Variant report

Variant	rs229095
Chromosome Location	chr21:28260111-28260112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr21:28259453-28260140	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr21:28259450-28260123	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr21:28259374-28260152	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000223563	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1497288	1.00[ASN][1000 genomes]
rs151056	0.83[EUR][1000 genomes]
rs162488	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162490	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162491	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162492	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162493	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162496	0.84[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs162497	0.84[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs162498	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162499	0.84[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs162501	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs162503	1.00[ASN][1000 genomes]
rs162504	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs162505	1.00[ASN][1000 genomes]
rs162506	0.80[TSI][hapmap]
rs162507	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs162508	1.00[ASN][1000 genomes]
rs162510	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs162516	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162520	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162521	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162531	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs162533	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162534	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162535	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162536	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162537	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162538	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162539	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162540	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162541	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229045	0.83[EUR][1000 genomes]
rs229046	0.83[EUR][1000 genomes]
rs229053	1.00[JPT][hapmap]
rs229060	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229061	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229063	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229064	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229069	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229071	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229076	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229078	0.91[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229079	0.88[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs229085	1.00[ASN][1000 genomes]
rs229087	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229088	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229089	0.96[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229090	0.83[EUR][1000 genomes]
rs229091	0.91[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229093	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229097	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229103	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229109	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229110	0.92[EUR][1000 genomes]
rs233899	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233900	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830556	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830558	0.84[EUR][1000 genomes]
rs2830584	0.83[EUR][1000 genomes]
rs2830589	0.83[CEU][hapmap]
rs389125	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs431134	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs457947	1.00[ASN][1000 genomes]
rs4817147	1.00[ASN][1000 genomes]
rs7281968	0.83[EUR][1000 genomes]
rs73358063	1.00[ASN][1000 genomes]
rs73358075	1.00[ASN][1000 genomes]
rs73899348	1.00[ASN][1000 genomes]
rs8127064	1.00[ASN][1000 genomes]
rs8131204	1.00[ASN][1000 genomes]
rs8992	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9647124	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 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	chr21:28256800-28260200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr21:28259600-28260200	Enhancers	Hela-S3	cervix
3	chr21:28260000-28261200	Weak transcription	Osteobl	bone

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