Variant report

Variant	rs2059536
Chromosome Location	chr8:6564810-6564811
allele	C/T
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	chr8:6563393-6568475	GM18505	blood:	n/a	n/a
2	POLR2A	chr8:6563702-6564833	GM12878	blood:	n/a	n/a
3	NFATC1	chr8:6563693-6564818	GM12878	blood:	n/a	chr8:6564768-6564781
4	ATF2	chr8:6563611-6564821	GM12878	blood:	n/a	n/a
5	POLR2A	chr8:6563528-6568801	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:6564760-6565041	K562	blood:	n/a	n/a
7	NFATC1	chr8:6563319-6564869	GM12878	blood:	n/a	chr8:6564768-6564781
8	POLR2A	chr8:6563793-6564821	GM12892	blood:	n/a	n/a
9	MTA3	chr8:6563318-6566068	GM12878	blood:	n/a	n/a
10	POLR2A	chr8:6563447-6564811	GM12892	blood:	n/a	n/a
11	POLR2A	chr8:6563500-6564850	GM12892	blood:	n/a	n/a
12	POLR2A	chr8:6563320-6569676	GM12878	blood:	n/a	n/a
13	POLR2A	chr8:6563688-6567085	K562	blood:	n/a	n/a
14	POLR2A	chr8:6559898-6568153	GM12892	blood:	n/a	n/a
15	POLR2A	chr8:6563623-6564825	GM12892	blood:	n/a	n/a
16	POLR2A	chr8:6563304-6568497	GM12891	blood:	n/a	n/a
17	POLR2A	chr8:6563551-6564826	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:6564149..6568070-chr8:6601682..6607895,12	K562	blood:
2	chr8:6564149..6568457-chr8:6601682..6605924,8	K562	blood:

Variant related genes	Relation type
AGPAT5	TF binding region
ENSG00000266038	Chromatin interaction
ENSG00000155189	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10108451	0.83[EUR][1000 genomes]
rs11986408	0.81[EUR][1000 genomes]
rs11986409	0.81[EUR][1000 genomes]
rs11996255	0.81[EUR][1000 genomes]
rs11996256	0.81[EUR][1000 genomes]
rs1365041	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1365042	0.90[EUR][1000 genomes]
rs1365043	0.89[EUR][1000 genomes]
rs1559748	0.88[EUR][1000 genomes]
rs1971312	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2911975	0.83[EUR][1000 genomes]
rs2911976	0.85[EUR][1000 genomes]
rs2911977	0.85[EUR][1000 genomes]
rs2911978	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2911983	0.88[EUR][1000 genomes]
rs2911987	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911992	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912054	0.83[EUR][1000 genomes]
rs2928617	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928618	0.90[EUR][1000 genomes]
rs2928619	0.90[EUR][1000 genomes]
rs2928621	0.90[EUR][1000 genomes]
rs2928623	0.88[EUR][1000 genomes]
rs2928626	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2928629	0.84[EUR][1000 genomes]
rs2928630	0.84[EUR][1000 genomes]
rs2936502	0.82[EUR][1000 genomes]
rs2980680	0.83[EUR][1000 genomes]
rs2980682	0.82[EUR][1000 genomes]
rs2980683	0.85[EUR][1000 genomes]
rs2980684	0.85[EUR][1000 genomes]
rs2980686	0.81[EUR][1000 genomes]
rs2980689	0.80[ASN][1000 genomes]
rs2980690	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2980692	0.88[EUR][1000 genomes]
rs992813	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv933768	chr8:6482944-6618221	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv831220	chr8:6527845-6728491	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv1030637	chr8:6545498-6669949	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1034115	chr8:6546984-6665832	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6543200-6565200	Weak transcription	Left Ventricle	heart
2	chr8:6549400-6565000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr8:6552000-6565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:6552000-6565200	Weak transcription	Pancreas	Pancrea
5	chr8:6554200-6565200	Weak transcription	Aorta	Aorta
6	chr8:6554600-6565000	Weak transcription	Brain Hippocampus Middle	brain
7	chr8:6555600-6565200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:6557000-6565200	Weak transcription	Lung	lung
9	chr8:6557400-6565000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:6558000-6565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:6562200-6565000	Weak transcription	Fetal Stomach	stomach
12	chr8:6563000-6565000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr8:6563200-6565000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr8:6563200-6565000	Enhancers	Primary B cells from cord blood	blood
15	chr8:6563400-6565000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:6563600-6565000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr8:6563600-6565000	Enhancers	Primary B cells from peripheral blood	blood
18	chr8:6563600-6565200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:6563600-6565200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr8:6563600-6565200	Flanking Active TSS	Dnd41	blood
21	chr8:6563800-6565000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr8:6563800-6565000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:6563800-6565000	Enhancers	Fetal Thymus	thymus
24	chr8:6563800-6565200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr8:6563800-6565600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:6564000-6565000	Enhancers	Primary hematopoietic stem cells	blood
27	chr8:6564000-6565000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr8:6564000-6565000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr8:6564000-6565000	Enhancers	HUVEC	blood vessel
30	chr8:6564000-6565200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr8:6564000-6565400	Active TSS	Colonic Mucosa	Colon
32	chr8:6564000-6566600	Active TSS	Rectal Smooth Muscle	rectum
33	chr8:6564000-6567400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:6564000-6567600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr8:6564000-6568400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr8:6564200-6565000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr8:6564200-6565000	Enhancers	Primary T cells from cord blood	blood
38	chr8:6564200-6565000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr8:6564200-6565000	Enhancers	Fetal Brain Male	brain
40	chr8:6564200-6565000	Enhancers	Fetal Brain Female	brain
41	chr8:6564200-6565000	Weak transcription	Placenta	Placenta
42	chr8:6564200-6565000	Enhancers	NH-A	brain
43	chr8:6564200-6565000	Enhancers	Osteobl	bone
44	chr8:6564200-6565400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:6564400-6565000	Enhancers	Brain Angular Gyrus	brain
46	chr8:6564400-6565000	Enhancers	Brain Cingulate Gyrus	brain
47	chr8:6564400-6565000	Enhancers	Brain Substantia Nigra	brain
48	chr8:6564400-6565000	Enhancers	Fetal Lung	lung
49	chr8:6564400-6565200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr8:6564400-6565200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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