Variant report

Variant	nsv874128
Chromosome Location	chr2:52814504-52859829
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	CEBPB	chr2:52834390-52834658	IMR90	lung:	n/a	chr2:52834518-52834527 chr2:52834516-52834527 chr2:52834517-52834528 chr2:52834518-52834527 chr2:52834518-52834527 chr2:52834518-52834527
2	CEBPB	chr2:52841343-52841411	A549	lung:	n/a	n/a
3	CEBPB	chr2:52834381-52834700	K562	blood:	n/a	chr2:52834518-52834527 chr2:52834516-52834527 chr2:52834517-52834528 chr2:52834518-52834527 chr2:52834518-52834527 chr2:52834518-52834527
4	CEBPB	chr2:52834371-52834680	HepG2	liver:	n/a	chr2:52834518-52834527 chr2:52834516-52834527 chr2:52834517-52834528 chr2:52834518-52834527 chr2:52834518-52834527 chr2:52834518-52834527
5	CTCF	chr2:52859780-52860019	H1-hESC	embryonic stem cell:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
6	CTCF	chr2:52840340-52840490	Caco-2	colon:	n/a	chr2:52840412-52840430
7	CTCF	chr2:52840360-52840510	HCT-116	colon:	n/a	chr2:52840412-52840430
8	CTCF	chr2:52840300-52840450	HEK293	kidney:	n/a	chr2:52840412-52840430
9	CTCF	chr2:52840340-52840490	NB4	blood:	n/a	chr2:52840412-52840430
10	CTCF	chr2:52840295-52840495	GM12878	blood:	n/a	chr2:52840412-52840430
11	CTCF	chr2:52859794-52859958	H1-hESC	embryonic stem cell:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
12	CTCF	chr2:52840250-52840511	H1-hESC	embryonic stem cell:	n/a	chr2:52840412-52840430
13	CTCF	chr2:52840340-52840490	MCF-7	breast:	n/a	chr2:52840412-52840430
14	CTCF	chr2:52840320-52840470	HBMEC	blood vessel:	n/a	chr2:52840412-52840430
15	CTCF	chr2:52859760-52859910	HBMEC	blood vessel:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
16	CTCF	chr2:52840349-52840416	MCF-7	breast:	n/a	n/a
17	CTCF	chr2:52840337-52840438	HepG2	liver:	n/a	chr2:52840412-52840430
18	CTCF	chr2:52840354-52840449	ProgFib	skin:	n/a	chr2:52840412-52840430
19	CTCF	chr2:52840340-52840490	HCPEpiC	choroid plexus:	n/a	chr2:52840412-52840430
20	CTCF	chr2:52840371-52840464	HepG2	liver:	n/a	chr2:52840412-52840430
21	CTCF	chr2:52859820-52859970	BE2_C	brain:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
22	CTCF	chr2:52840343-52840467	MCF-7	breast:	n/a	chr2:52840412-52840430
23	CTCF	chr2:52840360-52840510	HPF	lung:	n/a	chr2:52840412-52840430
24	CTCF	chr2:52840224-52840534	H1-hESC	embryonic stem cell:	n/a	chr2:52840412-52840430
25	CTCF	chr2:52859780-52859930	WERI-Rb-1	eye:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
26	CTCF	chr2:52840360-52840510	MCF-7	breast:	n/a	chr2:52840412-52840430
27	CTCF	chr2:52840360-52840510	A549	lung:	n/a	chr2:52840412-52840430
28	CTCF	chr2:52859820-52859942	MCF-7	breast:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
29	CTCF	chr2:52840300-52840450	AG04449	skin:	n/a	chr2:52840412-52840430
30	CTCF	chr2:52840369-52840451	H1-hESC	embryonic stem cell:	n/a	chr2:52840412-52840430
31	CTCF	chr2:52840320-52840470	HPAF	blood vessel:	n/a	chr2:52840412-52840430
32	CTCF	chr2:52828593-52828660	Lung_OC	lung:	n/a	n/a
33	CTCF	chr2:52840340-52840490	HCM	heart:	n/a	chr2:52840412-52840430
34	CTCF	chr2:52840300-52840450	HMEC	breast:	n/a	chr2:52840412-52840430
35	CTCF	chr2:52840334-52840452	MCF-7	breast:	n/a	chr2:52840412-52840430
36	CTCF	chr2:52840317-52840514	Hela-S3	cervix:	n/a	chr2:52840412-52840430
37	CTCF	chr2:52840306-52840516	MCF-7	breast:	n/a	chr2:52840412-52840430
38	CTCF	chr2:52840417-52840418	MCF-7	breast:	n/a	n/a
39	CTCF	chr2:52840360-52840510	Caco-2	colon:	n/a	chr2:52840412-52840430
40	CTCF	chr2:52840308-52840494	A549	lung:	n/a	chr2:52840412-52840430
41	CTCF	chr2:52840228-52840664	HCT-116	colon:	n/a	chr2:52840412-52840430
42	CTCF	chr2:52840282-52840600	IMR90	lung:	n/a	chr2:52840412-52840430
43	CTCF	chr2:52842660-52842810	HepG2	liver:	n/a	n/a
44	CTCF	chr2:52840360-52840510	Hela-S3	cervix:	n/a	chr2:52840412-52840430
45	CTCF	chr2:52840319-52840508	LNCaP	prostate:	n/a	chr2:52840412-52840430
46	CTCF	chr2:52840360-52840510	HCPEpiC	choroid plexus:	n/a	chr2:52840412-52840430
47	CTCF	chr2:52840400-52840550	A549	lung:	n/a	chr2:52840412-52840430
48	CTCF	chr2:52840340-52840490	HPF	lung:	n/a	chr2:52840412-52840430
49	CTCF	chr2:52840340-52840490	WERI-Rb-1	eye:	n/a	chr2:52840412-52840430
50	CTCF	chr2:52840300-52840450	HEEpiC	esophagus:	n/a	chr2:52840412-52840430

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:52857018-52857068	NHBE	bronchial:	n/a
2	chr2:52856495-52856545	AG04449	skin:	fetal
3	chr2:52856495-52856545	HCPEpiC	choroid plexus:	n/a
4	chr2:52856751-52856801	AG04449	skin:	fetal
5	chr2:52856495-52856545	SK-N-MC	brain:	n/a
6	chr2:52856751-52856801	AG10803	skin:	n/a
7	chr2:52856495-52856545	LNCaP	prostate:	n/a
8	chr2:52857018-52857068	SAEC	small airway:	n/a
9	chr2:52857018-52857068	SKMC	muscle:	n/a
10	chr2:52857018-52857068	ProgFib	skin:	n/a
11	chr2:52856918-52856968	SKMC	muscle:	n/a
12	chr2:52856751-52856801	SAEC	small airway:	n/a
13	chr2:52856495-52856545	AG04450	lung:	fetal
14	chr2:52856495-52856545	BE2_C	brain:	n/a
15	chr2:52856918-52856968	Caco-2	colon:	n/a
16	chr2:52856918-52856968	HCPEpiC	choroid plexus:	n/a
17	chr2:52856918-52856968	NHBE	bronchial:	n/a
18	chr2:52856751-52856801	AG04450	lung:	fetal
19	chr2:52856751-52856801	HRPEpiC	eye:	n/a
20	chr2:52856495-52856545	NHBE	bronchial:	n/a
21	chr2:52856918-52856968	HRE	kidney:	n/a
22	chr2:52856918-52856968	SK-N-SH_RA	brain:	n/a
23	chr2:52856495-52856545	AoSMC	blood vessel:	n/a
24	chr2:52857018-52857068	HCT-116	colon:	n/a
25	chr2:52857018-52857068	HRCEpiC	kidney:	n/a
26	chr2:52856918-52856968	AG09309	skin:	n/a
27	chr2:52856918-52856968	HL-60	blood:	n/a
28	chr2:52856918-52856968	PFSK-1	brain:	n/a
29	chr2:52856918-52856968	Jurkat	blood:	n/a
30	chr2:52856495-52856545	HCT-116	colon:	n/a
31	chr2:52856751-52856801	RPTEC	kidney:	n/a
32	chr2:52856918-52856968	ovcar-3	ovarian:	n/a
33	chr2:52856495-52856545	MCF10A-Er-Src	breast:	n/a
34	chr2:52856918-52856968	CMK	blood:	n/a
35	chr2:52856751-52856801	ovcar-3	ovarian:	n/a
36	chr2:52856918-52856968	AG09319	gingival:	n/a
37	chr2:52856918-52856968	AoSMC	blood vessel:	n/a
38	chr2:52856495-52856545	PrEC	prostate:	n/a
39	chr2:52857018-52857068	HMEC	breast:	n/a
40	chr2:52856751-52856801	HPAEpiC	pulmonary alveolar:	n/a
41	chr2:52856751-52856801	ProgFib	skin:	n/a
42	chr2:52856918-52856968	HRPEpiC	eye:	n/a
43	chr2:52856751-52856801	SK-N-SH_RA	brain:	n/a
44	chr2:52857018-52857068	AG09309	skin:	n/a
45	chr2:52856751-52856801	GM19239	blood:	n/a
46	chr2:52856495-52856545	NHDF-neo	bronchial:	n/a
47	chr2:52856918-52856968	NT2-D1	testis:	n/a
48	chr2:52857018-52857068	HIPEpiC	eye:	n/a
49	chr2:52857018-52857068	HAEpiC	amniotic membrane:	n/a
50	chr2:52856918-52856968	AG10803	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:52840541..52843528-chr2:52846569..52849939,3	K562	blood:
2	chr2:52859439..52860286-chr4:132071047..132072003,2	MCF-7	breast:
3	chr2:52644535..52645157-chr2:52839947..52840842,2	MCF-7	breast:
4	chr2:52840541..52843528-chr2:52846569..52849939,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC2-8	chr2:52857033-52857216	NONHSAT070675
2	lnc-CHAC2-8	chr2:52856881-52857016	NONHSAT070675

Variant related genes	Relation type
FTH1P6	TF binding region
FTH1P6	CpG island

Extended variants
information (count: 932 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:932 , 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	rs2170794	chr2:52814504-52814505	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs79939936	chr2:52814567-52814568	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs191543703	chr2:52814610-52814611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs575725023	chr2:52814623-52814624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs541233515	chr2:52814626-52814627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs544921993	chr2:52814655-52814656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs372553744	chr2:52814686-52814687	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs376460386	chr2:52814709-52814710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs371573106	chr2:52814712-52814713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs150472426	chr2:52814716-52814717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs564677626	chr2:52814717-52814718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs200216665	chr2:52814718-52814719	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs201656379	chr2:52814719-52814720	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs6730992	chr2:52814754-52814755	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs532149456	chr2:52814794-52814795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs575032545	chr2:52814799-52814800	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs184908998	chr2:52814804-52814805	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs559507907	chr2:52814834-52814835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs528170344	chr2:52814847-52814848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs547954703	chr2:52814858-52814859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188061028	chr2:52814883-52814884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs4672176	chr2:52814901-52814902	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs192827332	chr2:52814928-52814929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs567950930	chr2:52814957-52814958	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs539456444	chr2:52814967-52814968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs185308779	chr2:52814974-52814975	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs563734623	chr2:52814975-52814976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs142669342	chr2:52815114-52815115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs146019055	chr2:52815201-52815202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs555560399	chr2:52815204-52815205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs575833096	chr2:52815239-52815240	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs538050341	chr2:52815240-52815241	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs148722179	chr2:52815260-52815261	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs62128489	chr2:52815264-52815265	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs545839740	chr2:52815311-52815312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs559421869	chr2:52815312-52815313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs150859756	chr2:52815352-52815353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs2356464	chr2:52815370-52815371	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs559630235	chr2:52815399-52815400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs374615233	chr2:52815421-52815422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs376550112	chr2:52815433-52815434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs189422159	chr2:52815440-52815441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs530737771	chr2:52815470-52815471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs550461367	chr2:52815481-52815482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs114409991	chr2:52815500-52815501	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs2356465	chr2:52815505-52815506	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs546467910	chr2:52815527-52815528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs199943842	chr2:52815582-52815583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144405493	chr2:52815583-52815584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs368301753	chr2:52815584-52815585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	23813976	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52813200-52819200	Weak transcription	Dnd41	blood
2	chr2:52819200-52819600	ZNF genes & repeats	Dnd41	blood
3	chr2:52819600-52821200	Weak transcription	Dnd41	blood
4	chr2:52820600-52820800	Enhancers	HUVEC	blood vessel
5	chr2:52821000-52821400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr2:52821000-52821600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:52821000-52821600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:52821200-52821600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:52821200-52821600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:52821200-52821600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:52821200-52821600	Active TSS	Brain Hippocampus Middle	brain
12	chr2:52821200-52821800	Enhancers	Fetal Kidney	kidney
13	chr2:52821200-52822000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:52821200-52823000	Enhancers	Dnd41	blood
15	chr2:52827400-52827800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:52839000-52839400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:52839000-52839400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:52839000-52839400	Enhancers	Fetal Heart	heart
19	chr2:52839000-52839800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:52839000-52839800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:52839000-52840400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:52839200-52840000	Enhancers	Fetal Brain Male	brain
23	chr2:52839400-52844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:52839800-52840600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:52840600-52844800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:52844400-52845200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:52844600-52845000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:52844800-52845200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr2:52844800-52845400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr2:52844800-52845600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:52846000-52846600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:52846600-52847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:52847600-52848800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:52847800-52850600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:52848000-52848200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:52848400-52848800	Enhancers	Brain Cingulate Gyrus	brain
37	chr2:52848800-52849200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:52848800-52849200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:52849200-52850000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:52849200-52850000	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:52849400-52849600	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links