Variant report

Variant	nsv875954
Chromosome Location	chr2:231421531-231441828
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	ATF3	chr2:231440402-231440663	K562	blood:	n/a	n/a
2	BATF	chr2:231429516-231429826	GM12878	blood:	n/a	n/a
3	BATF	chr2:231434019-231434263	GM12878	blood:	n/a	chr2:231434114-231434125
4	BCL11A	chr2:231436984-231437184	GM12878	blood:	n/a	n/a
5	BCLAF1	chr2:231429404-231429865	GM12878	blood:	n/a	n/a
6	CBX3	chr2:231440344-231440726	K562	blood:	n/a	n/a
7	CEBPB	chr2:231430624-231430838	A549	lung:	n/a	chr2:231430738-231430749 chr2:231430740-231430751
8	CEBPB	chr2:231430730-231430785	K562	blood:	n/a	chr2:231430738-231430749 chr2:231430740-231430751
9	CEBPB	chr2:231430605-231430872	HepG2	liver:	n/a	chr2:231430738-231430749 chr2:231430740-231430751
10	CEBPB	chr2:231430617-231430885	IMR90	lung:	n/a	chr2:231430738-231430749 chr2:231430740-231430751
11	CHD2	chr2:231429655-231429740	GM12878	blood:	n/a	n/a
12	CTCF	chr2:231430240-231430390	GM12872	blood:	n/a	chr2:231430273-231430294
13	CTCF	chr2:231437087-231437168	LNCaP	prostate:	n/a	n/a
14	CTCF	chr2:231435900-231436050	GM12873	blood:	n/a	n/a
15	CTCF	chr2:231435840-231435990	GM12871	blood:	n/a	n/a
16	CTCF	chr2:231426486-231426533	GM13977	blood:	n/a	n/a
17	CTCF	chr2:231422340-231422490	NHDF-neo	bronchial:	n/a	n/a
18	CTCF	chr2:231435880-231436030	GM12864	blood:	n/a	n/a
19	CTCF	chr2:231426429-231426510	MCF-7	breast:	n/a	n/a
20	CTCF	chr2:231429016-231429168	K562	blood:	n/a	n/a
21	CTCF	chr2:231435720-231435870	HCT-116	colon:	n/a	n/a
22	CTCF	chr2:231435880-231436030	GM12873	blood:	n/a	n/a
23	CTCF	chr2:231430242-231430316	Fibrobl	skin:	n/a	chr2:231430273-231430294
24	CTCF	chr2:231440140-231440290	HepG2	liver:	n/a	n/a
25	CTCF	chr2:231435840-231435990	HMF	breast:	n/a	n/a
26	CTCF	chr2:231430180-231430330	GM12865	blood:	n/a	chr2:231430273-231430294
27	CTCF	chr2:231435820-231435970	GM12873	blood:	n/a	n/a
28	CTCF	chr2:231430140-231430290	GM12873	blood:	n/a	n/a
29	CTCF	chr2:231435880-231436030	GM12872	blood:	n/a	n/a
30	CTCF	chr2:231430180-231430330	GM12866	blood:	n/a	chr2:231430273-231430294
31	CTCF	chr2:231435800-231435950	GM12874	blood:	n/a	n/a
32	CTCF	chr2:231435840-231435990	GM12867	blood:	n/a	n/a
33	CTCF	chr2:231435820-231435970	GM12875	blood:	n/a	n/a
34	CTCF	chr2:231435800-231435950	HEK293	kidney:	n/a	n/a
35	CTCF	chr2:231435780-231435930	GM12872	blood:	n/a	n/a
36	CTCF	chr2:231441800-231441950	HepG2	liver:	n/a	n/a
37	CTCF	chr2:231435800-231435950	HepG2	liver:	n/a	n/a
38	CTCF	chr2:231429920-231430070	GM12869	blood:	n/a	n/a
39	CTCF	chr2:231435840-231435990	HCFaa	heart:	n/a	n/a
40	E2F4	chr2:231429744-231429823	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F6	chr2:231440466-231440616	K562	blood:	n/a	n/a
42	EBF1	chr2:231430009-231430370	GM12878	blood:	n/a	n/a
43	EP300	chr2:231429600-231429716	GM12878	blood:	n/a	n/a
44	EP300	chr2:231440532-231440642	K562	blood:	n/a	n/a
45	FOS	chr2:231429960-231430131	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr2:231429932-231430177	MCF10A-Er-Src	breast:	n/a	chr2:231430167-231430176
47	FOS	chr2:231429920-231430135	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr2:231430009-231430161	MCF10A-Er-Src	breast:	n/a	n/a
49	FOSL1	chr2:231440361-231440717	K562	blood:	n/a	chr2:231440575-231440584
50	FOXA1	chr2:231436473-231436931	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-1	chr2:231435355-231435430	ENSG00000235419.1
2	lnc-SP110-1	chr2:231440637-231440741	ENSG00000235419.1
3	lnc-SP110-1	chr2:231440637-231440741	ENSG00000235419.1

Variant related genes	Relation type
TPM3P8	TF binding region

Extended variants
information (count: 906 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:906 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1678154	chr2:231421531-231421532	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs115096102	chr2:231421535-231421536	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs189542592	chr2:231421552-231421553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs575475177	chr2:231421574-231421575	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs571910578	chr2:231421585-231421586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs373844247	chr2:231421592-231421593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs11680387	chr2:231421610-231421611	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs77576746	chr2:231421615-231421616	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs180943099	chr2:231421616-231421617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs544310043	chr2:231421677-231421678	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs1678155	chr2:231421683-231421684	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs577109264	chr2:231421701-231421702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs544227799	chr2:231421709-231421710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs564297869	chr2:231421724-231421725	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs577376138	chr2:231421725-231421726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs542549976	chr2:231421762-231421763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560721263	chr2:231421787-231421788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs80070702	chr2:231421831-231421832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs185014348	chr2:231421834-231421835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs564052665	chr2:231421838-231421839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs540040915	chr2:231421892-231421893	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs191079839	chr2:231421909-231421910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs181733664	chr2:231421915-231421916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs374572642	chr2:231421920-231421921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs572837358	chr2:231421938-231421939	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs535034429	chr2:231421954-231421955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs7584134	chr2:231421964-231421965	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs565606995	chr2:231421995-231421996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs539285020	chr2:231422040-231422041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs560502939	chr2:231422051-231422052	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs11406010	chr2:231422065-231422066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs7584149	chr2:231422075-231422076	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs80336114	chr2:231422098-231422099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs538329523	chr2:231422184-231422185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs35829056	chr2:231422244-231422245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs560184736	chr2:231422302-231422303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs574889789	chr2:231422335-231422336	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs111800614	chr2:231422337-231422338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs7584696	chr2:231422378-231422379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs560801051	chr2:231422385-231422386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs115295543	chr2:231422459-231422460	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs546126144	chr2:231422508-231422509	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs527460705	chr2:231422511-231422512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs529361844	chr2:231422518-231422519	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs564692291	chr2:231422529-231422530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs531769516	chr2:231422535-231422536	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs1678156	chr2:231422554-231422555	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs187010507	chr2:231422587-231422588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs386656136	chr2:231422629-231422630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs11687105	chr2:231422631-231422632	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231401000-231430200	Weak transcription	Pancreas	Pancrea
2	chr2:231410200-231428800	Weak transcription	Primary B cells from cord blood	blood
3	chr2:231426600-231427200	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:231427200-231429000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:231428800-231429400	Enhancers	Primary B cells from cord blood	blood
6	chr2:231429000-231429400	Enhancers	GM12878-XiMat	blood
7	chr2:231429000-231429800	Enhancers	K562	blood
8	chr2:231429000-231430600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:231429000-231430600	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:231429200-231429400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:231429200-231429400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr2:231429400-231429600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr2:231429400-231429800	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr2:231429400-231429800	Flanking Active TSS	GM12878-XiMat	blood
15	chr2:231429400-231430200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr2:231429400-231430600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:231429400-231430600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:231429400-231431000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr2:231429600-231429800	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:231429600-231430400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:231429600-231430400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:231429600-231430400	Enhancers	Fetal Thymus	thymus
23	chr2:231429600-231430600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:231429800-231430200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:231429800-231430600	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:231429800-231430600	Enhancers	GM12878-XiMat	blood
27	chr2:231429800-231431000	Enhancers	Primary B cells from cord blood	blood
28	chr2:231430000-231430400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:231430000-231430400	Enhancers	Psoas Muscle	Psoas
30	chr2:231430200-231430400	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr2:231430200-231430400	Enhancers	Pancreas	Pancrea
32	chr2:231430200-231430600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr2:231430200-231430600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:231430200-231430600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr2:231431000-231434000	Weak transcription	Primary B cells from cord blood	blood
36	chr2:231436200-231436600	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr2:231436600-231440000	Weak transcription	Primary T cells from cord blood	blood
38	chr2:231439400-231440800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr2:231439800-231440200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr2:231439800-231440600	Enhancers	Placenta	Placenta
41	chr2:231439800-231440800	Enhancers	Fetal Thymus	thymus
42	chr2:231439800-231443800	Enhancers	Primary T cells fromperipheralblood	blood
43	chr2:231440000-231440200	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr2:231440000-231440600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:231440000-231440800	Enhancers	K562	blood
46	chr2:231440000-231441000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:231440000-231441000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:231440000-231442200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:231440000-231442600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:231440200-231440400	Enhancers	Primary T cells from cord blood	blood

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