Variant report

Variant	rs6042689
Chromosome Location	chr20:1487758-1487759
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	chr20:1445622..1448578-chr20:1487118..1490074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11697322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11699494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163	1.00[CHB][hapmap]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1883933	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883936	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs57094926	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033911	1.00[ASN][1000 genomes]
rs6033914	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033918	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs6033923	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033935	0.88[ASW][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.89[AFR][1000 genomes]
rs6033936	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6042588	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs6042647	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042676	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042682	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs60645920	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110193	1.00[CHB][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs66715055	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117719	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118276	1.00[CHB][hapmap]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1482000-1497600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:1484200-1488600	Enhancers	HMEC	breast
3	chr20:1484200-1489200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:1485600-1489400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:1486800-1489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:1486800-1489600	Enhancers	NHEK	skin
7	chr20:1487200-1489200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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