Variant report

Variant	rs3759399
Chromosome Location	chr12:120516507-120516508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:120516491-120518244	MCF-7	breast:	n/a	chr12:120517377-120517393
2	GATA3	chr12:120516423-120518031	MCF-7	breast:	n/a	chr12:120517377-120517393
3	SIN3AK20	chr12:120516451-120518177	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:120515805..120518721-chr12:120536191..120539691,3	MCF-7	breast:
2	chr12:120500334..120503561-chr12:120515815..120519326,4	MCF-7	breast:
3	chr12:120513658..120516518-chr12:120532561..120535483,2	MCF-7	breast:
4	chr12:120515699..120519633-chr12:120727984..120732928,6	MCF-7	breast:
5	chr12:120514645..120518172-chr12:120553447..120556638,5	MCF-7	breast:
6	chr12:120515251..120520638-chr12:120728491..120731370,5	MCF-7	breast:
7	chr12:120509994..120511912-chr12:120515778..120517839,2	K562	blood:
8	chr12:120425757..120429620-chr12:120514242..120517556,6	MCF-7	breast:
9	chr12:120426905..120428468-chr12:120515496..120517085,2	MCF-7	breast:
10	chr12:120515678..120517305-chr12:120637350..120639266,3	MCF-7	breast:
11	chr12:120516359..120519600-chr12:120552938..120556302,7	MCF-7	breast:
12	chr12:120472729..120475362-chr12:120515779..120517962,2	MCF-7	breast:
13	chr12:120442635..120444845-chr12:120516019..120517526,2	MCF-7	breast:
14	chr12:120484290..120487162-chr12:120516019..120517962,3	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC64	TF binding region
ENSG00000200795	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000272464	Chromatin interaction
ENSG00000089157	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10744747	0.85[ASN][1000 genomes]
rs10774542	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11064986	0.80[ASN][1000 genomes]
rs11064998	0.82[ASN][1000 genomes]
rs11065004	0.87[ASN][1000 genomes]
rs11065014	0.98[ASN][1000 genomes]
rs11065017	0.95[ASN][1000 genomes]
rs11065018	0.95[ASN][1000 genomes]
rs12311327	0.86[ASN][1000 genomes]
rs12320072	0.93[ASN][1000 genomes]
rs2240311	0.94[ASN][1000 genomes]
rs2393570	0.87[ASN][1000 genomes]
rs2893812	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3742044	0.81[ASN][1000 genomes]
rs3852586	0.97[ASN][1000 genomes]
rs3852588	0.94[ASN][1000 genomes]
rs3886910	0.81[ASN][1000 genomes]
rs3999575	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4351876	0.81[ASN][1000 genomes]
rs4767870	0.83[ASN][1000 genomes]
rs4767873	0.81[ASN][1000 genomes]
rs6490278	0.81[ASN][1000 genomes]
rs6490283	0.93[ASN][1000 genomes]
rs6490284	0.97[ASN][1000 genomes]
rs7295717	0.87[ASN][1000 genomes]
rs7302874	0.81[ASN][1000 genomes]
rs7305625	0.92[ASN][1000 genomes]
rs7306739	0.94[ASN][1000 genomes]
rs7312811	0.82[ASN][1000 genomes]
rs7314959	0.92[ASN][1000 genomes]
rs7956436	0.87[ASN][1000 genomes]
rs7960725	0.87[ASN][1000 genomes]
rs7961738	0.81[ASN][1000 genomes]
rs7962812	0.82[ASN][1000 genomes]
rs7971249	0.90[ASN][1000 genomes]
rs7977281	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120493800-120523800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:120494800-120517800	Weak transcription	Lung	lung
3	chr12:120498800-120516600	Weak transcription	Fetal Brain Male	brain
4	chr12:120502000-120523400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:120502200-120516600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:120502200-120517800	Weak transcription	Gastric	stomach
7	chr12:120502400-120523200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:120502400-120523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:120502400-120524400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:120502600-120518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:120502600-120524400	Weak transcription	Brain Anterior Caudate	brain
12	chr12:120502600-120525200	Weak transcription	Spleen	Spleen
13	chr12:120503000-120517000	Weak transcription	Dnd41	blood
14	chr12:120503800-120518000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:120504600-120516800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:120504600-120516800	Weak transcription	HMEC	breast
17	chr12:120505800-120516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:120507400-120516800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:120508400-120518200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:120509800-120524600	Weak transcription	Pancreas	Pancrea
21	chr12:120510000-120524600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:120510200-120523000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:120510400-120517600	Weak transcription	Fetal Brain Female	brain
24	chr12:120510400-120517800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:120510600-120524600	Weak transcription	Brain Germinal Matrix	brain
26	chr12:120511000-120516600	Weak transcription	NHEK	skin
27	chr12:120511200-120516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:120511600-120523200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:120512800-120524400	Weak transcription	Brain Angular Gyrus	brain
30	chr12:120513200-120516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:120513200-120517800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:120513400-120516800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:120513400-120524200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:120513600-120517000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:120513800-120524400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:120514200-120523600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:120514600-120518600	Enhancers	Placenta	Placenta
38	chr12:120514600-120518800	Enhancers	Stomach Mucosa	stomach
39	chr12:120514800-120516600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:120514800-120524600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:120515000-120523200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr12:120515200-120516800	Genic enhancers	Primary T cells from cord blood	blood
43	chr12:120515200-120517800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:120515200-120518200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:120515200-120521200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:120515400-120517400	Weak transcription	Thymus	Thymus
47	chr12:120515600-120517000	Enhancers	Esophagus	oesophagus
48	chr12:120515800-120516600	Enhancers	Hela-S3	cervix
49	chr12:120515800-120516800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:120515800-120517800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links