Variant report

Variant	rs2209553
Chromosome Location	chr10:90286617-90286618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:90284453..90286680-chr10:90293279..90295834,2	MCF-7	breast:
2	chr10:90285144..90287206-chr10:90288284..90290388,2	MCF-7	breast:
3	chr10:89620501..89622600-chr10:90285256..90287404,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10736351	1.00[YRI][hapmap]
rs10749590	1.00[MEX][hapmap]
rs10788598	1.00[MEX][hapmap]
rs10788599	1.00[MEX][hapmap]
rs1750274	0.81[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs1935579	1.00[MEX][hapmap]
rs2185786	0.82[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs2437875	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs2477954	0.84[AMR][1000 genomes]
rs2477956	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2576159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576169	0.84[AMR][1000 genomes]
rs2576170	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs2576171	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs2576172	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs2576176	0.86[JPT][hapmap]
rs2576181	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs2765440	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs2765454	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3740279	1.00[YRI][hapmap]
rs4934404	1.00[MEX][hapmap]
rs7921352	0.93[MEX][hapmap]
rs796945	0.85[MEX][hapmap]
rs813782	0.93[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2209553	LIPM	cis	cerebellum	SCAN
rs2209553	RNLS	cis	cerebellum	SCAN
rs2209553	CLCN1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90281800-90286800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr10:90282000-90286800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr10:90283800-90288800	Weak transcription	Fetal Lung	lung
4	chr10:90284000-90288000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:90284800-90286800	Enhancers	Osteobl	bone
6	chr10:90285000-90287000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr10:90285600-90287000	Enhancers	Thymus	Thymus
8	chr10:90285600-90287600	Enhancers	Fetal Thymus	thymus
9	chr10:90285800-90289800	Weak transcription	HSMM	muscle
10	chr10:90286000-90290000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr10:90286000-90290800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:90286000-90291200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr10:90286200-90291200	Weak transcription	Liver	Liver
14	chr10:90286400-90286800	Weak transcription	Hela-S3	cervix
15	chr10:90286400-90287000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr10:90286400-90288200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:90286600-90288000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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