Variant report

Variant	rs2275683
Chromosome Location	chr9:104075427-104075428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104069628..104072510-chr9:104073819..104075636,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10125731	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10512279	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10989462	0.85[JPT][hapmap]
rs10989469	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10989471	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11790209	0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11790501	0.94[ASN][1000 genomes]
rs11792655	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12341244	0.80[JPT][hapmap]
rs12341316	0.85[JPT][hapmap]
rs12553507	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12683393	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12683674	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684829	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13289023	0.85[JPT][hapmap]
rs13296052	0.85[JPT][hapmap]
rs1341769	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1891219	0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1935240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34553293	0.96[ASN][1000 genomes]
rs35846126	0.86[ASN][1000 genomes]
rs3780531	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3944892	0.85[JPT][hapmap]
rs4480176	0.85[ASN][1000 genomes]
rs6479049	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7023477	0.85[JPT][hapmap]
rs7023799	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7034058	0.85[JPT][hapmap]
rs7035407	0.84[JPT][hapmap]
rs7040055	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7848242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7861116	1.00[ASN][1000 genomes]
rs7865487	0.84[EUR][1000 genomes]
rs7868832	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs7869625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][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	nsv1037157	chr9:104045761-104149233	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1049740	chr9:104049624-104075825	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104072400-104075800	Enhancers	Brain Hippocampus Middle	brain
2	chr9:104073000-104088600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:104073800-104082600	Weak transcription	Brain Anterior Caudate	brain
4	chr9:104074200-104080800	Enhancers	Liver	Liver
5	chr9:104074400-104081200	Weak transcription	Brain Substantia Nigra	brain
6	chr9:104074600-104077200	Weak transcription	A549	lung
7	chr9:104074800-104075800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:104075000-104075600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:104075000-104075600	Enhancers	Brain Germinal Matrix	brain
10	chr9:104075000-104075600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr9:104075000-104075600	Enhancers	Fetal Brain Male	brain
12	chr9:104075000-104075600	Enhancers	Fetal Muscle Leg	muscle
13	chr9:104075200-104075600	Weak transcription	Brain Angular Gyrus	brain
14	chr9:104075200-104076600	Genic enhancers	HepG2	liver
15	chr9:104075400-104077600	Weak transcription	Fetal Lung	lung
16	chr9:104075400-104077600	Weak transcription	HSMMtube	muscle
17	chr9:104075400-104079600	Weak transcription	Fetal Brain Female	brain

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