Variant report

Variant	rs458563
Chromosome Location	chr21:45991877-45991878
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	chr21:45989841..45993258-chr21:45994452..45997591,3	MCF-7	breast:
2	chr21:45987563..45989403-chr21:45990992..45992920,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs115728	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1211057	0.84[EUR][1000 genomes]
rs1211059	0.84[EUR][1000 genomes]
rs1211060	0.84[EUR][1000 genomes]
rs1211061	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs144266	0.84[EUR][1000 genomes]
rs144267	0.84[EUR][1000 genomes]
rs170848	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs182854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233252	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs233253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233254	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233255	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233256	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233257	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233258	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233259	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs369111	0.84[EUR][1000 genomes]
rs379858	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs380585	0.84[EUR][1000 genomes]
rs396912	0.84[EUR][1000 genomes]
rs400368	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs401727	0.84[EUR][1000 genomes]
rs403940	0.84[EUR][1000 genomes]
rs426512	0.84[EUR][1000 genomes]
rs426973	0.84[EUR][1000 genomes]
rs430609	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs432174	0.84[EUR][1000 genomes]
rs434716	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs455413	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs455562	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs455714	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs455777	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs455911	0.84[EUR][1000 genomes]
rs456444	0.82[CEU][hapmap];0.87[GIH][hapmap];0.84[EUR][1000 genomes]
rs456780	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs457322	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs457647	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs457697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs457698	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459667	0.84[EUR][1000 genomes]
rs459845	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs459915	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs460064	0.82[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs460085	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs460122	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs460166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460546	0.88[EUR][1000 genomes]
rs461436	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs461815	0.84[EUR][1000 genomes]
rs462025	0.84[EUR][1000 genomes]
rs462254	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs462349	0.84[EUR][1000 genomes]
rs462697	0.84[EUR][1000 genomes]
rs462711	0.84[EUR][1000 genomes]
rs463239	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs463267	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs463668	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs463966	0.84[EUR][1000 genomes]
rs464281	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs464391	0.84[EUR][1000 genomes]
rs464504	0.82[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs464684	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs465079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs465333	0.84[EUR][1000 genomes]
rs465930	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs466094	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs466560	0.82[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	esv3361489	chr21:45669073-46013747	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv913943	chr21:45740823-46031810	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv913946	chr21:45838632-46031810	Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv913948	chr21:45860912-46031810	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1056424	chr21:45894901-46031810	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544475	chr21:45894901-46031810	Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1055163	chr21:45895663-46031810	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1061423	chr21:45985068-46009217	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv913951	chr21:45985068-46012524	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	nsv913952	chr21:45988426-46031810	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2751931	chr21:45990446-46031810	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45978400-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:45989000-45994200	Weak transcription	Gastric	stomach
3	chr21:45991200-45992200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:45991600-45992000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:45991800-45994400	Enhancers	HepG2	liver

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