Variant report

Variant	rs11239305
Chromosome Location	chr10:45489224-45489225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45423081..45426439-chr10:45487238..45490931,4	K562	blood:
2	chr10:45472874..45476114-chr10:45485945..45489321,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165507	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11239299	1.00[AMR][1000 genomes]
rs11239303	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239306	1.00[AMR][1000 genomes]
rs11239307	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239308	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239309	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239311	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239315	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239319	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239323	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239324	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11239342	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11239343	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11239345	0.91[EUR][1000 genomes]
rs11239346	0.91[EUR][1000 genomes]
rs12354652	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12358699	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12359377	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12359697	1.00[EUR][1000 genomes]
rs12359954	1.00[AMR][1000 genomes]
rs17157322	1.00[EUR][1000 genomes]
rs35521977	1.00[AMR][1000 genomes]
rs3740092	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3740093	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3758399	1.00[AMR][1000 genomes]
rs3758400	1.00[AMR][1000 genomes]
rs41301599	1.00[AMR][1000 genomes]
rs41301601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41301609	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41301611	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41306544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41306546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59381196	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61269477	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45474400-45490800	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr10:45474400-45490800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr10:45474800-45490200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:45476800-45491400	Weak transcription	Fetal Kidney	kidney
5	chr10:45477800-45489400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr10:45478800-45495800	Weak transcription	HMEC	breast
7	chr10:45480800-45489400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:45482200-45490800	Weak transcription	GM12878-XiMat	blood
9	chr10:45482200-45491200	Weak transcription	Fetal Lung	lung
10	chr10:45482400-45495600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:45484000-45490400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:45484000-45491000	Genic enhancers	Left Ventricle	heart
13	chr10:45484200-45494200	Enhancers	Right Atrium	heart
14	chr10:45484400-45490800	Genic enhancers	Fetal Muscle Leg	muscle
15	chr10:45484600-45490000	Genic enhancers	Right Ventricle	heart
16	chr10:45484600-45494200	Enhancers	Ovary	ovary
17	chr10:45484800-45490000	Genic enhancers	Pancreas	Pancrea
18	chr10:45484800-45491000	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr10:45485200-45490000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr10:45485200-45493600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:45485400-45490000	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:45485600-45490600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:45485800-45489600	Genic enhancers	Adipose Nuclei	Adipose
24	chr10:45486000-45495600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr10:45486000-45495600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr10:45486400-45489600	Genic enhancers	HepG2	liver
27	chr10:45486400-45490000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr10:45486400-45490000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:45486400-45490200	Weak transcription	Fetal Thymus	thymus
30	chr10:45486400-45490400	Genic enhancers	Brain Hippocampus Middle	brain
31	chr10:45486400-45491000	Strong transcription	Fetal Intestine Small	intestine
32	chr10:45486600-45489400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:45486600-45489600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:45486600-45489600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr10:45486600-45490000	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr10:45487000-45489600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:45487200-45489400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:45487200-45489600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr10:45487200-45495600	Weak transcription	Brain Germinal Matrix	brain
40	chr10:45487200-45496200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:45487400-45489400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:45487400-45489400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr10:45487400-45489400	Strong transcription	HSMM	muscle
44	chr10:45487400-45490600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:45487400-45495600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:45487600-45489400	Strong transcription	Brain Substantia Nigra	brain
47	chr10:45487600-45489600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr10:45487800-45489600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr10:45487800-45489800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:45487800-45491200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links