Variant report

Variant	rs12209009
Chromosome Location	chr6:131100970-131100971
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10457557	0.89[EUR][1000 genomes]
rs10872374	0.87[EUR][1000 genomes]
rs11154603	0.88[EUR][1000 genomes]
rs11966663	0.87[EUR][1000 genomes]
rs12173491	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12191209	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191580	0.87[EUR][1000 genomes]
rs12206483	0.86[EUR][1000 genomes]
rs12207178	0.86[EUR][1000 genomes]
rs12210679	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907589	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375762	0.86[EUR][1000 genomes]
rs9375765	0.89[EUR][1000 genomes]
rs9388832	0.85[EUR][1000 genomes]
rs9398960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9402269	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9402274	0.89[EUR][1000 genomes]
rs9402276	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533971	chr6:130490694-131172051	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv830806	chr6:130938330-131107137	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv604664	chr6:131004998-131115817	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1025019	chr6:131074711-131116070	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv604665	chr6:131077027-131115817	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv604666	chr6:131078180-131122295	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131099600-131101600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr6:131099800-131101000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:131099800-131101000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:131099800-131101200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:131099800-131101600	Enhancers	Colon Smooth Muscle	Colon
6	chr6:131099800-131103200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:131099800-131103600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:131099800-131103800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:131100000-131101200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr6:131100000-131101400	Enhancers	Rectal Smooth Muscle	rectum
11	chr6:131100000-131101600	Enhancers	Fetal Stomach	stomach
12	chr6:131100000-131101600	Enhancers	NHLF	lung
13	chr6:131100000-131103600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:131100200-131103600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr6:131100400-131101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:131100400-131101200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:131100400-131101200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:131100400-131103600	Enhancers	Primary T cells from cord blood	blood
19	chr6:131100400-131103600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:131100600-131101000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:131100600-131101000	Active TSS	Stomach Smooth Muscle	stomach
22	chr6:131100600-131101000	Flanking Active TSS	NHDF-Ad	bronchial
23	chr6:131100600-131101200	Enhancers	Adipose Nuclei	Adipose
24	chr6:131100600-131101400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:131100600-131101800	Enhancers	HSMM	muscle
26	chr6:131100600-131103600	Enhancers	Fetal Thymus	thymus
27	chr6:131100800-131101200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:131100800-131101800	Enhancers	HSMMtube	muscle
29	chr6:131100800-131102000	Enhancers	Osteobl	bone
30	chr6:131100800-131102400	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links