Variant report

Variant	esv3496928
Chromosome Location	chr2:173179937-173186324
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr2:173185901-173186116	GM12878	blood:	n/a	n/a
2	FOXA2	chr2:173185923-173186231	A549	lung:	n/a	n/a
3	FOXA2	chr2:173180149-173180735	A549	lung:	n/a	n/a
4	FOXA2	chr2:173180175-173180704	A549	lung:	n/a	n/a
5	HEY1	chr2:173179915-173180125	K562	blood:	n/a	n/a
6	NR3C1	chr2:173185975-173186161	A549	lung:	n/a	n/a
7	POLR2A	chr2:173179947-173180176	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:173180018-173180064	K562	blood:	n/a	n/a
9	REST	chr2:173186011-173186104	GM12878	blood:	n/a	n/a
10	REST	chr2:173185974-173186111	PANC-1	pancreas:	n/a	n/a
11	SRF	chr2:173185966-173186070	GM12878	blood:	n/a	n/a
12	YY1	chr2:173179882-173180075	K562	blood:	n/a	n/a
13	YY1	chr2:173179915-173180118	K562	blood:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA6-2	chr2:173180016-173180136	NONHSAT075499
2	lnc-ITGA6-1	chr2:173180015-173180136	XLOC_001757

No data

Variant related genes	Relation type
ENSG00000232555	TF binding region
KIAA0319L	miRNA target sites

Extended variants
information (count: 62 )
Associated
traits (count: 44 )

Variant overlapped rSNPs/rCNVs (count:62 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540998048	chr2:173179973-173179974	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs71407944	chr2:173179996-173179997	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs4972791	chr2:173179998-173179999	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs544776065	chr2:173180016-173180017	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs563402531	chr2:173180030-173180031	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs4972485	chr2:173180034-173180035	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs549570540	chr2:173180049-173180050	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs112878802	chr2:173180162-173180163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs567592698	chr2:173180166-173180167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs528739707	chr2:173180167-173180168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs546923062	chr2:173180205-173180206	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs370280428	chr2:173180248-173180249	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs374608022	chr2:173180347-173180348	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs368166127	chr2:173180364-173180365	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs538694432	chr2:173180368-173180369	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs371863133	chr2:173180391-173180392	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs575584818	chr2:173180440-173180441	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs13030719	chr2:173180458-173180459	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs200468739	chr2:173180629-173180630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs12998902	chr2:173180646-173180647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs6719299	chr2:173180699-173180700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs200798838	chr2:173180763-173180764	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs201626864	chr2:173180788-173180789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs528908594	chr2:173181148-173181149	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs201028152	chr2:173181327-173181328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs558971417	chr2:173181329-173181330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs569341308	chr2:173181330-173181331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs199591505	chr2:173181403-173181404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs374117885	chr2:173185908-173185909	Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs377613149	chr2:173185944-173185945	Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs373343780	chr2:173186011-173186012	Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs377523136	chr2:173186012-173186013	Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs35494823	chr2:173186039-173186040	Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs368110758	chr2:173186040-173186041	Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs28719067	chr2:173186049-173186050	Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs28446979	chr2:173186051-173186052	Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs372033584	chr2:173186055-173186056	Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs373995236	chr2:173186056-173186057	Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs28551668	chr2:173186066-173186067	Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs28626782	chr2:173186070-173186071	Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs28538810	chr2:173186076-173186077	Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs555556838	chr2:173186077-173186078	Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs76150554	chr2:173186080-173186081	Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs11679316	chr2:173186081-173186082	Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs573907184	chr2:173186090-173186091	Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs138268051	chr2:173186096-173186097	Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs397705216	chr2:173186104-173186105	Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs11450856	chr2:173186105-173186106	Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs201551731	chr2:173186130-173186131	Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs199598044	chr2:173186131-173186132	Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:44)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	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
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	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
Colorectal cancer	16272173	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Glioblastoma	21080181	CNVD
small cell lung cancer	20016488	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Prostate cancer	16573809	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Donnai-Barrow syndrome	21085971	CNVD
Breast cancer	21045282	CNVD
Limb abnormalities	22140379	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173173000-173181600	Weak transcription	Right Atrium	heart
2	chr2:173180200-173180600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:173185800-173186200	Active TSS	GM12878-XiMat	blood
4	chr2:173186200-173186600	ZNF genes & repeats	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links