Variant report

Variant	rs11539377
Chromosome Location	chr3:119219573-119219574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119219400-119219667	HepG2	liver:	n/a	n/a
2	IRF1	chr3:119219067-119219777	K562	blood:	n/a	n/a
3	POLR2A	chr3:119218321-119220778	K562	blood:	n/a	n/a
4	POLR2A	chr3:119219244-119219840	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr3:119216044-119220289	SK-N-SH	brain:	n/a	n/a
6	NFYB	chr3:119219426-119219668	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:119215979-119219829	SK-N-MC	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119219516..119223386-chr3:119224346..119229091,6	K562	blood:
2	chr3:119218133..119220642-chr3:119277892..119280066,2	K562	blood:
3	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
4	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
5	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272662	TF binding region
ENSG00000121594	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11709468	0.89[YRI][hapmap]
rs11915398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916272	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916344	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11917446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917642	0.85[EUR][1000 genomes]
rs11918271	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919404	0.85[EUR][1000 genomes]
rs11919541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919760	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11921098	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11922005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11923882	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11925305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829840	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16829878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16829888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2049500	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs3732414	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4461452	0.89[YRI][hapmap]
rs4687863	0.89[YRI][hapmap]
rs503083	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55696355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55853418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55968892	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56149432	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56195264	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56413426	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56710033	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57168946	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57389809	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57935532	0.95[EUR][1000 genomes]
rs58398719	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58639515	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58843212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58978800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59482964	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60006470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6762095	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6763716	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6764495	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6779137	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6783100	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6802790	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6808654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs716649	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs72952928	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72952932	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72952934	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72952950	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72970333	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72970352	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73857028	0.89[EUR][1000 genomes]
rs7621149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7626731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642792	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7650975	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7653469	1.00[TSI][hapmap]
rs9850413	0.89[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119216200-119219600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr3:119216200-119219600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:119216200-119219800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:119216200-119220000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:119216400-119219600	Active TSS	Psoas Muscle	Psoas
6	chr3:119216400-119220200	Active TSS	K562	blood
7	chr3:119216600-119219800	Active TSS	Left Ventricle	heart
8	chr3:119218000-119220400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:119218000-119224400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:119218000-119225000	Weak transcription	Gastric	stomach
11	chr3:119218000-119231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
13	chr3:119218200-119219600	Flanking Active TSS	Dnd41	blood
14	chr3:119218200-119219800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:119218200-119219800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:119218200-119219800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:119218200-119220000	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:119218200-119220000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:119218200-119220000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr3:119218200-119220000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:119218200-119220800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:119218400-119219600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:119218400-119219600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:119218400-119219600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr3:119218400-119219800	Flanking Active TSS	HUVEC	blood vessel
26	chr3:119218400-119219800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:119218400-119220000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:119218400-119220000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:119218400-119220000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:119218400-119220000	Enhancers	Pancreas	Pancrea
31	chr3:119218400-119220000	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:119218400-119220000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:119218400-119220000	Enhancers	HSMMtube	muscle
34	chr3:119218400-119220200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:119218400-119220200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr3:119218400-119220400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:119218400-119220800	Enhancers	Brain Cingulate Gyrus	brain
38	chr3:119218600-119219600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:119218600-119219600	Enhancers	Small Intestine	intestine
40	chr3:119218600-119219800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:119218600-119219800	Enhancers	Brain Angular Gyrus	brain
42	chr3:119218600-119219800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr3:119218600-119220000	Enhancers	Colon Smooth Muscle	Colon
44	chr3:119218600-119220000	Enhancers	Fetal Lung	lung
45	chr3:119218600-119220000	Active TSS	Right Atrium	heart
46	chr3:119218600-119220000	Active TSS	Right Ventricle	heart
47	chr3:119218600-119220200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:119218600-119220200	Enhancers	Brain Hippocampus Middle	brain
49	chr3:119218600-119220200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:119218600-119220200	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links