Variant report

Variant	nsv963232
Chromosome Location	chr2:54249008-54261054
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	ARID3A	chr2:54257321-54257392	K562	blood:	n/a	n/a
2	CCNT2	chr2:54257215-54257395	K562	blood:	n/a	n/a
3	CEBPD	chr2:54257122-54257484	K562	blood:	n/a	n/a
4	CTCF	chr2:54259880-54260030	Caco-2	colon:	n/a	n/a
5	EP300	chr2:54257248-54257463	K562	blood:	n/a	n/a
6	FOS	chr2:54260911-54261199	MCF10A-Er-Src	breast:	n/a	chr2:54261050-54261061
7	FOS	chr2:54260920-54261187	MCF10A-Er-Src	breast:	n/a	chr2:54261050-54261061
8	FOS	chr2:54260901-54261179	MCF10A-Er-Src	breast:	n/a	chr2:54261050-54261061
9	FOS	chr2:54260927-54261213	HUVEC	blood vessel:	n/a	chr2:54261050-54261061
10	GATA1	chr2:54257085-54257505	PBDE	blood:	n/a	n/a
11	GATA2	chr2:54257205-54257568	K562	blood:	n/a	n/a
12	KAP1	chr2:54257241-54257714	HEK293	kidney:	n/a	n/a
13	KAP1	chr2:54252477-54252839	U2OS	brain:	n/a	n/a
14	POLR2A	chr2:54259939-54259985	MCF10A-Er-Src	breast:	n/a	n/a
15	RCOR1	chr2:54257279-54257491	K562	blood:	n/a	n/a
16	SETDB1	chr2:54252378-54252861	U2OS	brain:	n/a	n/a
17	STAT3	chr2:54260775-54261211	MCF10A-Er-Src	breast:	n/a	chr2:54261023-54261031 chr2:54261051-54261060 chr2:54261020-54261034 chr2:54261021-54261032 chr2:54261017-54261037
18	STAT3	chr2:54250354-54250510	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr2:54260834-54261186	MCF10A-Er-Src	breast:	n/a	chr2:54261023-54261031 chr2:54261051-54261060 chr2:54261020-54261034 chr2:54261021-54261032 chr2:54261017-54261037
20	STAT3	chr2:54260890-54261186	MCF10A-Er-Src	breast:	n/a	chr2:54261023-54261031 chr2:54261051-54261060 chr2:54261020-54261034 chr2:54261021-54261032 chr2:54261017-54261037
21	TAL1	chr2:54257292-54257475	K562	blood:	n/a	n/a
22	TEAD4	chr2:54252869-54253136	ECC-1	luminal epithelium:	n/a	n/a
23	TEAD4	chr2:54257187-54257543	K562	blood:	n/a	n/a
24	TEAD4	chr2:54252919-54253122	ECC-1	luminal epithelium:	n/a	n/a
25	TEAD4	chr2:54252898-54253100	H1-hESC	embryonic stem cell:	n/a	n/a
26	TEAD4	chr2:54252794-54253135	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54247772..54249970-chr2:54252060..54254811,2	MCF-7	breast:
2	chr2:54247772..54249970-chr2:54252060..54254811,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSME4-2	chr2:54249535-54249668	NONHSAT070719
2	lnc-PSME4-1	chr2:54256689-54257003	NONHSAT070721
3	lnc-PSME4-1	chr2:54257723-54257819	NONHSAT070721
4	lnc-ACYP2-5	chr2:54254065-54254992	NONHSAT070720
5	lnc-ACYP2-4	chr2:54259644-54261288	NONHSAT070722
6	lnc-PSME4-2	chr2:54248557-54249107	NONHSAT070719

Variant related genes	Relation type
ENSG00000235937	TF binding region

Extended variants
information (count: 541 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:541 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs376369100	chr2:54249021-54249022	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
2	rs141094387	chr2:54249041-54249042	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
3	rs547548551	chr2:54249045-54249046	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
4	rs567481467	chr2:54249076-54249077	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
5	rs530017183	chr2:54249088-54249089	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
6	rs535617538	chr2:54249116-54249117	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs569680399	chr2:54249120-54249121	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs546269741	chr2:54249141-54249142	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs186422358	chr2:54249180-54249181	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs10084374	chr2:54249312-54249313	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs374604340	chr2:54249374-54249375	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs190825373	chr2:54249409-54249410	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs555162540	chr2:54249416-54249417	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs11694388	chr2:54249433-54249434	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs574908917	chr2:54249450-54249451	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs544096533	chr2:54249472-54249473	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs62140983	chr2:54249496-54249497	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs557189475	chr2:54249517-54249518	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs576863915	chr2:54249544-54249545	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
20	rs368884278	chr2:54249562-54249563	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
21	rs114643987	chr2:54249624-54249625	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
22	rs528903742	chr2:54249632-54249633	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
23	rs182975029	chr2:54249666-54249667	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
24	rs561139988	chr2:54249668-54249669	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
25	rs143495646	chr2:54249685-54249686	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs529811706	chr2:54249687-54249688	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs550140352	chr2:54249707-54249708	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs11688581	chr2:54249728-54249729	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs188540995	chr2:54249754-54249755	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs552188973	chr2:54249770-54249771	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs555036822	chr2:54249804-54249805	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs565509183	chr2:54249817-54249818	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs534741299	chr2:54249863-54249864	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs554318561	chr2:54249866-54249867	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs74387700	chr2:54249868-54249869	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs192732700	chr2:54249875-54249876	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs114083596	chr2:54249922-54249923	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs149879026	chr2:54249958-54249959	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs551648844	chr2:54249960-54249961	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs538098122	chr2:54249975-54249976	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs552965604	chr2:54249981-54249982	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs115088502	chr2:54250002-54250003	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs542318797	chr2:54250025-54250026	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs562032553	chr2:54250038-54250039	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs115908461	chr2:54250051-54250052	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs527449005	chr2:54250098-54250099	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs35807551	chr2:54250102-54250103	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs563611803	chr2:54250173-54250174	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs542848714	chr2:54250191-54250192	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs183088255	chr2:54250193-54250194	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

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
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
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
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
2	chr2:54240200-54257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:54242200-54251800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:54243400-54254200	Weak transcription	Fetal Stomach	stomach
5	chr2:54243800-54249200	Weak transcription	HSMMtube	muscle
6	chr2:54243800-54255400	Weak transcription	HepG2	liver
7	chr2:54243800-54268000	Weak transcription	Osteobl	bone
8	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:54244400-54254200	Weak transcription	Ovary	ovary
11	chr2:54246600-54249600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:54247200-54250000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:54247600-54249400	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr2:54248200-54250200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:54248400-54249800	Weak transcription	Gastric	stomach
17	chr2:54248400-54254600	Weak transcription	Liver	Liver
18	chr2:54248400-54256800	Weak transcription	Pancreas	Pancrea
19	chr2:54248400-54257400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:54248600-54252000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:54248600-54256800	Weak transcription	Psoas Muscle	Psoas
22	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
24	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
25	chr2:54249400-54251600	Strong transcription	Primary T cells from cord blood	blood
26	chr2:54249800-54250000	Enhancers	Gastric	stomach
27	chr2:54249800-54250000	Enhancers	Left Ventricle	heart
28	chr2:54250000-54257600	Weak transcription	Gastric	stomach
29	chr2:54250000-54257600	Weak transcription	Left Ventricle	heart
30	chr2:54251600-54263800	Weak transcription	Primary T cells from cord blood	blood
31	chr2:54252000-54252600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:54252600-54258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:54253800-54254800	Enhancers	Colon Smooth Muscle	Colon
34	chr2:54254000-54254400	Enhancers	Fetal Kidney	kidney
35	chr2:54254200-54254400	Enhancers	Fetal Stomach	stomach
36	chr2:54254200-54254600	Enhancers	Ovary	ovary
37	chr2:54254400-54254600	Enhancers	Brain Substantia Nigra	brain
38	chr2:54254600-54256800	Weak transcription	Ovary	ovary
39	chr2:54254600-54267400	Weak transcription	Brain Substantia Nigra	brain
40	chr2:54254600-54269800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:54254800-54256600	Weak transcription	Fetal Heart	heart
42	chr2:54254800-54269600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:54255400-54256000	Enhancers	HepG2	liver
44	chr2:54256000-54257600	Weak transcription	HepG2	liver
45	chr2:54256200-54258400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:54256600-54258200	Enhancers	Fetal Heart	heart
47	chr2:54256800-54257800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:54256800-54257800	Enhancers	Pancreas	Pancrea
49	chr2:54256800-54258200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:54256800-54258200	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links