Variant report

Variant	nsv820061
Chromosome Location	chr3:56648862-56650174
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	CTCF	chr3:56649436-56649475	ProgFib	skin:	n/a	n/a
2	FOS	chr3:56649395-56649664	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:56649450-56649587	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA2	chr3:56648935-56649091	HepG2	liver:	n/a	n/a
5	MAFK	chr3:56650162-56651062	GM12878	blood:	n/a	chr3:56650692-56650707
6	POLR2A	chr3:56649481-56649510	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:56649188-56649638	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:56649140-56649193	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:56648967-56664047	K562	blood:	n/a	n/a
10	POLR2A	chr3:56649132-56649587	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:56649770-56650050	K562	blood:	n/a	n/a
12	POLR2A	chr3:56649121-56649139	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:56650093-56650979	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:56649161-56649167	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:69 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571573632	chr3:56648862-56648863	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs34723346	chr3:56648869-56648870	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs188791343	chr3:56648991-56648992	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs536915076	chr3:56649030-56649031	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs62256023	chr3:56649033-56649034	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs368606194	chr3:56649073-56649074	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs567510457	chr3:56649099-56649100	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs375700553	chr3:56649117-56649118	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs6768855	chr3:56649126-56649127	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs372886360	chr3:56649141-56649142	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs147410213	chr3:56649146-56649147	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs140838811	chr3:56649165-56649166	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs139701955	chr3:56649192-56649193	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs147405993	chr3:56649206-56649207	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs201097901	chr3:56649219-56649220	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs142612378	chr3:56649229-56649230	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs61743975	chr3:56649252-56649253	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs61743979	chr3:56649256-56649257	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs145123713	chr3:56649257-56649258	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs6807338	chr3:56649282-56649283	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs368059707	chr3:56649304-56649305	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs201708195	chr3:56649305-56649306	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs6807408	chr3:56649309-56649310	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs184859178	chr3:56649313-56649314	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs36051378	chr3:56649320-56649321	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs374993386	chr3:56649346-56649347	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs563354906	chr3:56649360-56649361	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs561027079	chr3:56649369-56649370	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs531805142	chr3:56649387-56649388	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs551612354	chr3:56649389-56649390	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs571600193	chr3:56649391-56649392	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs564505852	chr3:56649423-56649424	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs547681479	chr3:56649469-56649470	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs6445801	chr3:56649594-56649595	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs536556614	chr3:56649604-56649605	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs187761786	chr3:56649639-56649640	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs570175069	chr3:56649658-56649659	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs113252705	chr3:56649719-56649720	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs538702387	chr3:56649739-56649740	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs558399974	chr3:56649746-56649747	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs4681903	chr3:56649759-56649760	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs113644977	chr3:56649762-56649763	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs192325874	chr3:56649767-56649768	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs540982044	chr3:56649812-56649813	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs202139142	chr3:56649909-56649910	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs112775968	chr3:56649919-56649920	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs559949584	chr3:56649920-56649921	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs369681089	chr3:56649950-56649951	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs543762687	chr3:56649971-56649972	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs375152503	chr3:56649972-56649973	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Cancer	20164919	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Lung adenocarcinoma	21935476	CNVD
Breast cancer	22522925	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
10	chr3:56640000-56650000	Weak transcription	HMEC	breast
11	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:56640800-56649400	Weak transcription	Osteobl	bone
16	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
17	chr3:56640800-56650400	Weak transcription	NHLF	lung
18	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
19	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood
24	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
26	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:56644800-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:56644800-56649600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:56645000-56650600	Weak transcription	A549	lung
37	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr3:56645600-56649200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:56645600-56650600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:56645600-56653400	Weak transcription	Fetal Heart	heart
46	chr3:56645600-56656000	Strong transcription	Fetal Intestine Large	intestine
47	chr3:56645600-56656000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
50	chr3:56645800-56662000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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