Variant report

Variant	rs9979633
Chromosome Location	chr21:47185080-47185081
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	chr21:46974937..46977900-chr21:47183608..47186473,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11089022	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11702443	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11702478	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11702850	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11911839	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12627257	1.00[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs1556335	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1783075	1.00[ASW][hapmap];0.88[MKK][hapmap]
rs2075885	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2150452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297293	0.80[ASN][1000 genomes]
rs2330245	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2838984	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2839006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839007	1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839015	0.90[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2839027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2839028	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2839034	0.91[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs28438591	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs373617	0.85[MKK][hapmap]
rs3788219	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs431609	1.00[ASW][hapmap];0.88[MKK][hapmap]
rs4819145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819146	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4819150	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62213280	0.82[ASN][1000 genomes]
rs7278438	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7281669	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743352	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs8129118	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8129304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8134872	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap]
rs914243	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs9306138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9306141	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs971977	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977795	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9978181	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9979633	COL6A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47166200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr21:47168600-47187000	Weak transcription	NHDF-Ad	bronchial
3	chr21:47170200-47188800	Weak transcription	Spleen	Spleen
4	chr21:47170800-47188200	Weak transcription	Right Atrium	heart
5	chr21:47171800-47186600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr21:47175600-47186000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr21:47177200-47187400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr21:47180000-47186600	Strong transcription	Thymus	Thymus
9	chr21:47180400-47187000	Weak transcription	HSMMtube	muscle
10	chr21:47180600-47186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr21:47182000-47186600	Weak transcription	Primary T cells from cord blood	blood
12	chr21:47182400-47186400	Strong transcription	Fetal Thymus	thymus
13	chr21:47183600-47186800	Weak transcription	NH-A	brain
14	chr21:47183800-47186400	Weak transcription	Fetal Stomach	stomach
15	chr21:47183800-47187800	Weak transcription	Brain Substantia Nigra	brain
16	chr21:47183800-47188200	Weak transcription	Fetal Lung	lung
17	chr21:47183800-47188600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:47184000-47187600	Weak transcription	Brain Hippocampus Middle	brain
19	chr21:47184400-47185400	Enhancers	Fetal Muscle Trunk	muscle
20	chr21:47184400-47189000	Enhancers	Fetal Muscle Leg	muscle
21	chr21:47185000-47185200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr21:47185000-47187600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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