Heart	heart
30	chr2:99083200-99094200	Weak transcription	Placenta	Placenta
31	chr2:99083400-99087600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:99083400-99088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:99083400-99088600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:99083600-99088200	Weak transcription	Right Atrium	heart
35	chr2:99083600-99088200	Weak transcription	Stomach Mucosa	stomach
36	chr2:99083600-99088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:99083600-99090000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:99083600-99090800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:99083800-99090000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:99083800-99094400	Weak transcription	Dnd41	blood
41	chr2:99084000-99088800	Weak transcription	Brain Angular Gyrus	brain
42	chr2:99084000-99088800	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:99084000-99090000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:99084000-99090400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:99084000-99091600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:99084200-99087600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:99084200-99090000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:99084200-99090000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr2:99084200-99090600	Weak transcription	Fetal Brain Female	brain
50	chr2:99084800-99095600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links