Variant report

Variant	nsv2904
Chromosome Location	chr2:126428107-126467337
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	BACH1	chr2:126458745-126458939	K562	blood:	n/a	n/a
2	BACH1	chr2:126458688-126458954	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr2:126462546-126463195	HepG2	liver:	n/a	chr2:126462632-126462645 chr2:126463016-126463027
4	CEBPB	chr2:126459761-126460068	HepG2	liver:	n/a	chr2:126459891-126459902
5	CEBPB	chr2:126462893-126463185	A549	lung:	n/a	chr2:126463016-126463027
6	CEBPB	chr2:126462938-126463121	H1-hESC	embryonic stem cell:	n/a	chr2:126463016-126463027
7	CEBPB	chr2:126430195-126430582	HepG2	liver:	n/a	chr2:126430336-126430347
8	CEBPB	chr2:126459773-126460015	A549	lung:	n/a	chr2:126459891-126459902
9	CEBPB	chr2:126464113-126464382	HepG2	liver:	n/a	n/a
10	CEBPB	chr2:126462587-126463186	IMR90	lung:	n/a	chr2:126462632-126462645 chr2:126463016-126463027
11	CEBPB	chr2:126456504-126456579	HepG2	liver:	n/a	n/a
12	CEBPB	chr2:126459757-126460046	Hela-S3	cervix:	n/a	chr2:126459891-126459902
13	CEBPB	chr2:126430277-126430417	H1-hESC	embryonic stem cell:	n/a	chr2:126430336-126430347
14	CEBPB	chr2:126457168-126457434	A549	lung:	n/a	chr2:126457350-126457363 chr2:126457351-126457362
15	CEBPB	chr2:126430155-126430949	Hela-S3	cervix:	n/a	chr2:126430336-126430347
16	CEBPB	chr2:126457190-126457461	HepG2	liver:	n/a	chr2:126457350-126457363 chr2:126457351-126457362
17	CHD2	chr2:126437689-126437846	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr2:126460860-126461010	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr2:126463740-126463890	GM12866	blood:	n/a	n/a
20	CTCF	chr2:126454081-126454105	HepG2	liver:	n/a	n/a
21	CTCF	chr2:126435289-126435369	GM13976	blood:	n/a	n/a
22	CTCF	chr2:126456540-126456690	GM12867	blood:	n/a	n/a
23	CTCF	chr2:126454040-126454190	GM06990	blood:	n/a	n/a
24	CTCF	chr2:126432669-126432760	GM13976	blood:	n/a	n/a
25	E2F4	chr2:126436783-126436890	MCF10A-Er-Src	breast:	n/a	n/a
26	E2F4	chr2:126454291-126454606	MCF10A-Er-Src	breast:	n/a	n/a
27	EP300	chr2:126454112-126454580	T-47D	breast:	n/a	chr2:126454451-126454461
28	EP300	chr2:126428276-126428457	GM12878	blood:	n/a	n/a
29	EP300	chr2:126454138-126454736	T-47D	breast:	n/a	chr2:126454657-126454671 chr2:126454451-126454461
30	EP300	chr2:126454248-126454492	Hela-S3	cervix:	n/a	chr2:126454451-126454461
31	FOS	chr2:126430217-126430509	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr2:126454306-126454540	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr2:126458740-126458941	MCF10A-Er-Src	breast:	n/a	chr2:126458841-126458849 chr2:126458841-126458849 chr2:126458841-126458848
34	FOS	chr2:126437715-126437897	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr2:126430249-126430500	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr2:126459855-126459917	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr2:126430733-126431067	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr2:126459799-126460042	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr2:126454166-126454578	MCF10A-Er-Src	breast:	n/a	n/a
40	FOS	chr2:126454166-126454610	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr2:126459885-126459902	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr2:126454246-126454511	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr2:126430733-126431063	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr2:126430309-126430416	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr2:126430163-126430510	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr2:126430749-126431054	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr2:126430733-126431335	MCF10A-Er-Src	breast:	n/a	n/a
48	FOXA1	chr2:126453929-126454598	T-47D	breast:	n/a	chr2:126454063-126454075 chr2:126454446-126454461
49	FOXA1	chr2:126454035-126454601	T-47D	breast:	n/a	chr2:126454063-126454075 chr2:126454446-126454461
50	FOXA1	chr2:126452821-126453113	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:126441721..126443799-chr2:126451980..126453632,2	K562	blood:
2	chr2:126441149..126442866-chr2:126450432..126451944,2	K562	blood:
3	chr2:126441149..126442866-chr2:126450432..126451944,2	K562	blood:
4	chr2:126423393..126427272-chr2:126428665..126431892,3	K562	blood:
5	chr2:126441721..126443799-chr2:126451980..126453632,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTNAP5-2	chr2:126456152-126456276	FPKM1_group_17139_transcript_1
2	lnc-CNTNAP5-2	chr2:126457983-126458113	FPKM1_group_17139_transcript_1
3	lnc-BIN1-3	chr2:126464387-126464754	XLOC_002307
4	lnc-BIN1-3	chr2:126464386-126464754	NONHSAT074119
5	lnc-CNTNAP5-2	chr2:126456152-126456276	NONHSAT074117

Variant related genes	Relation type
ENSG00000235491	TF binding region
KCNC4	miRNA target sites

Extended variants
information (count: 626 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:626 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs371367990	chr2:126428142-126428143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs574168070	chr2:126428177-126428178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs541906112	chr2:126437210-126437211	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs561777830	chr2:126437277-126437278	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs527661427	chr2:126437304-126437305	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs147702946	chr2:126437309-126437310	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs57441255	chr2:126437315-126437316	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs191908241	chr2:126437317-126437318	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs532207959	chr2:126437360-126437361	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs552445701	chr2:126437365-126437366	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs564170077	chr2:126437384-126437385	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs183230899	chr2:126437402-126437403	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs531466095	chr2:126437405-126437406	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs142149363	chr2:126437445-126437446	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs559915833	chr2:126437473-126437474	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs533746133	chr2:126437474-126437475	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs145919511	chr2:126437483-126437484	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs11896494	chr2:126437498-126437499	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs539735511	chr2:126437575-126437576	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs11896542	chr2:126437623-126437624	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs576209906	chr2:126437667-126437668	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs73953965	chr2:126437703-126437704	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs138844155	chr2:126437708-126437709	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs572360454	chr2:126437738-126437739	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs148892438	chr2:126437763-126437764	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs7425477	chr2:126437766-126437767	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs561650138	chr2:126437773-126437774	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs12996707	chr2:126437781-126437782	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs565177303	chr2:126437815-126437816	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs562699940	chr2:126437825-126437826	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs531505054	chr2:126437828-126437829	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs143604456	chr2:126437832-126437833	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs147980425	chr2:126437857-126437858	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs371143929	chr2:126437886-126437887	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs527392057	chr2:126437922-126437923	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs113338319	chr2:126437923-126437924	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs187834611	chr2:126437941-126437942	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs192347729	chr2:126437951-126437952	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs372711972	chr2:126437975-126437976	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs550269789	chr2:126437982-126437983	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs550035430	chr2:126438016-126438017	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs569934497	chr2:126438034-126438035	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs535613937	chr2:126438055-126438056	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs555446245	chr2:126438062-126438063	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs572546400	chr2:126438087-126438088	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs534797658	chr2:126438101-126438102	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs114426295	chr2:126438103-126438104	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs1529380	chr2:126438106-126438107	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs73953966	chr2:126438107-126438108	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs539036844	chr2:126438157-126438158	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	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
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
Splenic marginal zone lymphoma	21957467	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Colorectal cancer	16272173	CNVD
myoclonus epilepsy	18472482	CNVD
Benign familial neonatal-infantile seizures	18472482	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Mental retardation	17621639	CNVD
Acute myeloid leukemia	21251322	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Medulloblastoma	16968546	CNVD
Neurocytoma	17123091	CNVD
Developmental delay	21147756	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:126427800-126428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:126437200-126437600	Enhancers	Adipose Nuclei	Adipose
3	chr2:126437200-126438600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:126437600-126438000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:126437600-126438600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr2:126437800-126438200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr2:126437800-126438200	Enhancers	Hela-S3	cervix
8	chr2:126438000-126438600	Enhancers	Colonic Mucosa	Colon
9	chr2:126438000-126439200	Enhancers	Brain Substantia Nigra	brain
10	chr2:126438200-126438400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr2:126438200-126438600	Enhancers	Brain Anterior Caudate	brain
12	chr2:126438200-126439400	Enhancers	Brain Hippocampus Middle	brain
13	chr2:126438400-126439400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:126438600-126439000	Enhancers	Adipose Nuclei	Adipose
15	chr2:126438600-126440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:126438800-126439200	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:126439000-126439400	Weak transcription	Adipose Nuclei	Adipose
18	chr2:126439400-126440800	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr2:126439400-126441200	Enhancers	Adipose Nuclei	Adipose
20	chr2:126440000-126440200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:126440600-126441400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:126441400-126443000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:126441600-126443200	Enhancers	GM12878-XiMat	blood
24	chr2:126442800-126443200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr2:126443000-126443200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:126451800-126453200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:126453800-126454200	Enhancers	Brain Substantia Nigra	brain
28	chr2:126453800-126454600	Enhancers	Brain Hippocampus Middle	brain
29	chr2:126454000-126455200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr2:126454000-126455200	Enhancers	Hela-S3	cervix
31	chr2:126454200-126455200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:126462200-126463000	Enhancers	Brain Germinal Matrix	brain
33	chr2:126463000-126466200	Weak transcription	Brain Germinal Matrix	brain
34	chr2:126466200-126466400	Enhancers	Brain Germinal Matrix	brain
35	chr2:126466600-126467200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:126467200-126470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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