Variant report

Variant	esv3335327
Chromosome Location	chr3:195662155-195665953
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr3:195662910-195663112	GM12878	blood:	n/a	n/a
2	BCL11A	chr3:195663537-195663765	GM12878	blood:	n/a	chr3:195663586-195663595
3	CTCF	chr3:195664133-195664188	Spleen_OC	spleen:	n/a	n/a
4	CTCF	chr3:195664081-195664162	LNCaP	prostate:	n/a	n/a
5	CTCF	chr3:195664124-195664199	Medullo	brain:	n/a	n/a
6	CTCF	chr3:195664112-195664146	GM13977	blood:	n/a	n/a
7	CTCF	chr3:195664112-195664202	K562	blood:	n/a	n/a
8	CTCF	chr3:195664130-195664171	GM13976	blood:	n/a	n/a
9	CTCF	chr3:195664114-195664118	Medullo	brain:	n/a	n/a
10	CTCF	chr3:195664104-195664164	GM10266	blood:	n/a	n/a
11	CTCF	chr3:195664075-195664161	GM10248	blood:	n/a	n/a
12	CTCF	chr3:195664029-195664219	K562	blood:	n/a	n/a
13	EBF1	chr3:195663974-195664237	GM12878	blood:	n/a	n/a
14	FOSL2	chr3:195662879-195663171	HepG2	liver:	n/a	n/a
15	FOSL2	chr3:195663500-195663777	HepG2	liver:	n/a	n/a
16	FOXA1	chr3:195662758-195663052	HepG2	liver:	n/a	n/a
17	GABPA	chr3:195663518-195663672	Hela-S3	cervix:	n/a	n/a
18	HEY1	chr3:195662447-195662835	K562	blood:	n/a	n/a
19	PAX5	chr3:195663404-195663897	GM12878	blood:	n/a	n/a
20	PAX5	chr3:195663468-195663774	GM12878	blood:	n/a	n/a
21	PAX5	chr3:195662923-195663159	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:195663936-195664213	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:195663862-195664113	A549	lung:	n/a	n/a
24	POLR2A	chr3:195663986-195664137	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:195664028-195664153	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:195663816-195664191	A549	lung:	n/a	n/a
27	POLR2A	chr3:195664442-195664489	K562	blood:	n/a	n/a
28	POLR2A	chr3:195662062-195662191	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:195663997-195664150	A549	lung:	n/a	n/a
30	POLR2A	chr3:195663391-195664302	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:195663467-195663664	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:195663460-195663871	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:195662795-195663168	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:195662032-195662164	K562	blood:	n/a	n/a
35	POLR2A	chr3:195663831-195664143	A549	lung:	n/a	n/a
36	POU2F2	chr3:195662809-195663261	GM12878	blood:	n/a	n/a
37	POU2F2	chr3:195663418-195663845	GM12878	blood:	n/a	n/a
38	SIX5	chr3:195664474-195664699	K562	blood:	n/a	n/a
39	SIX5	chr3:195662802-195663052	K562	blood:	n/a	n/a
40	SPI1	chr3:195664529-195664702	K562	blood:	n/a	n/a
41	TCF3	chr3:195663832-195664078	GM12878	blood:	n/a	n/a
42	ZBTB33	chr3:195663697-195664052	K562	blood:	n/a	n/a
43	ZBTB33	chr3:195663510-195663822	GM12878	blood:	n/a	n/a
44	ZBTB33	chr3:195663699-195664057	K562	blood:	n/a	n/a
45	ZBTB33	chr3:195662823-195663119	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195655412..195657166-chr3:195660620..195663176,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNK2-2	chr3:195665538-195665609	NONHSAT094271

No data

Variant related genes	Relation type
ENSG00000231443	TF binding region
ENSG00000239122	chromatin interactions

Extended variants
information (count: 200 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:200 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138645674	chr3:195662165-195662166	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs543564646	chr3:195662187-195662188	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs149330613	chr3:195662197-195662198	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs182922011	chr3:195662198-195662199	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs564823132	chr3:195662200-195662201	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs534196981	chr3:195662209-195662210	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs558566160	chr3:195662215-195662216	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs576795580	chr3:195662221-195662222	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs537977410	chr3:195662253-195662254	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs554162859	chr3:195662269-195662270	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs188874965	chr3:195662289-195662290	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs369095600	chr3:195662308-195662309	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs373281591	chr3:195662332-195662333	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs560923640	chr3:195662337-195662338	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs144578309	chr3:195662358-195662359	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs540498936	chr3:195662386-195662387	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs564895548	chr3:195662394-195662395	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs532095815	chr3:195662398-195662399	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs550412187	chr3:195662399-195662400	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs562641233	chr3:195662468-195662469	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs193283168	chr3:195662472-195662473	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs548789428	chr3:195662476-195662477	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs566710740	chr3:195662505-195662506	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs534239396	chr3:195662519-195662520	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs115199576	chr3:195662520-195662521	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs570516722	chr3:195662607-195662608	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs6791537	chr3:195662617-195662618	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs556274674	chr3:195662666-195662667	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs574924061	chr3:195662678-195662679	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs540712268	chr3:195662682-195662683	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs9325425	chr3:195662694-195662695	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs142508176	chr3:195662698-195662699	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs573045697	chr3:195662712-195662713	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs540535729	chr3:195662713-195662714	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs565134860	chr3:195662715-195662716	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs577051861	chr3:195662716-195662717	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs544240781	chr3:195662730-195662731	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs72499654	chr3:195662770-195662771	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs563162215	chr3:195662785-195662786	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs530863726	chr3:195662793-195662794	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs112906500	chr3:195662812-195662813	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs2448529	chr3:195662858-195662859	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs140383223	chr3:195662866-195662867	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs6791829	chr3:195662887-195662888	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs552462592	chr3:195662902-195662903	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs200155733	chr3:195662906-195662907	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs570852196	chr3:195662942-195662943	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs531909661	chr3:195662946-195662947	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs550177013	chr3:195662953-195662954	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs376257412	chr3:195662961-195662962	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195647200-195681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:195648600-195666600	Weak transcription	Lung	lung
3	chr3:195648600-195666600	Weak transcription	Spleen	Spleen
4	chr3:195648600-195680600	Weak transcription	Pancreas	Pancrea
5	chr3:195648800-195666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:195648800-195666800	Weak transcription	Esophagus	oesophagus
7	chr3:195651200-195671200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:195651800-195673800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:195653000-195666800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:195656600-195681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:195656800-195666600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:195656800-195666600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:195656800-195669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:195656800-195671200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:195656800-195676400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:195656800-195679400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:195657000-195666800	Weak transcription	Primary T cells from cord blood	blood
18	chr3:195657200-195666800	Weak transcription	Thymus	Thymus
19	chr3:195657400-195670000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:195657800-195681400	Weak transcription	GM12878-XiMat	blood
21	chr3:195658400-195666800	Weak transcription	Gastric	stomach
22	chr3:195658800-195666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:195659000-195667200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:195659000-195676400	Weak transcription	Hela-S3	cervix
25	chr3:195659600-195666600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:195659600-195666800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:195659600-195681200	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:195659600-195685600	Weak transcription	Small Intestine	intestine
29	chr3:195660000-195666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:195660000-195666600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:195660000-195666600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:195660000-195666600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:195660000-195666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:195660000-195666800	Weak transcription	Brain Substantia Nigra	brain
35	chr3:195660000-195666800	Weak transcription	Fetal Intestine Large	intestine
36	chr3:195660000-195666800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:195660000-195669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:195660000-195681200	Weak transcription	Colonic Mucosa	Colon
39	chr3:195660200-195666600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:195660400-195666600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:195660400-195666800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:195660400-195666800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:195660400-195680600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:195660600-195666400	Weak transcription	Fetal Intestine Small	intestine
45	chr3:195660600-195666800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:195660600-195669600	Weak transcription	A549	lung
47	chr3:195660600-195681200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:195660800-195666800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:195660800-195667000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:195660800-195669400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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