Variant report

Variant	rs2836741
Chromosome Location	chr21:40271392-40271393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40268536..40271467-chr21:40282576..40285415,2	K562	blood:
2	chr21:40270467..40272211-chr21:40279287..40280872,2	MCF-7	breast:
3	chr21:40268911..40271660-chr21:40277159..40278899,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1734596	0.95[ASN][1000 genomes]
rs2836724	0.82[MEX][hapmap]
rs2836731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2836734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836738	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836739	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425931	0.86[ASN][1000 genomes]
rs455426	0.90[JPT][hapmap]
rs456489	0.88[ASN][1000 genomes]
rs456508	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs458748	0.90[JPT][hapmap]
rs458885	0.99[ASN][1000 genomes]
rs458933	0.99[ASN][1000 genomes]
rs463032	0.90[JPT][hapmap]
rs465189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs465214	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs465612	0.99[ASN][1000 genomes]
rs467872	0.99[ASN][1000 genomes]
rs468641	0.99[ASN][1000 genomes]
rs468708	0.99[ASN][1000 genomes]
rs468939	0.99[ASN][1000 genomes]
rs469190	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469221	0.96[ASN][1000 genomes]
rs469242	0.99[ASN][1000 genomes]
rs469495	0.99[ASN][1000 genomes]
rs469589	0.99[ASN][1000 genomes]
rs62217841	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7283319	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7283582	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9983650	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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	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
4	nsv587478	chr21:40243459-40275033	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2836741	NCRNA00257	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40260000-40275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:40269400-40271600	Enhancers	Hela-S3	cervix
3	chr21:40269400-40271600	Enhancers	HSMMtube	muscle
4	chr21:40269600-40273000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr21:40269800-40271600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr21:40270000-40274800	Weak transcription	Psoas Muscle	Psoas
7	chr21:40270200-40271400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:40270200-40271400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr21:40270400-40273200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:40270600-40274400	Weak transcription	NHEK	skin
11	chr21:40270600-40278600	Weak transcription	Liver	Liver
12	chr21:40270800-40274400	Weak transcription	HMEC	breast
13	chr21:40271000-40274600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr21:40271200-40274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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