Variant report

Variant	esv2590986
Chromosome Location	chr3:177395894-177397383
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	chr3:177397308-177397855	K562	blood:	n/a	n/a
2	EP300	chr3:177397220-177398065	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr3:177397268-177398108	SK-N-SH	brain:	n/a	n/a
4	EP300	chr3:177397225-177399260	SK-N-SH	brain:	n/a	chr3:177398807-177398821 chr3:177398406-177398415
5	EP300	chr3:177397310-177398048	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr3:177397266-177398031	SK-N-SH	brain:	n/a	n/a
7	FOS	chr3:177397284-177398592	HUVEC	blood vessel:	n/a	chr3:177397630-177397637 chr3:177398406-177398415 chr3:177397630-177397638 chr3:177398405-177398414 chr3:177397630-177397638 chr3:177398405-177398415
8	FOSL2	chr3:177397310-177397893	SK-N-SH	brain:	n/a	chr3:177397630-177397637 chr3:177397630-177397638 chr3:177397630-177397638
9	FOXM1	chr3:177397015-177398097	SK-N-SH	brain:	n/a	n/a
10	FOXM1	chr3:177397249-177397998	SK-N-SH	brain:	n/a	n/a
11	GATA1	chr3:177397323-177398346	PBDE	blood:	n/a	chr3:177398197-177398207 chr3:177398197-177398206 chr3:177398260-177398269 chr3:177398199-177398206 chr3:177398260-177398269 chr3:177398192-177398213 chr3:177398251-177398268 chr3:177398199-177398206 chr3:177397523-177397534 chr3:177398199-177398206
12	GATA2	chr3:177396460-177396821	HUVEC	blood vessel:	n/a	n/a
13	GATA2	chr3:177397276-177398330	HUVEC	blood vessel:	n/a	chr3:177398197-177398207 chr3:177398197-177398206 chr3:177398260-177398269 chr3:177398199-177398206 chr3:177398260-177398269 chr3:177398192-177398213 chr3:177398251-177398268 chr3:177398199-177398206 chr3:177397523-177397534 chr3:177398199-177398206
14	GATA2	chr3:177397342-177397937	K562	blood:	n/a	chr3:177397523-177397534
15	GATA3	chr3:177397209-177398697	SK-N-SH	brain:	n/a	chr3:177398197-177398207 chr3:177398197-177398206 chr3:177398260-177398269 chr3:177398199-177398206 chr3:177398260-177398269 chr3:177398192-177398213 chr3:177398251-177398268 chr3:177398199-177398206 chr3:177397523-177397534 chr3:177398199-177398206
16	GATA3	chr3:177397260-177398554	SK-N-SH	brain:	n/a	chr3:177398197-177398207 chr3:177398197-177398206 chr3:177398260-177398269 chr3:177398199-177398206 chr3:177398260-177398269 chr3:177398192-177398213 chr3:177398251-177398268 chr3:177398199-177398206 chr3:177397523-177397534 chr3:177398199-177398206
17	JUND	chr3:177397270-177397967	SK-N-SH	brain:	n/a	chr3:177397630-177397637 chr3:177397630-177397638 chr3:177397630-177397638
18	JUND	chr3:177397315-177397906	SK-N-SH	brain:	n/a	chr3:177397630-177397637 chr3:177397630-177397638 chr3:177397630-177397638
19	NFIC	chr3:177397139-177398061	SK-N-SH	brain:	n/a	n/a
20	PBX3	chr3:177397328-177398030	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr3:177397356-177397925	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr3:177397330-177397857	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr3:177397218-177398120	SK-N-SH_RA	brain:	n/a	n/a
24	RAD21	chr3:177397268-177398172	SK-N-SH_RA	brain:	n/a	n/a
25	RAD21	chr3:177396390-177398716	SK-N-SH	brain:	n/a	n/a
26	RFX5	chr3:177396233-177396287	K562	blood:	n/a	n/a
27	TCF12	chr3:177397238-177398118	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr3:177397168-177398627	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr3:177397371-177398079	SK-N-SH	brain:	n/a	n/a
30	TEAD4	chr3:177397244-177398022	SK-N-SH	brain:	n/a	n/a
31	TEAD4	chr3:177397308-177397944	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177395868..177398215-chr3:177400550..177402752,2	MCF-7	breast:
2	chr3:177396417..177398253-chr3:177403984..177405833,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228561	TF binding region
ENSG00000228561	chromatin interactions

Extended variants
information (count: 49 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:49 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62283321	chr3:177395949-177395950	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs552187022	chr3:177395973-177395974	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs568899903	chr3:177396001-177396002	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs33964414	chr3:177396058-177396059	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs78694389	chr3:177396085-177396086	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs568073260	chr3:177396093-177396094	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs551061019	chr3:177396123-177396124	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs375948913	chr3:177396209-177396210	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs149515596	chr3:177396217-177396218	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs576695506	chr3:177396275-177396276	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs115963549	chr3:177396304-177396305	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs558503792	chr3:177396322-177396323	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs62283322	chr3:177396338-177396339	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs148363878	chr3:177396395-177396396	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs141579066	chr3:177396396-177396397	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs77461012	chr3:177396397-177396398	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs561391829	chr3:177396404-177396405	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs560663819	chr3:177396413-177396414	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs574839259	chr3:177396479-177396480	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs540801902	chr3:177396493-177396494	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs34491022	chr3:177396516-177396517	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs532833499	chr3:177396572-177396573	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs552952503	chr3:177396587-177396588	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs62283323	chr3:177396683-177396684	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs531298764	chr3:177396726-177396727	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs565961939	chr3:177396734-177396735	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs116322740	chr3:177396777-177396778	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs369096521	chr3:177396809-177396810	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs568122925	chr3:177396812-177396813	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs55993565	chr3:177396826-177396827	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs547171437	chr3:177396869-177396870	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs370601746	chr3:177396883-177396884	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs570337862	chr3:177396906-177396907	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs539343899	chr3:177396916-177396917	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs528438931	chr3:177396947-177396948	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs551601438	chr3:177397006-177397007	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs571473033	chr3:177397022-177397023	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs7614252	chr3:177397042-177397043	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs557036824	chr3:177397048-177397049	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs116905684	chr3:177397061-177397062	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs574842070	chr3:177397080-177397081	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs150544531	chr3:177397091-177397092	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs540758963	chr3:177397146-177397147	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs567124095	chr3:177397190-177397191	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs80071291	chr3:177397217-177397218	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs71992691	chr3:177397221-177397222	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs549948145	chr3:177397225-177397226	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs560666026	chr3:177397245-177397246	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs577555076	chr3:177397362-177397363	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:76)

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	22032731	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
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Anaplastic thyroid cancer	17989125	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Ovarian cancer	18208621	CNVD
Thyroid cancer	17317825	CNVD
Thyroid cancer	17989125	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Breast cancer	21806811	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	19653912	CNVD
Cancer	20164920	CNVD
Endometrial cancer	19261849	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Esophageal squamous carcinoma	17470683	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21611746	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Myelofibrosis	22110671	CNVD
Prostate cancer	17217626	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Neurodevelopmental disorder	22521361	CNVD
Cancer	20164919	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177383800-177397800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:177391200-177397600	Weak transcription	Right Atrium	heart
3	chr3:177391600-177396400	Weak transcription	HUVEC	blood vessel
4	chr3:177391600-177396800	Weak transcription	Dnd41	blood
5	chr3:177391800-177397600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:177392000-177405400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:177392200-177396800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:177392200-177397200	Weak transcription	HMEC	breast
9	chr3:177392200-177397200	Weak transcription	Osteobl	bone
10	chr3:177392200-177397400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:177392200-177397600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:177392200-177397600	Weak transcription	Adipose Nuclei	Adipose
13	chr3:177392200-177397800	Weak transcription	NHLF	lung
14	chr3:177392200-177404400	Weak transcription	Ovary	ovary
15	chr3:177392400-177396000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:177392400-177396600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:177392400-177397200	Weak transcription	K562	blood
18	chr3:177392400-177397200	Weak transcription	NH-A	brain
19	chr3:177392400-177397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:177392400-177397600	Weak transcription	NHDF-Ad	bronchial
21	chr3:177392400-177397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:177392600-177396000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:177392600-177396200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:177392600-177396400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:177392600-177397400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:177392600-177397400	Weak transcription	Fetal Thymus	thymus
28	chr3:177392600-177397600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:177392600-177398600	Weak transcription	Spleen	Spleen
30	chr3:177392600-177399600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:177393200-177396000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:177394000-177401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:177394800-177404800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:177395000-177396600	Weak transcription	Fetal Heart	heart
35	chr3:177395000-177396800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:177395000-177396800	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:177395000-177397000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:177395000-177406000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:177395200-177396000	Enhancers	Fetal Brain Male	brain
41	chr3:177395200-177396400	Weak transcription	Fetal Kidney	kidney
42	chr3:177395200-177397000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr3:177395200-177397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:177395200-177399600	Weak transcription	Stomach Mucosa	stomach
45	chr3:177395200-177400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:177395400-177399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:177395400-177400200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:177395600-177397400	Weak transcription	Fetal Lung	lung
49	chr3:177395800-177396600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:177396000-177398600	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links