Variant report

Variant	rs6072773
Chromosome Location	chr20:41162875-41162876
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	chr20:41156659..41159808-chr20:41161331..41164447,3	MCF-7	breast:
2	chr20:41161976..41163501-chr20:41178008..41179846,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1033642	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1033643	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12106011	1.00[CEU][hapmap]
rs12106099	0.83[ASN][1000 genomes]
rs1569908	0.83[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs2064676	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064677	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064678	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2205939	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[ASN][1000 genomes]
rs230153	0.82[JPT][hapmap]
rs230161	1.00[YRI][hapmap]
rs6016816	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap]
rs6065496	0.87[JPT][hapmap]
rs6072758	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs6072759	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6072767	0.83[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs6072768	0.81[CEU][hapmap]
rs6072771	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6072775	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6093656	0.82[CHD][hapmap];0.89[TSI][hapmap]
rs6093657	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs6093669	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6093670	0.90[ASN][1000 genomes]
rs6093672	0.94[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs6093673	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6102888	0.80[MEX][hapmap]
rs6102894	0.90[ASN][1000 genomes]
rs6102895	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs6102897	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6102899	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6102904	1.00[CEU][hapmap]
rs61055710	0.86[AMR][1000 genomes]
rs73127302	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv833987	chr20:41007663-41184914	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1059852	chr20:41087948-41217672	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv544276	chr20:41087948-41217672	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1055546	chr20:41102999-41260749	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1064253	chr20:41120425-41379706	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1061449	chr20:41126720-41212178	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv586006	chr20:41157707-41290936	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv828726	chr20:41161919-41166198	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6072773	SYS1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41160800-41173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41161000-41163000	Weak transcription	Pancreas	Pancrea

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