Variant report

Variant	rs11088585
Chromosome Location	chr21:17798960-17798961
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	chr21:17793428..17795619-chr21:17796309..17799030,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11911745	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11911959	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1349226	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1375625	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1375626	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1449517	0.86[CHB][hapmap]
rs1974157	0.88[ASN][1000 genomes]
rs1992970	0.86[CHB][hapmap]
rs2017357	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051270	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs240453	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs240455	0.80[EUR][1000 genomes]
rs240461	0.96[CEU][hapmap]
rs240492	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs2823784	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs2823790	0.89[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823791	0.95[EUR][1000 genomes]
rs2823795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2823798	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2823799	0.96[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2823801	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3928806	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57190849	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61514219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6517700	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs8126683	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs8126881	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8128973	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs9305765	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs996175	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9979472	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9980917	0.80[EUR][1000 genomes]
rs9984548	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	nsv913416	chr21:17728224-17863882	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv913419	chr21:17775056-17826260	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv470880	chr21:17777827-17820111	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv459100	chr21:17777966-17826260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv587077	chr21:17777966-17826260	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv913420	chr21:17777966-17826260	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv913421	chr21:17786219-17826260	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv913422	chr21:17791751-17826260	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv459101	chr21:17794432-17819036	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv587078	chr21:17794432-17819036	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11088585	CHODL	cis	parietal	SCAN
rs11088585	CHODL	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17795400-17803200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:17796000-17800800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr21:17797000-17799200	Weak transcription	A549	lung
4	chr21:17797200-17799000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr21:17797200-17799000	Enhancers	Fetal Brain Male	brain
6	chr21:17797200-17799600	Enhancers	Hela-S3	cervix
7	chr21:17797200-17799800	Enhancers	NH-A	brain
8	chr21:17797200-17803200	Weak transcription	Colon Smooth Muscle	Colon
9	chr21:17797200-17813000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr21:17797200-17813400	Weak transcription	Fetal Muscle Leg	muscle
11	chr21:17797400-17800400	Weak transcription	HSMM	muscle
12	chr21:17797600-17799600	Weak transcription	Brain Substantia Nigra	brain
13	chr21:17797600-17800000	Weak transcription	Liver	Liver
14	chr21:17797800-17799000	Weak transcription	Ovary	ovary
15	chr21:17797800-17799200	Weak transcription	Psoas Muscle	Psoas
16	chr21:17797800-17808400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr21:17798000-17799200	Weak transcription	Fetal Lung	lung
18	chr21:17798200-17799400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:17798400-17799200	Weak transcription	Brain Anterior Caudate	brain
20	chr21:17798400-17799800	Enhancers	Fetal Heart	heart
21	chr21:17798800-17799000	Enhancers	HUVEC	blood vessel
22	chr21:17798800-17799800	Enhancers	Muscle Satellite Cultured Cells	--

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