Variant report

Variant	rs6049976
Chromosome Location	chr20:24771791-24771792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24771567..24773890-chr20:24790007..24791908,2	MCF-7	breast:
2	chr17:72982681..72985188-chr20:24771420..24774172,2	MCF-7	breast:
3	chr20:24771465..24772208-chr20:24898686..24899202,2	MCF-7	breast:
4	chr20:24770878..24773860-chr20:24773955..24776847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109089	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12480651	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226667	0.82[ASN][1000 genomes]
rs226668	0.82[ASN][1000 genomes]
rs226669	0.82[ASN][1000 genomes]
rs226670	0.82[ASN][1000 genomes]
rs226671	0.82[ASN][1000 genomes]
rs226672	0.82[ASN][1000 genomes]
rs226674	0.82[ASN][1000 genomes]
rs226675	0.82[ASN][1000 genomes]
rs226676	0.82[ASN][1000 genomes]
rs226677	0.82[ASN][1000 genomes]
rs226678	0.82[ASN][1000 genomes]
rs226679	0.82[ASN][1000 genomes]
rs226680	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs226681	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs226687	0.82[ASN][1000 genomes]
rs226688	0.82[ASN][1000 genomes]
rs226690	0.82[ASN][1000 genomes]
rs226697	0.82[ASN][1000 genomes]
rs226699	0.82[ASN][1000 genomes]
rs4813538	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4813539	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4813540	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815303	0.88[EUR][1000 genomes]
rs4815308	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4815312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815315	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56103836	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036904	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6036910	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036911	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049933	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049943	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049956	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6049971	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6049977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049983	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61059580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114868	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7264934	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7271933	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73335420	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335440	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335460	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73612620	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs743191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs85804	0.82[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	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1059270	chr20:24741923-24787243	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24767400-24772400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr20:24770600-24771800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:24771600-24771800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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