Variant report

Variant	rs56254477
Chromosome Location	chr6:73332537-73332538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:73331830..73337292-chr6:73338860..73341706,8	K562	blood:
2	chr6:73262215..73264630-chr6:73332275..73334908,2	K562	blood:
3	chr6:73332489..73334434-chr6:73351844..73354373,2	K562	blood:

Variant related genes	Relation type
ENSG00000233844	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10484913	0.84[EUR][1000 genomes]
rs10485213	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10943043	1.00[ASN][1000 genomes]
rs10943048	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10943051	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10943055	0.86[EUR][1000 genomes]
rs11758568	1.00[ASN][1000 genomes]
rs11759937	0.87[EUR][1000 genomes]
rs12189974	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12190091	1.00[ASN][1000 genomes]
rs12191216	0.82[EUR][1000 genomes]
rs12197962	0.82[EUR][1000 genomes]
rs12200468	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204989	0.84[EUR][1000 genomes]
rs12205254	1.00[ASN][1000 genomes]
rs12205834	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12208907	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12212562	1.00[ASN][1000 genomes]
rs12214894	1.00[ASN][1000 genomes]
rs12214895	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12215865	0.82[EUR][1000 genomes]
rs12374630	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17692715	1.00[ASN][1000 genomes]
rs17692874	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17692898	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17729195	0.86[EUR][1000 genomes]
rs17749408	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17749420	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796704	0.81[EUR][1000 genomes]
rs34821312	1.00[ASN][1000 genomes]
rs55633371	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55826353	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56086224	1.00[ASN][1000 genomes]
rs56316829	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411984	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411990	0.81[EUR][1000 genomes]
rs6453592	1.00[ASN][1000 genomes]
rs6453593	1.00[ASN][1000 genomes]
rs6453594	1.00[ASN][1000 genomes]
rs6922524	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922932	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935174	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs719830	0.81[EUR][1000 genomes]
rs72935423	0.87[EUR][1000 genomes]
rs7768673	1.00[ASN][1000 genomes]
rs7776215	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3412497	chr6:73330856-73333404	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73329200-73333800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:73329400-73333200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
3	chr6:73329400-73334400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:73329600-73332600	Active TSS	Brain Anterior Caudate	brain
5	chr6:73329600-73332600	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:73329600-73332800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:73329600-73333200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:73329600-73333200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr6:73329600-73333200	Active TSS	Aorta	Aorta
10	chr6:73329600-73333600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:73329600-73333600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:73329600-73333800	Active TSS	Brain Angular Gyrus	brain
13	chr6:73329800-73332800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:73329800-73333200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr6:73329800-73333200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:73329800-73333200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:73329800-73333200	Active TSS	Psoas Muscle	Psoas
18	chr6:73329800-73333400	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr6:73329800-73333400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:73330000-73333200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:73330200-73333200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:73330400-73333000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:73330600-73332800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:73330600-73333200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:73330800-73333200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:73330800-73333200	Flanking Active TSS	Pancreas	Pancrea
27	chr6:73330800-73333400	Bivalent/Poised TSS	NHDF-Ad	bronchial
28	chr6:73330800-73333400	Active TSS	Osteobl	bone
29	chr6:73331000-73333000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:73331000-73333000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:73331000-73333000	Bivalent Enhancer	Fetal Brain Male	brain
32	chr6:73331000-73333200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:73331000-73333200	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr6:73331000-73333200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr6:73331000-73333600	Bivalent/Poised TSS	A549	lung
36	chr6:73331000-73334000	Active TSS	HSMMtube	muscle
37	chr6:73331200-73332800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr6:73331200-73332800	Bivalent/Poised TSS	Small Intestine	intestine
39	chr6:73331200-73333000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
40	chr6:73331200-73333400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:73331200-73333400	Active TSS	Primary B cells from peripheral blood	blood
42	chr6:73331400-73332600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr6:73331400-73332800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr6:73331400-73332800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:73331400-73332800	Active TSS	Right Atrium	heart
46	chr6:73331400-73333000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr6:73331400-73333200	Active TSS	Primary T cells from cord blood	blood
48	chr6:73331400-73333200	Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:73331400-73333200	Active TSS	Lung	lung
50	chr6:73331400-73333200	Active TSS	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links