Variant report

Variant	rs12197537
Chromosome Location	chr6:24228787-24228788
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24227048..24229838-chr6:24232947..24235192,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12189861	0.90[EUR][1000 genomes]
rs12190103	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12190202	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12199068	0.96[EUR][1000 genomes]
rs12201442	0.93[EUR][1000 genomes]
rs12205083	0.91[EUR][1000 genomes]
rs12215082	0.89[EUR][1000 genomes]
rs1541190	0.96[EUR][1000 genomes]
rs1591997	0.97[EUR][1000 genomes]
rs28993075	0.95[EUR][1000 genomes]
rs28993077	0.95[EUR][1000 genomes]
rs28993078	0.91[EUR][1000 genomes]
rs28993079	0.91[EUR][1000 genomes]
rs3789226	0.89[EUR][1000 genomes]
rs3846828	0.85[EUR][1000 genomes]
rs4612153	0.96[EUR][1000 genomes]
rs6907864	0.88[EUR][1000 genomes]
rs6923278	0.95[EUR][1000 genomes]
rs6923473	0.95[EUR][1000 genomes]
rs72830866	0.89[EUR][1000 genomes]
rs7774208	0.85[ASN][1000 genomes]
rs9295616	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9460976	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9460977	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9460983	0.95[EUR][1000 genomes]
rs9460984	0.96[EUR][1000 genomes]
rs9467076	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9467078	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9467079	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9467081	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9467087	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467090	0.96[EUR][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	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427746	chr6:24221299-24305709	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24206200-24231400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:24214600-24235400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24217800-24231600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:24224800-24228800	Strong transcription	HepG2	liver
5	chr6:24225000-24229000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:24225000-24229200	Weak transcription	Pancreas	Pancrea
7	chr6:24226800-24229600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:24227000-24228800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:24227000-24230400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:24227200-24229200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:24227600-24229000	Enhancers	Brain Germinal Matrix	brain
12	chr6:24227600-24229200	Enhancers	Brain Anterior Caudate	brain
13	chr6:24227600-24229400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:24227600-24229400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:24227600-24229400	Enhancers	Fetal Kidney	kidney
16	chr6:24227600-24229600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:24227800-24229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:24227800-24229000	Weak transcription	Ovary	ovary
19	chr6:24227800-24229400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:24227800-24229600	Enhancers	Fetal Lung	lung
21	chr6:24228000-24228800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:24228000-24229200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:24228000-24229200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:24228000-24229200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:24228000-24229200	Enhancers	Fetal Stomach	stomach
26	chr6:24228000-24229400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:24228000-24229600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:24228000-24229600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:24228200-24229200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr6:24228400-24228800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:24228400-24229400	Enhancers	H9 Cell Line	embryonic stem cell
32	chr6:24228400-24229800	Enhancers	NHDF-Ad	bronchial
33	chr6:24228400-24230000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:24228400-24230600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:24228600-24229400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr6:24228600-24229600	Enhancers	HSMM	muscle
37	chr6:24228600-24229800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr6:24228600-24230400	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links