Variant report

Variant	rs2961685
Chromosome Location	chr5:177654452-177654453
allele	A/G
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	POLR2A	chr5:177654353-177654773	HepG2	liver:	n/a	n/a
2	STAT3	chr5:177654356-177654536	MCF10A-Er-Src	breast:	n/a	chr5:177654494-177654505
3	POLR2A	chr5:177654447-177654970	HepG2	liver:	n/a	n/a
4	STAT3	chr5:177654411-177654642	MCF10A-Er-Src	breast:	n/a	chr5:177654494-177654505
5	POLR2A	chr5:177654428-177655024	HL-60	blood:	n/a	n/a
6	FOS	chr5:177654269-177654661	HUVEC	blood vessel:	n/a	chr5:177654462-177654473
7	FOS	chr5:177654338-177654611	MCF10A-Er-Src	breast:	n/a	chr5:177654462-177654473
8	POLR2A	chr5:177653417-177655906	K562	blood:	n/a	n/a
9	POLR2A	chr5:177654090-177654847	K562	blood:	n/a	n/a
10	FOS	chr5:177654300-177654611	MCF10A-Er-Src	breast:	n/a	chr5:177654462-177654473
11	POLR2A	chr5:177654107-177655211	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr5:177653368-177655971	A549	lung:	n/a	n/a

Variant related genes	Relation type
PHYKPL	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2913747	0.94[ASN][1000 genomes]
rs2913752	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2913862	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913864	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913867	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2961674	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2961675	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2961676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2961677	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2961679	0.94[ASN][1000 genomes]
rs2961682	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2961686	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177635800-177657000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:177639400-177657600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:177640400-177655600	Weak transcription	Right Atrium	heart
4	chr5:177643400-177656400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:177643600-177655200	Weak transcription	Stomach Mucosa	stomach
6	chr5:177644200-177654800	Weak transcription	NHDF-Ad	bronchial
7	chr5:177645400-177654800	Strong transcription	Hela-S3	cervix
8	chr5:177645400-177656800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr5:177645400-177656800	Strong transcription	Dnd41	blood
10	chr5:177645600-177654800	Weak transcription	HSMM	muscle
11	chr5:177646200-177657000	Weak transcription	Fetal Brain Male	brain
12	chr5:177646600-177657400	Strong transcription	Thymus	Thymus
13	chr5:177646800-177658000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:177647800-177657000	Strong transcription	Brain Germinal Matrix	brain
15	chr5:177648000-177656000	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr5:177648000-177656800	Strong transcription	Primary B cells from cord blood	blood
17	chr5:177648000-177658000	Strong transcription	Fetal Thymus	thymus
18	chr5:177648200-177654800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:177648200-177657000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:177648200-177657000	Strong transcription	NHLF	lung
21	chr5:177648200-177657400	Strong transcription	Fetal Brain Female	brain
22	chr5:177648200-177657800	Genic enhancers	Fetal Intestine Large	intestine
23	chr5:177648400-177654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:177648400-177654800	Strong transcription	NHEK	skin
25	chr5:177648400-177655000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:177648600-177656400	Strong transcription	GM12878-XiMat	blood
27	chr5:177648600-177658000	Strong transcription	Spleen	Spleen
28	chr5:177649000-177655000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:177649000-177657400	Strong transcription	Primary T cells from cord blood	blood
30	chr5:177649400-177654600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:177649400-177654600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:177649400-177655000	Weak transcription	Small Intestine	intestine
33	chr5:177649400-177655200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:177649400-177655600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:177649400-177657000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:177649400-177657200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:177649400-177657200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr5:177649600-177654600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:177649600-177654800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:177649600-177657800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr5:177650000-177654800	Weak transcription	Brain Substantia Nigra	brain
42	chr5:177650200-177656600	Weak transcription	Brain Angular Gyrus	brain
43	chr5:177650600-177655400	Weak transcription	HUVEC	blood vessel
44	chr5:177651000-177654600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:177651000-177657000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr5:177651200-177656200	Strong transcription	Lung	lung
47	chr5:177651400-177654600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:177651400-177655600	Strong transcription	Adipose Nuclei	Adipose
49	chr5:177651400-177658000	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr5:177651600-177657800	Strong transcription	Fetal Muscle Leg	muscle

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