Variant report

Variant	rs239036
Chromosome Location	chr21:17550915-17550916
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	CUX1	chr21:17550901-17550946	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LINC00478	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10854413	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11908760	0.92[EUR][1000 genomes]
rs11911225	0.92[EUR][1000 genomes]
rs11911677	0.89[EUR][1000 genomes]
rs1543773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16995014	1.00[CHB][hapmap]
rs2187061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs239035	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs239037	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs239043	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2823625	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2823626	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823628	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs7275630	0.92[EUR][1000 genomes]
rs7275690	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7277202	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7281053	0.94[EUR][1000 genomes]
rs7281143	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7282315	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs7283583	1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066951	chr21:17458978-17603160	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv544381	chr21:17458978-17603160	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1065028	chr21:17522588-17572535	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17527200-17553000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:17543200-17551200	Weak transcription	A549	lung
3	chr21:17543400-17552600	Weak transcription	Brain Anterior Caudate	brain
4	chr21:17543400-17553000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr21:17548800-17556200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr21:17549200-17552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr21:17549200-17552200	Weak transcription	Ovary	ovary
8	chr21:17549800-17553200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:17550800-17553800	Enhancers	Hela-S3	cervix

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