Variant report

Variant	esv2763113
Chromosome Location	chr2:231441828-231445303
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr2:231442774-231443381	GM12878	blood:	n/a	n/a
2	ATF2	chr2:231442846-231443279	GM12878	blood:	n/a	n/a
3	BATF	chr2:231442929-231443221	GM12878	blood:	n/a	n/a
4	BATF	chr2:231442925-231443233	GM12878	blood:	n/a	n/a
5	BCL11A	chr2:231442887-231443253	GM12878	blood:	n/a	chr2:231443028-231443037 chr2:231443168-231443177
6	BCLAF1	chr2:231442812-231443426	GM12878	blood:	n/a	chr2:231443028-231443037 chr2:231443168-231443177
7	BHLHE40	chr2:231441953-231442155	K562	blood:	n/a	chr2:231442091-231442104 chr2:231442094-231442103 chr2:231442087-231442108
8	BHLHE40	chr2:231442912-231443163	GM12878	blood:	n/a	n/a
9	CEBPB	chr2:231442781-231443370	GM12878	blood:	n/a	n/a
10	CTCF	chr2:231444500-231444650	GM12875	blood:	n/a	n/a
11	CTCF	chr2:231444440-231444590	GM12875	blood:	n/a	n/a
12	CTCF	chr2:231444460-231444610	GM12864	blood:	n/a	n/a
13	CTCF	chr2:231444420-231444570	GM12873	blood:	n/a	n/a
14	CTCF	chr2:231441800-231441950	HepG2	liver:	n/a	n/a
15	CTCF	chr2:231444520-231444670	GM12870	blood:	n/a	n/a
16	EP300	chr2:231442910-231443184	GM12878	blood:	n/a	chr2:231443168-231443182
17	ETS1	chr2:231442837-231443198	GM12878	blood:	n/a	chr2:231443168-231443179 chr2:231443028-231443039 chr2:231443172-231443179 chr2:231443166-231443180 chr2:231443028-231443041 chr2:231443168-231443183 chr2:231443168-231443181
18	FOXM1	chr2:231442846-231443342	GM12878	blood:	n/a	n/a
19	IKZF1	chr2:231442828-231443297	GM12878	blood:	n/a	n/a
20	IRF4	chr2:231442846-231443308	GM12878	blood:	n/a	n/a
21	MAX	chr2:231441890-231442024	K562	blood:	n/a	n/a
22	MEF2A	chr2:231442857-231443213	GM12878	blood:	n/a	n/a
23	MTA3	chr2:231442750-231443326	GM12878	blood:	n/a	n/a
24	NFATC1	chr2:231442781-231443652	GM12878	blood:	n/a	n/a
25	NFATC1	chr2:231442826-231443502	GM12878	blood:	n/a	n/a
26	NFATC1	chr2:231444157-231444651	GM12878	blood:	n/a	n/a
27	NFIC	chr2:231442654-231443515	GM12878	blood:	n/a	n/a
28	NFIC	chr2:231442824-231443298	GM12878	blood:	n/a	n/a
29	PML	chr2:231443657-231444635	GM12878	blood:	n/a	chr2:231443791-231443799
30	PML	chr2:231442724-231443580	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:231441874-231442044	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:231444024-231444116	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:231444528-231444587	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:231445078-231445373	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:231444453-231444682	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:231445100-231445314	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:231444030-231444152	GM12878	blood:	n/a	n/a
38	RUNX3	chr2:231442670-231443316	GM12878	blood:	n/a	n/a
39	RUNX3	chr2:231442748-231443281	GM12878	blood:	n/a	n/a
40	SMC3	chr2:231442908-231443363	GM12878	blood:	n/a	n/a
41	SPI1	chr2:231442813-231443343	GM12891	blood:	n/a	chr2:231443168-231443177 chr2:231443028-231443037
42	SPI1	chr2:231442746-231443425	GM12878	blood:	n/a	chr2:231443168-231443177 chr2:231443028-231443037
43	SPI1	chr2:231442816-231443282	GM12878	blood:	n/a	chr2:231443168-231443177 chr2:231443028-231443037
44	SPI1	chr2:231442796-231443271	GM12891	blood:	n/a	chr2:231443168-231443177 chr2:231443028-231443037
45	SPI1	chr2:231442931-231443258	GM12878	blood:	n/a	chr2:231443168-231443177 chr2:231443028-231443037
46	STAT5A	chr2:231442909-231443265	GM12878	blood:	n/a	chr2:231443034-231443042 chr2:231443171-231443183
47	STAT5A	chr2:231443416-231443862	GM12878	blood:	n/a	chr2:231443801-231443809 chr2:231443774-231443786
48	TBL1XR1	chr2:231443000-231443256	GM12878	blood:	n/a	n/a
49	USF1	chr2:231441992-231442169	SK-N-SH_RA	brain:	n/a	chr2:231442091-231442104 chr2:231442094-231442103 chr2:231442087-231442108

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-1	chr2:231442842-231442911	ENSG00000235419.1
2	lnc-SP110-1	chr2:231443869-231443952	ENSG00000235419.1
3	lnc-SP110-1	chr2:231443869-231443952	ENSG00000235419.1
4	lnc-SP110-1	chr2:231444616-231444648	ENSG00000235419.1
5	lnc-SP110-1	chr2:231444620-231444721	ENSG00000235419.1
6	lnc-SP110-1	chr2:231442842-231442911	ENSG00000235419.1

Variant related genes	Relation type
TPM3P8	TF binding region
ENSG00000235419	TF binding region

Extended variants
information (count: 171 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:171 , 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	rs13418016	chr2:231441828-231441829	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs141931119	chr2:231441831-231441832	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs373891604	chr2:231441864-231441865	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs144307799	chr2:231441866-231441867	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs535187849	chr2:231441910-231441911	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs73104901	chr2:231441979-231441980	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs147786792	chr2:231441994-231441995	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs557815848	chr2:231442004-231442005	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs13418228	chr2:231442026-231442027	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs76162714	chr2:231442071-231442072	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs535089983	chr2:231442076-231442077	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs10933341	chr2:231442079-231442080	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs11689558	chr2:231442084-231442085	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs182195017	chr2:231442097-231442098	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs560553072	chr2:231442098-231442099	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs141378789	chr2:231442108-231442109	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs10804366	chr2:231442134-231442135	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs11898876	chr2:231442212-231442213	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs189194850	chr2:231442281-231442282	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs193084301	chr2:231442326-231442327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs10933342	chr2:231442359-231442360	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs112144278	chr2:231442362-231442363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs370390397	chr2:231442374-231442375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs547132778	chr2:231442396-231442397	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs553582954	chr2:231442416-231442417	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs574344195	chr2:231442449-231442450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs117952811	chr2:231442485-231442486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs150349414	chr2:231442487-231442488	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs7562389	chr2:231442496-231442497	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs575913354	chr2:231442512-231442513	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs372219757	chr2:231442552-231442553	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs528192561	chr2:231442563-231442564	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs10933343	chr2:231442572-231442573	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs113214710	chr2:231442593-231442594	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs541216839	chr2:231442634-231442635	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs560615012	chr2:231442635-231442636	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs375433209	chr2:231442647-231442648	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs572504155	chr2:231442654-231442655	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs28648648	chr2:231442663-231442664	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs7604318	chr2:231442682-231442683	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs564517981	chr2:231442691-231442692	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs531577416	chr2:231442709-231442710	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs550499778	chr2:231442710-231442711	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs13384122	chr2:231442722-231442723	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs550098413	chr2:231442753-231442754	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs562037103	chr2:231442768-231442769	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs111704343	chr2:231442769-231442770	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs547590295	chr2:231442779-231442780	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs11679760	chr2:231442787-231442788	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs146336136	chr2:231442796-231442797	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	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
Lung cancer	18438408	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cervical cancer	21062161	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Chordoma	18071362	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	22429812	CNVD
Bladder cancer	21909424	CNVD
Renal cell carcinoma	21668985	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Wilms tumour	21544195	CNVD
Esophageal adenocarcinoma	18519675	CNVD
prenatal diagnosis	22389664	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Mental retardation	20152051	CNVD
Cancer	21183584	CNVD
Albright''s disease	22277900	CNVD
Brachydactyly-Mental Retardation Syndrome	22470819	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Colorectal cancer	19359472	CNVD
Autism	18414403	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231439800-231443800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr2:231440000-231442200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:231440000-231442600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:231440200-231443400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:231440600-231443400	Enhancers	Primary T cells from cord blood	blood
6	chr2:231440800-231443000	Weak transcription	GM12878-XiMat	blood
7	chr2:231440800-231443400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:231441000-231442200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:231441000-231447200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:231441600-231442400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:231441800-231442000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:231441800-231443400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:231442000-231443000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:231442000-231443600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:231442200-231442400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:231442200-231443200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:231442400-231442800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:231442400-231442800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:231442600-231445000	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:231442800-231443400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:231442800-231443400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:231442800-231444000	Enhancers	Primary B cells from cord blood	blood
23	chr2:231442800-231444200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:231443000-231443200	Enhancers	GM12878-XiMat	blood
25	chr2:231443000-231443200	Bivalent Enhancer	HepG2	liver
26	chr2:231443000-231443400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr2:231443000-231443400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:231443200-231443400	Flanking Active TSS	GM12878-XiMat	blood
29	chr2:231443200-231443600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr2:231443200-231444000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:231443400-231443600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
32	chr2:231443400-231451000	Weak transcription	Primary T cells from cord blood	blood
33	chr2:231443400-231453800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:231443400-231454400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:231443400-231454600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:231443600-231445800	Genic enhancers	GM12878-XiMat	blood
37	chr2:231443800-231447600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:231444000-231447400	Weak transcription	Primary B cells from cord blood	blood
39	chr2:231444000-231447600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:231445000-231445400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:231445200-231445400	Enhancers	Spleen	Spleen

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