Variant report

Variant	nsv961776
Chromosome Location	chr2:54755470-54757189
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:54756642-54756956	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:54756554-54757039	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:54756665-54756960	HepG2	liver:	n/a	n/a
4	FOXA1	chr2:54756599-54757113	HepG2	liver:	n/a	n/a
5	FOXA2	chr2:54756624-54756931	HepG2	liver:	n/a	n/a
6	GATA3	chr2:54757015-54757490	MCF-7	breast:	n/a	chr2:54757215-54757225 chr2:54757336-54757349
7	GATA3	chr2:54757141-54757320	SH-SY5Y	brain:	n/a	chr2:54757215-54757225
8	MAFF	chr2:54757086-54757340	HepG2	liver:	n/a	n/a
9	MAFK	chr2:54757014-54757330	HepG2	liver:	n/a	n/a
10	MAFK	chr2:54757041-54757329	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:54757020-54757382	SK-N-MC	brain:	n/a	n/a
12	ZNF384	chr2:54757034-54757057	GM12878	blood:	n/a	n/a
13	ZNF384	chr2:54756937-54757496	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:54756403-54756453	NHDF-neo	bronchial:	n/a
2	chr2:54756247-54756297	RPTEC	kidney:	n/a
3	chr2:54756247-54756297	NT2-D1	testis:	n/a
4	chr2:54756247-54756297	HCF	heart:	n/a
5	chr2:54756247-54756297	K562	blood:	n/a
6	chr2:54756247-54756297	SKMC	muscle:	n/a
7	chr2:54756403-54756453	AG04449	skin:	fetal
8	chr2:54756403-54756453	ProgFib	skin:	n/a
9	chr2:54756247-54756297	CMK	blood:	n/a
10	chr2:54756247-54756297	AG09309	skin:	n/a
11	chr2:54756403-54756453	K562	blood:	n/a
12	chr2:54756403-54756453	HEEpiC	esophagus:	n/a
13	chr2:54756247-54756297	GM12892	blood:	n/a
14	chr2:54756403-54756453	HUVEC	blood vessel:	n/a
15	chr2:54756247-54756297	NH-A	brain:	n/a
16	chr2:54756403-54756453	HPAEpiC	pulmonary alveolar:	n/a
17	chr2:54756403-54756453	SK-N-SH_RA	brain:	n/a
18	chr2:54756247-54756297	HCPEpiC	choroid plexus:	n/a
19	chr2:54756247-54756297	HCT-116	colon:	n/a
20	chr2:54756403-54756453	NHBE	bronchial:	n/a
21	chr2:54756247-54756297	HUVEC	blood vessel:	n/a
22	chr2:54756247-54756297	A549	lung:	n/a
23	chr2:54756403-54756453	HRE	kidney:	n/a
24	chr2:54756247-54756297	AG10803	skin:	n/a
25	chr2:54756247-54756297	AG04449	skin:	fetal
26	chr2:54756403-54756453	A549	lung:	n/a
27	chr2:54756247-54756297	GM12878	blood:	n/a
28	chr2:54756403-54756453	Hepatocyte	liver:	n/a
29	chr2:54756247-54756297	LNCaP	prostate:	n/a
30	chr2:54756403-54756453	HNPCEpiC	eye:	n/a
31	chr2:54756403-54756453	PANC-1	pancreas:	n/a
32	chr2:54756247-54756297	HMEC	breast:	n/a
33	chr2:54756247-54756297	Jurkat	blood:	n/a
34	chr2:54756403-54756453	IMR90	lung:	fetal
35	chr2:54756403-54756453	MCF10A-Er-Src	breast:	n/a
36	chr2:54756247-54756297	PFSK-1	brain:	n/a
37	chr2:54756403-54756453	BJ	skin:	n/a
38	chr2:54756403-54756453	HCT-116	colon:	n/a
39	chr2:54756403-54756453	BE2_C	brain:	n/a
40	chr2:54756403-54756453	AG09309	skin:	n/a
41	chr2:54756247-54756297	HIPEpiC	eye:	n/a
42	chr2:54756403-54756453	U87	brain:	n/a
43	chr2:54756403-54756453	HAEpiC	amniotic membrane:	n/a
44	chr2:54756247-54756297	HNPCEpiC	eye:	n/a
45	chr2:54756247-54756297	BE2_C	brain:	n/a
46	chr2:54756247-54756297	HRCEpiC	kidney:	n/a
47	chr2:54756403-54756453	SKMC	muscle:	n/a
48	chr2:54756247-54756297	NHBE	bronchial:	n/a
49	chr2:54756403-54756453	HepG2	liver:	n/a
50	chr2:54756403-54756453	Hela-S3	cervix:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:
2	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:

No data

Variant related genes	Relation type
RPL23AP32	TF binding region
RPL23AP32	CpG island
ENSG00000115306	chromatin interactions

Extended variants
information (count: 94 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:94 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192376358	chr2:54755551-54755552	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs541157801	chr2:54755569-54755570	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs560854732	chr2:54755652-54755653	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs529760086	chr2:54755653-54755654	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs568711534	chr2:54755675-54755676	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs549804105	chr2:54755678-54755679	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs570286803	chr2:54755683-54755684	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs532707973	chr2:54755687-54755688	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs184538193	chr2:54755698-54755699	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs373952751	chr2:54755704-54755705	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs544351805	chr2:54755721-54755722	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs371284257	chr2:54755735-54755736	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs376736777	chr2:54755760-54755761	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs566169979	chr2:54755780-54755781	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs534778599	chr2:54755804-54755805	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs557655997	chr2:54755812-54755813	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs147265083	chr2:54755815-54755816	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs199545647	chr2:54755835-54755836	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs10591541	chr2:54755837-54755838	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs571163284	chr2:54755838-54755839	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs397869606	chr2:54755852-54755853	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs4319969	chr2:54755878-54755879	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs537003236	chr2:54755948-54755949	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs569657241	chr2:54755975-54755976	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs557088188	chr2:54756006-54756007	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs150543482	chr2:54756010-54756011	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs200337687	chr2:54756049-54756050	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs13415931	chr2:54756084-54756085	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs4519565	chr2:54756086-54756087	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs560470203	chr2:54756087-54756088	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs375508207	chr2:54756101-54756102	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs199674248	chr2:54756125-54756126	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs145841076	chr2:54756126-54756127	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs572307261	chr2:54756200-54756201	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs541121007	chr2:54756204-54756205	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs369314693	chr2:54756232-54756233	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs560915991	chr2:54756248-54756249	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs140836730	chr2:54756275-54756276	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs543406235	chr2:54756277-54756278	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs192732406	chr2:54756284-54756285	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs532818589	chr2:54756285-54756286	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs142265861	chr2:54756287-54756288	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs566253477	chr2:54756288-54756289	Weak transcription Genic enhancers Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs528707278	chr2:54756333-54756334	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs573654094	chr2:54756356-54756357	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs115643541	chr2:54756364-54756365	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs542261860	chr2:54756372-54756373	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs568176679	chr2:54756375-54756376	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs537165667	chr2:54756386-54756387	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs185021373	chr2:54756388-54756389	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

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
Pancreatic cancer	17952125	CNVD

Chromatin state (count:157 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
11	chr2:54750600-54757000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:54751000-54756800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:54752000-54756200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
20	chr2:54752000-54764600	Weak transcription	Gastric	stomach
21	chr2:54752200-54759600	Weak transcription	Small Intestine	intestine
22	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:54752400-54757000	Weak transcription	Hela-S3	cervix
25	chr2:54752400-54758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:54752400-54758000	Weak transcription	Aorta	Aorta
27	chr2:54752400-54758000	Weak transcription	NHEK	skin
28	chr2:54752400-54758200	Weak transcription	Fetal Thymus	thymus
29	chr2:54752400-54759600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:54752600-54758000	Weak transcription	HMEC	breast
31	chr2:54752600-54758600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:54752600-54759800	Weak transcription	GM12878-XiMat	blood
33	chr2:54753000-54755800	Strong transcription	NHLF	lung
34	chr2:54753000-54758800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:54753000-54759000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:54753200-54755600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:54753200-54755600	Genic enhancers	Fetal Heart	heart
38	chr2:54753200-54756200	Strong transcription	HepG2	liver
39	chr2:54753200-54756400	Genic enhancers	HSMMtube	muscle
40	chr2:54753200-54756800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:54753200-54756800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:54753200-54757000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:54753200-54757400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:54753200-54757400	Strong transcription	Fetal Brain Female	brain
45	chr2:54753200-54758000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:54753200-54758200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:54753200-54759800	Strong transcription	Adipose Nuclei	Adipose
48	chr2:54753400-54755600	Genic enhancers	Brain Anterior Caudate	brain
49	chr2:54753400-54755800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:54753400-54756800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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