Variant report

Variant	rs469190
Chromosome Location	chr21:40241282-40241283
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	chr21:40240674..40242419-chr21:40245224..40247812,2	MCF-7	breast:
2	chr21:40237649..40239379-chr21:40240190..40242974,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1734596	0.96[ASN][1000 genomes]
rs2836724	0.81[MEX][hapmap]
rs2836731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836738	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836739	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs425931	0.87[ASN][1000 genomes]
rs455426	0.90[JPT][hapmap]
rs456489	0.89[ASN][1000 genomes]
rs456508	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs458748	0.90[JPT][hapmap]
rs458885	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs458933	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs463032	0.90[JPT][hapmap]
rs465189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs465214	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs465612	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs467872	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs468641	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs468708	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs468939	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs469221	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs469242	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs469495	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs469589	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62217841	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7283319	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7283582	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983650	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs469190	NCRNA00257	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40226000-40242200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:40229600-40245400	Weak transcription	Left Ventricle	heart
3	chr21:40233600-40245400	Weak transcription	Right Atrium	heart
4	chr21:40235600-40247600	Weak transcription	Spleen	Spleen
5	chr21:40240800-40242200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr21:40241000-40241600	Enhancers	Primary B cells from peripheral blood	blood
7	chr21:40241000-40241600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr21:40241000-40241600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr21:40241000-40242200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr21:40241000-40242800	Bivalent Enhancer	Primary B cells from cord blood	blood
11	chr21:40241000-40243000	Enhancers	Primary neutrophils fromperipheralblood	blood

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