Variant report

Variant	esv3487502
Chromosome Location	chr12:65017334-65018585
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr12:65017923-65017924	K562	blood:	n/a	n/a
2	CTCF	chr12:65018511-65018560	ProgFib	skin:	n/a	n/a
3	CUX1	chr12:65017838-65018037	K562	blood:	n/a	n/a
4	FOSL2	chr12:65016990-65017454	MCF-7	breast:	n/a	n/a
5	GTF2F1	chr12:65017837-65017857	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr12:65018064-65018113	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF1	chr12:65017614-65017978	H1-hESC	embryonic stem cell:	n/a	chr12:65017772-65017793 chr12:65017776-65017789 chr12:65017778-65017787 chr12:65017777-65017786
8	USF1	chr12:65017619-65017978	H1-hESC	embryonic stem cell:	n/a	chr12:65017772-65017793 chr12:65017776-65017789 chr12:65017778-65017787 chr12:65017777-65017786
9	WRNIP1	chr12:65017630-65017830	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:65011462..65014885-chr12:65017332..65020916,6	MCF-7	breast:
2	chr12:65018029..65021346-chr12:65072247..65076410,6	MCF-7	breast:
3	chr12:65018258..65020873-chr12:65068837..65071390,2	MCF-7	breast:
4	chr12:65016442..65019284-chr12:65019658..65023232,4	MCF-7	breast:
5	chr12:65017129..65019171-chr12:65067339..65069384,2	MCF-7	breast:
6	chr12:65010556..65012937-chr12:65017376..65021348,4	K562	blood:
7	chr12:65013129..65015693-chr12:65017473..65019068,2	K562	blood:
8	chr12:65001678..65008078-chr12:65013108..65023657,17	MCF-7	breast:
9	chr12:65008839..65011429-chr12:65017334..65019705,2	MCF-7	breast:
10	chr12:64989403..64992125-chr12:65016566..65018354,2	MCF-7	breast:
11	chr12:65017089..65019712-chr12:65042869..65045588,2	MCF-7	breast:
12	chr12:65018061..65020835-chr12:65174615..65176151,2	MCF-7	breast:
13	chr12:65001526..65007900-chr12:65015799..65021807,8	K562	blood:
14	chr12:65018082..65020499-chr12:65056309..65058062,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225195	TF binding region
ENSG00000256670	chromatin interactions
ENSG00000225195	chromatin interactions
ENSG00000111490	chromatin interactions
ENSG00000153179	chromatin interactions

Extended variants
information (count: 59 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:59 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553056057	chr12:65017341-65017342	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs561034841	chr12:65017369-65017370	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs59219879	chr12:65017484-65017485	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs56185632	chr12:65017491-65017492	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs60649666	chr12:65017502-65017503	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs549760714	chr12:65017503-65017504	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs563241924	chr12:65017504-65017505	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs532470335	chr12:65017505-65017506	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs57471087	chr12:65017506-65017507	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs552478010	chr12:65017518-65017519	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs58422857	chr12:65017543-65017544	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs55923537	chr12:65017586-65017587	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs55905863	chr12:65017595-65017596	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs55663246	chr12:65017601-65017602	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs181190042	chr12:65017621-65017622	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs56257033	chr12:65017628-65017629	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs55789996	chr12:65017634-65017635	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs55983611	chr12:65017640-65017641	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs55727547	chr12:65017641-65017642	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs59044636	chr12:65017681-65017682	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs377387942	chr12:65017695-65017696	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs1245169	chr12:65017698-65017699	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs534803488	chr12:65017723-65017724	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs554058033	chr12:65017732-65017733	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs79461001	chr12:65017733-65017734	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs185594395	chr12:65017751-65017752	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs528353179	chr12:65017782-65017783	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs189655998	chr12:65017811-65017812	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs1245168	chr12:65017844-65017845	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs538978677	chr12:65017854-65017855	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs139977520	chr12:65017899-65017900	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs554376196	chr12:65017919-65017920	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs574281880	chr12:65017924-65017925	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs116778842	chr12:65017948-65017949	Flanking Active TSS Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs572695183	chr12:65018008-65018009	Flanking Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs138083982	chr12:65018013-65018014	Flanking Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs369112461	chr12:65018023-65018024	Flanking Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs7302505	chr12:65018121-65018122	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs11175471	chr12:65018137-65018138	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs11175472	chr12:65018173-65018174	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs2682714	chr12:65018192-65018193	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs559684583	chr12:65018233-65018234	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs528329935	chr12:65018255-65018256	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs548379407	chr12:65018256-65018257	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs568132257	chr12:65018272-65018273	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs545806152	chr12:65018349-65018350	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs544166743	chr12:65018368-65018369	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs549989049	chr12:65018434-65018435	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
49	rs569754956	chr12:65018435-65018436	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs181001172	chr12:65018445-65018446	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:83)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Metanephric adenoma	20802469	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Multiple myeloma	16616336	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Mental retardation	17220210	CNVD
Osteopoikilosis	17220210	CNVD
short stature	17220210	CNVD
Burkitt''s lymphoma	20823134	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Heart disease	21282601	CNVD
Ovarian neoplasms	16753589	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	16620391	CNVD
Intracranial arachnoid cysts	20187927	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:169 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65005800-65017800	Weak transcription	Gastric	stomach
2	chr12:65006200-65017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:65006200-65017600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:65006200-65018800	Weak transcription	Fetal Thymus	thymus
5	chr12:65006200-65019000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:65006200-65019000	Weak transcription	NHEK	skin
7	chr12:65006200-65019400	Weak transcription	Psoas Muscle	Psoas
8	chr12:65006600-65017400	Weak transcription	Small Intestine	intestine
9	chr12:65006600-65018200	Weak transcription	Fetal Intestine Large	intestine
10	chr12:65006800-65031800	Weak transcription	Dnd41	blood
11	chr12:65007000-65018800	Weak transcription	HMEC	breast
12	chr12:65007000-65019200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:65007200-65017600	Weak transcription	Stomach Mucosa	stomach
14	chr12:65007800-65017600	Weak transcription	Lung	lung
15	chr12:65008600-65019000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:65009200-65019200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:65009800-65019200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:65009800-65019400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:65010000-65023200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:65010200-65019400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:65010400-65018200	Weak transcription	Colonic Mucosa	Colon
22	chr12:65010400-65019000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:65010600-65017800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:65010600-65018800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:65010600-65018800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:65010600-65018800	Weak transcription	Fetal Lung	lung
27	chr12:65010600-65019000	Weak transcription	Fetal Stomach	stomach
28	chr12:65010800-65018600	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:65010800-65022200	Weak transcription	Spleen	Spleen
30	chr12:65011000-65018400	Weak transcription	Brain Substantia Nigra	brain
31	chr12:65011200-65018800	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:65011600-65019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:65011800-65019000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:65012000-65017600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:65012400-65018200	Weak transcription	Fetal Intestine Small	intestine
36	chr12:65012400-65019200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:65012600-65019200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:65013000-65019200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:65013200-65019000	Weak transcription	Right Ventricle	heart
40	chr12:65013200-65019200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:65013200-65019400	Weak transcription	Esophagus	oesophagus
42	chr12:65013200-65019400	Weak transcription	Ovary	ovary
43	chr12:65013400-65018200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:65013400-65018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:65013400-65018800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:65013400-65018800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:65013400-65018800	Weak transcription	Osteobl	bone
48	chr12:65013400-65019200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:65013600-65018400	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:65013600-65018400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links