Variant report

Variant	rs12481496
Chromosome Location	chr20:41638098-41638099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:41637939..41639575-chr20:41640283..41642711,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11696908	0.85[ASN][1000 genomes]
rs11907665	0.85[ASN][1000 genomes]
rs12625239	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs16987668	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2206455	0.90[CEU][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2206456	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2223556	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2223558	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs2223559	0.85[ASN][1000 genomes]
rs2294589	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294591	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867594	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35069072	0.85[ASN][1000 genomes]
rs3950170	0.85[ASN][1000 genomes]
rs56319720	0.83[ASN][1000 genomes]
rs56348412	0.83[ASN][1000 genomes]
rs56941535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58199388	0.81[ASN][1000 genomes]
rs6016936	0.83[ASN][1000 genomes]
rs6016937	0.91[CEU][hapmap];0.90[CHD][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap]
rs6016938	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6030592	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6030593	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6030596	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs6030601	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6030604	0.87[ASN][1000 genomes]
rs6065558	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6065559	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6065560	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6065561	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6065562	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs6065564	0.85[ASN][1000 genomes]
rs6065565	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap]
rs6072923	1.00[CHB][hapmap]
rs6072924	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6072925	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6072926	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6072928	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6072933	0.83[ASN][1000 genomes]
rs6072934	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs6072936	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs6072937	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs6072938	0.85[ASN][1000 genomes]
rs6072940	0.85[ASN][1000 genomes]
rs6072947	0.95[CEU][hapmap];0.86[YRI][hapmap]
rs6072948	0.85[ASN][1000 genomes]
rs62205279	0.83[ASN][1000 genomes]
rs7262225	1.00[ASW][hapmap];0.90[CHD][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73281237	0.83[ASN][1000 genomes]
rs73281239	0.83[ASN][1000 genomes]
rs7354318	0.85[ASN][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	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060468	chr20:41518010-41700012	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1061053	chr20:41521471-41704874	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv949221	chr20:41594025-41742176	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv869774	chr20:41595567-41746533	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2762078	chr20:41598181-41745491	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv948829	chr20:41598995-41742176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv912889	chr20:41609188-41666379	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1061219	chr20:41613071-41673335	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1065908	chr20:41620966-41735969	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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