Variant report

Variant	rs867520
Chromosome Location	chr6:73330586-73330587
allele	G/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	MTA3	chr6:73329476-73330787	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:73329493-73333253	NB4	blood:	n/a	n/a
3	MYC	chr6:73329525-73333814	NB4	blood:	n/a	chr6:73332416-73332426 chr6:73332439-73332454 chr6:73332995-73333005 chr6:73329906-73329916 chr6:73332443-73332450
4	POLR2A	chr6:73329777-73330737	GM12878	blood:	n/a	n/a
5	RELA	chr6:73329635-73330614	GM18951	blood:	n/a	n/a
6	ELF1	chr6:73330586-73333174	GM12878	blood:	n/a	chr6:73331869-73331881
7	POLR2A	chr6:73329606-73333225	GM19193	blood:	n/a	n/a
8	MAX	chr6:73329345-73333802	NB4	blood:	n/a	chr6:73332416-73332426 chr6:73332439-73332454 chr6:73332995-73333005 chr6:73329906-73329916 chr6:73332443-73332450
9	POLR2A	chr6:73329772-73330620	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr6:73329618-73333267	GM19099	blood:	n/a	n/a
11	RELA	chr6:73329373-73333198	GM15510	blood:	n/a	n/a
12	CHD1	chr6:73329602-73330883	GM12878	blood:	n/a	n/a
13	RELA	chr6:73329519-73330637	GM10847	blood:	n/a	n/a
14	POLR2A	chr6:73329758-73330732	GM12878	blood:	n/a	n/a
15	CHD2	chr6:73329622-73330608	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:73329606-73333307	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:73328381..73330856-chr6:73331571..73334005,2	MCF-7	breast:
2	chr6:73306231..73308470-chr6:73328760..73331273,2	K562	blood:
3	chr6:73326755..73329181-chr6:73329336..73331379,2	K562	blood:
4	chr6:73114115..73116045-chr6:73329072..73331095,2	K562	blood:

Variant related genes	Relation type
KCNQ5	TF binding region
ENSG00000185760	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10485212	0.88[YRI][hapmap]
rs10943047	1.00[CEU][hapmap]
rs11967126	1.00[CEU][hapmap]
rs12110561	1.00[CEU][hapmap]
rs16882707	1.00[CEU][hapmap]
rs2039107	1.00[CEU][hapmap]
rs4311478	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs4403240	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs6453595	1.00[CEU][hapmap]
rs6903897	1.00[CEU][hapmap]
rs6918190	1.00[CEU][hapmap]
rs6924417	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs73756006	0.83[AMR][1000 genomes]
rs73756512	1.00[EUR][1000 genomes]
rs7746456	1.00[CEU][hapmap]
rs7749673	1.00[CEU][hapmap]
rs9293893	1.00[CEU][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	nsv1023809	chr6:73157813-73477997	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv538303	chr6:73157813-73477997	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3347486	chr6:73283590-73445976	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73329200-73331600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:73329200-73331600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr6:73329200-73333800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:73329400-73331400	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr6:73329400-73331400	Flanking Active TSS	GM12878-XiMat	blood
6	chr6:73329400-73333200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
7	chr6:73329400-73334400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:73329600-73330600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
9	chr6:73329600-73330600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:73329600-73330800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:73329600-73330800	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:73329600-73330800	Flanking Active TSS	K562	blood
13	chr6:73329600-73330800	Flanking Active TSS	NHLF	lung
14	chr6:73329600-73331000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
15	chr6:73329600-73331000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr6:73329600-73331000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:73329600-73331000	Enhancers	Liver	Liver
18	chr6:73329600-73331000	Flanking Active TSS	Thymus	Thymus
19	chr6:73329600-73331200	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr6:73329600-73331200	Bivalent Enhancer	Placenta	Placenta
21	chr6:73329600-73331400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:73329600-73331600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr6:73329600-73331600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr6:73329600-73331600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:73329600-73331600	Flanking Active TSS	HSMM	muscle
26	chr6:73329600-73331800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr6:73329600-73331800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr6:73329600-73331800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:73329600-73331800	Flanking Active TSS	Dnd41	blood
30	chr6:73329600-73331800	Flanking Active TSS	NH-A	brain
31	chr6:73329600-73332000	Active TSS	Brain Hippocampus Middle	brain
32	chr6:73329600-73332400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:73329600-73332600	Active TSS	Brain Anterior Caudate	brain
34	chr6:73329600-73332600	Active TSS	Brain Cingulate Gyrus	brain
35	chr6:73329600-73332800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:73329600-73333200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:73329600-73333200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr6:73329600-73333200	Active TSS	Aorta	Aorta
39	chr6:73329600-73333600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:73329600-73333600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:73329600-73333800	Active TSS	Brain Angular Gyrus	brain
42	chr6:73329800-73330600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
43	chr6:73329800-73330600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:73329800-73330600	Active TSS	Colonic Mucosa	Colon
45	chr6:73329800-73330600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr6:73329800-73330800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:73329800-73330800	Active TSS	Brain Substantia Nigra	brain
48	chr6:73329800-73330800	Enhancers	Pancreas	Pancrea
49	chr6:73329800-73331000	Active TSS	Right Atrium	heart
50	chr6:73329800-73331000	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links