Variant report

Variant	rs12711084
Chromosome Location	chr4:120989853-120989854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:120986908-120989985	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:120987163-120989871	K562	blood:	n/a	n/a
3	POLR2A	chr4:120989769-120989911	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:120987112-120989933	K562	blood:	n/a	n/a
5	POLR2A	chr4:120989851-120990027	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
2	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC110373.1-6	chr4:120988015-120991623	NONHSAT098115

No data

Variant related genes	Relation type
MAD2L1	TF binding region
ENSG00000145390	Chromatin interaction
ENSG00000164096	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10010446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075717	0.83[ASN][1000 genomes]
rs11727480	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs11942060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112411	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs13121806	0.90[CHB][hapmap];0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs13136371	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1972014	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs2058765	0.80[GIH][hapmap]
rs2892890	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2904883	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2904884	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2934379	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs3113988	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs4834834	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534168	0.83[ASN][1000 genomes]
rs6810690	0.87[ASN][1000 genomes]
rs7660900	0.81[ASN][1000 genomes]
rs903147	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs972311	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]

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	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120989000-120990600	Flanking Active TSS	Dnd41	blood
2	chr4:120989000-120991000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:120989200-120990200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr4:120989200-120990400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr4:120989200-120990400	Flanking Active TSS	GM12878-XiMat	blood
6	chr4:120989200-120990600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:120989200-120991000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:120989400-120990000	Enhancers	HMEC	breast
9	chr4:120989400-120990200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr4:120989400-120990400	Enhancers	Primary T cells from cord blood	blood
11	chr4:120989400-120990400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr4:120989400-120990400	Weak transcription	A549	lung
13	chr4:120989400-120990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:120989400-120990600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:120989400-120990600	Enhancers	Primary hematopoietic stem cells	blood
16	chr4:120989400-120990600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr4:120989400-120990800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:120989400-120991000	Weak transcription	NH-A	brain
19	chr4:120989400-120992200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:120989400-120992400	Enhancers	NHLF	lung
21	chr4:120989400-121012600	Weak transcription	Aorta	Aorta
22	chr4:120989600-120990000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:120989600-120990400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:120989600-120990600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr4:120989600-120990600	Enhancers	HepG2	liver
26	chr4:120989600-120991000	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr4:120989600-120991000	Weak transcription	HUVEC	blood vessel
28	chr4:120989600-120991200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:120989600-120991600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:120989600-120991800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:120989600-120992200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr4:120989600-120992200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:120989600-120992200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:120989600-120992400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:120989600-120992400	Enhancers	Osteobl	bone
36	chr4:120989600-120992800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:120989600-120993000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:120989800-120990000	Active TSS	K562	blood
39	chr4:120989800-120990000	Enhancers	NHEK	skin
40	chr4:120989800-120990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:120989800-120990800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:120989800-120990800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:120989800-120990800	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:120989800-120990800	Weak transcription	NHDF-Ad	bronchial
45	chr4:120989800-120991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:120989800-120991000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:120989800-120991000	Weak transcription	HSMM	muscle
48	chr4:120989800-120991200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:120989800-120991400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:120989800-120991600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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